1
|
Zhao B, Hu L, Kaundal S, Neetu N, Lee CH, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Venkataram Prasad BV. Structure of orthoreovirus RNA chaperone σNS, a component of viral replication factories. Nat Commun 2024; 15:2460. [PMID: 38503747 PMCID: PMC10950856 DOI: 10.1038/s41467-024-46627-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
The mammalian orthoreovirus (reovirus) σNS protein is required for formation of replication compartments that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of a σNS mutant that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure shows that dimers interact with each other using N-terminal arms to form a helical assembly resembling WT σNS filaments in complex with RNA observed using cryo-EM. The interior of the helical assembly is of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same site as the N-terminal arm. This finding suggests that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS, which is supported by the structure of σNS lacking an N-terminal arm. We further observed that σNS has RNA chaperone activity likely essential for presenting mRNA to the viral polymerase for genome replication. This activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
Collapse
Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Soni Kaundal
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Neetu Neetu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Christopher H Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Xayathed Somoulay
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Gwen M Taylor
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA
| | - Terence S Dermody
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
- Institute of Infection, Inflammation, and Immunity, UPMC Children's Hospital of Pittsburgh, Pittsburg, PA, USA.
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburg, PA, USA.
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Verna and Marrs Mclean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
2
|
Judge A, Sankaran B, Hu L, Palaniappan M, Birgy A, Prasad BVV, Palzkill T. Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning. Proc Natl Acad Sci U S A 2024; 121:e2313513121. [PMID: 38483989 PMCID: PMC10962969 DOI: 10.1073/pnas.2313513121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
Cooperative interactions between amino acids are critical for protein function. A genetic reflection of cooperativity is epistasis, which is when a change in the amino acid at one position changes the sequence requirements at another position. To assess epistasis within an enzyme active site, we utilized CTX-M β-lactamase as a model system. CTX-M hydrolyzes β-lactam antibiotics to provide antibiotic resistance, allowing a simple functional selection for rapid sorting of modified enzymes. We created all pairwise mutations across 17 active site positions in the β-lactamase enzyme and quantitated the function of variants against two β-lactam antibiotics using next-generation sequencing. Context-dependent sequence requirements were determined by comparing the antibiotic resistance function of double mutations across the CTX-M active site to their predicted function based on the constituent single mutations, revealing both positive epistasis (synergistic interactions) and negative epistasis (antagonistic interactions) between amino acid substitutions. The resulting trends demonstrate that positive epistasis is present throughout the active site, that epistasis between residues is mediated through substrate interactions, and that residues more tolerant to substitutions serve as generic compensators which are responsible for many cases of positive epistasis. Additionally, we show that a key catalytic residue (Glu166) is amenable to compensatory mutations, and we characterize one such double mutant (E166Y/N170G) that acts by an altered catalytic mechanism. These findings shed light on the unique biochemical factors that drive epistasis within an enzyme active site and will inform enzyme engineering efforts by bridging the gap between amino acid sequence and catalytic function.
Collapse
Affiliation(s)
- Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Murugesan Palaniappan
- Department of Pathology and Immunology, Center for Drug Discovery, Baylor College of Medicine, Houston, TX77030
| | - André Birgy
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
- Infections, Antimicrobials, Modelling, Evolution, UMR 1137, French Insitute for Medical Research (INSERM), Faculty of Health, Université Paris Cité, Paris75006, France
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX77030
| |
Collapse
|
3
|
Dodd-O J, Roy A, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P, Kumar V. Author Correction: Antiviral fibrils of self-assembled peptides with tunable compositions. Nat Commun 2024; 15:1505. [PMID: 38374216 PMCID: PMC10876924 DOI: 10.1038/s41467-024-46005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Dilip Kumar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Soni Kaundal
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Boyang Zhao
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Li
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Varun Pai
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Amanda Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
- SAPHTx Inc, Newark, NJ, 07104, USA
| | - Alexandra Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E, Tempe, AZ, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- SAPHTx Inc, Newark, NJ, 07104, USA.
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
| |
Collapse
|
4
|
Dodd-O J, Roy A, Siddiqui Z, Jafari R, Coppola F, Ramasamy S, Kolloli A, Kumar D, Kaundal S, Zhao B, Kumar R, Robang AS, Li J, Azizogli AR, Pai V, Acevedo-Jake A, Heffernan C, Lucas A, McShan AC, Paravastu AK, Prasad BVV, Subbian S, Král P, Kumar V. Antiviral fibrils of self-assembled peptides with tunable compositions. Nat Commun 2024; 15:1142. [PMID: 38326301 PMCID: PMC10850501 DOI: 10.1038/s41467-024-45193-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
The lasting threat of viral pandemics necessitates the development of tailorable first-response antivirals with specific but adaptive architectures for treatment of novel viral infections. Here, such an antiviral platform has been developed based on a mixture of hetero-peptides self-assembled into functionalized β-sheets capable of specific multivalent binding to viral protein complexes. One domain of each hetero-peptide is designed to specifically bind to certain viral proteins, while another domain self-assembles into fibrils with epitope binding characteristics determined by the types of peptides and their molar fractions. The self-assembled fibrils maintain enhanced binding to viral protein complexes and retain high resilience to viral mutations. This method is experimentally and computationally tested using short peptides that specifically bind to Spike proteins of SARS-CoV-2. This platform is efficacious, inexpensive, and stable with excellent tolerability.
Collapse
Affiliation(s)
- Joseph Dodd-O
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Abhishek Roy
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Roya Jafari
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Francesco Coppola
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Dilip Kumar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Soni Kaundal
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Boyang Zhao
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jeffrey Li
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Varun Pai
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Amanda Acevedo-Jake
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Corey Heffernan
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA
- SAPHTx Inc, Newark, NJ, 07104, USA
| | - Alexandra Lucas
- Center for Personalized Diagnostics and Center for Immunotherapy Vaccines and Virotherapy, Biodesign Institute, Arizona State University, 727 E, Tempe, AZ, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA.
| | - Vivek Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- SAPHTx Inc, Newark, NJ, 07104, USA.
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA.
| |
Collapse
|
5
|
Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
Collapse
Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| |
Collapse
|
6
|
Sun Z, Lin H, Hu L, Neetu N, Sankaran B, Wang J, Prasad BVV, Palzkill T. Klebsiella pneumoniae carbapenemase variant 44 acquires ceftazidime-avibactam resistance by altering the conformation of active-site loops. J Biol Chem 2024; 300:105493. [PMID: 38000656 PMCID: PMC10716778 DOI: 10.1016/j.jbc.2023.105493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
Klebsiella pneumoniae carbapenemase 2 (KPC-2) is an important source of drug resistance as it can hydrolyze and inactivate virtually all β-lactam antibiotics. KPC-2 is potently inhibited by avibactam via formation of a reversible carbamyl linkage of the inhibitor with the catalytic serine of the enzyme. However, the use of avibactam in combination with ceftazidime (CAZ-AVI) has led to the emergence of CAZ-AVI-resistant variants of KPC-2 in clinical settings. One such variant, KPC-44, bears a 15 amino acid duplication in one of the active-site loops (270-loop). Here, we show that the KPC-44 variant exhibits higher catalytic efficiency in hydrolyzing ceftazidime, lower efficiency toward imipenem and meropenem, and a similar efficiency in hydrolyzing ampicillin, than the WT KPC-2 enzyme. In addition, the KPC-44 variant enzyme exhibits 12-fold lower AVI carbamylation efficiency than the KPC-2 enzyme. An X-ray crystal structure of KPC-44 showed that the 15 amino acid duplication results in an extended and partially disordered 270-loop and also changes the conformation of the adjacent 240-loop, which in turn has altered interactions with the active-site omega loop. Furthermore, a structure of KPC-44 with avibactam revealed that formation of the covalent complex results in further disorder in the 270-loop, suggesting that rearrangement of the 270-loop of KPC-44 facilitates AVI carbamylation. These results suggest that the duplication of 15 amino acids in the KPC-44 enzyme leads to resistance to CAZ-AVI by modulating the stability and conformation of the 270-, 240-, and omega-loops.
Collapse
Affiliation(s)
- Zhizeng Sun
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Hanfeng Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Neetu Neetu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA.
| |
Collapse
|
7
|
Salmen W, Hu L, Bok M, Chaimongkol N, Ettayebi K, Sosnovtsev SV, Soni K, Ayyar BV, Shanker S, Neill FH, Sankaran B, Atmar RL, Estes MK, Green KY, Parreño V, Prasad BVV. A single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity. Nat Commun 2023; 14:6516. [PMID: 37845211 PMCID: PMC10579229 DOI: 10.1038/s41467-023-42146-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/28/2023] [Indexed: 10/18/2023] Open
Abstract
Acute gastroenteritis caused by human noroviruses (HuNoVs) is a significant global health and economic burden and is without licensed vaccines or antiviral drugs. The GII.4 HuNoV causes most epidemics worldwide. This virus undergoes epochal evolution with periodic emergence of variants with new antigenic profiles and altered specificity for histo-blood group antigens (HBGA), the determinants of cell attachment and susceptibility, hampering the development of immunotherapeutics. Here, we show that a llama-derived nanobody M4 neutralizes multiple GII.4 variants with high potency in human intestinal enteroids. The crystal structure of M4 complexed with the protruding domain of the GII.4 capsid protein VP1 revealed a conserved epitope, away from the HBGA binding site, fully accessible only when VP1 transitions to a "raised" conformation in the capsid. Together with dynamic light scattering and electron microscopy of the GII.4 VLPs, our studies suggest a mechanism in which M4 accesses the epitope by altering the conformational dynamics of the capsid and triggering its disassembly to neutralize GII.4 infection.
Collapse
Affiliation(s)
- Wilhelm Salmen
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Marina Bok
- Virology Institute and Technology Innovation, IVIT, CONICET-INTA, Hurlingham, Buenos Aires, Argentina
| | - Natthawan Chaimongkol
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Stanislav V Sosnovtsev
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kaundal Soni
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - B Vijayalakshmi Ayyar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sreejesh Shanker
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Kim Y Green
- Caliciviruses Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Viviana Parreño
- Virology Institute and Technology Innovation, IVIT, CONICET-INTA, Hurlingham, Buenos Aires, Argentina
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
8
|
Short JM, Palmer CM, Burnley T, Winn MD, Zhang Q, Venkataram Prasad BV, Chen S, Crowther RA, Unwin PNT, Henderson R. MRC2020: improvements to Ximdisp and the MRC image-processing programs. IUCrJ 2023; 10:579-583. [PMID: 37493524 PMCID: PMC10478516 DOI: 10.1107/s2052252523006309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023]
Abstract
The great success of single-particle electron cryo-microscopy (cryoEM) during the last decade has involved the development of powerful new computer programs and packages that guide the user along a recommended processing workflow, in which the wisdom and choices made by the developers help everyone, especially new users, to obtain excellent results. The ability to carry out novel, non-standard or unusual combinations of image-processing steps is sometimes compromised by the convenience of a standard procedure. Some of the older programs were written with great flexibility and are still very valuable. Among these, the original MRC image-processing programs for structure determination by 2D crystal and helical processing alongside general-purpose utility programs such as Ximdisp, label, imedit and twofile are still available. This work describes an updated version of the MRC software package (MRC2020) that is freely available from CCP-EM. It includes new features and improvements such as extensions to the MRC format that retain the versatility of the package and make it particularly useful for testing novel computational procedures in cryoEM.
Collapse
Affiliation(s)
- J. M. Short
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - C. M. Palmer
- Science & Technology Facilities Council, Research Complex at Harwell, Harwell, Didcot OX11 0FA, United Kingdom
| | - T. Burnley
- Science & Technology Facilities Council, Research Complex at Harwell, Harwell, Didcot OX11 0FA, United Kingdom
| | - M. D. Winn
- Science & Technology Facilities Council, Research Complex at Harwell, Harwell, Didcot OX11 0FA, United Kingdom
| | - Q. Zhang
- Sun Yat Sen University, School of Life Science, State Key Laboratory of Biocontrol, Guangzhou 510275, People’s Republic of China
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - S. Chen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - R. A. Crowther
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - P. N. T. Unwin
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - R. Henderson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| |
Collapse
|
9
|
Zhao B, Hu L, Kuandal S, Neetu N, Lee C, Somoulay X, Sankaran B, Taylor GM, Dermody TS, Prasad BVV. Structure of Orthoreovirus RNA Chaperone σNS, a Component of Viral Replication Factories. bioRxiv 2023:2023.07.31.551319. [PMID: 37577609 PMCID: PMC10418060 DOI: 10.1101/2023.07.31.551319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The reovirus σNS RNA-binding protein is required for formation of intracellular compartments during viral infection that support viral genome replication and capsid assembly. Despite its functional importance, a mechanistic understanding of σNS is lacking. We conducted structural and biochemical analyses of an R6A mutant of σNS that forms dimers instead of the higher-order oligomers formed by wildtype (WT) σNS. The crystal structure of selenomethionine-substituted σNS-R6A reveals that the mutant protein forms a stable antiparallel dimer, with each subunit having a well-folded central core and a projecting N-terminal arm. The dimers interact with each other by inserting the N-terminal arms into a hydrophobic pocket of the neighboring dimers on either side to form a helical assembly that resembles filaments of WT σNS in complex with RNA observed using cryo-EM. The interior of the crystallographic helical assembly is positively charged and of appropriate diameter to bind RNA. The helical assembly is disrupted by bile acids, which bind to the same hydrophobic pocket as the N-terminal arm, as demonstrated in the crystal structure of σNS-R6A in complex with bile acid, suggesting that the N-terminal arm functions in conferring context-dependent oligomeric states of σNS. This idea is supported by the structure of σNS lacking the N-terminal arm. We discovered that σNS displays RNA helix destabilizing and annealing activities, likely essential for presenting mRNA to the viral RNA-dependent RNA polymerase for genome replication. The RNA chaperone activity is reduced by bile acids and abolished by N-terminal arm deletion, suggesting that the activity requires formation of σNS oligomers. Our studies provide structural and mechanistic insights into the function of σNS in reovirus replication.
Collapse
|
10
|
Sutherland DM, Strebl M, Koehler M, Welsh OL, Yu X, Hu L, dos Santos Natividade R, Knowlton JJ, Taylor GM, Moreno RA, Wörz P, Lonergan ZR, Aravamudhan P, Guzman-Cardozo C, Kour S, Pandey UB, Alsteens D, Wang Z, Prasad BVV, Stehle T, Dermody TS. NgR1 binding to reovirus reveals an unusual bivalent interaction and a new viral attachment protein. Proc Natl Acad Sci U S A 2023; 120:e2219404120. [PMID: 37276413 PMCID: PMC10268256 DOI: 10.1073/pnas.2219404120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/19/2023] [Indexed: 06/07/2023] Open
Abstract
Nogo-66 receptor 1 (NgR1) binds a variety of structurally dissimilar ligands in the adult central nervous system to inhibit axon extension. Disruption of ligand binding to NgR1 and subsequent signaling can improve neuron outgrowth, making NgR1 an important therapeutic target for diverse neurological conditions such as spinal crush injuries and Alzheimer's disease. Human NgR1 serves as a receptor for mammalian orthoreovirus (reovirus), but the mechanism of virus-receptor engagement is unknown. To elucidate how NgR1 mediates cell binding and entry of reovirus, we defined the affinity of interaction between virus and receptor, determined the structure of the virus-receptor complex, and identified residues in the receptor required for virus binding and infection. These studies revealed that central NgR1 surfaces form a bridge between two copies of viral capsid protein σ3, establishing that σ3 serves as a receptor ligand for reovirus. This unusual binding interface produces high-avidity interactions between virus and receptor to prime early entry steps. These studies refine models of reovirus cell-attachment and highlight the evolution of viruses to engage multiple receptors using distinct capsid components.
Collapse
Affiliation(s)
- Danica M. Sutherland
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Michael Strebl
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Olivia L. Welsh
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Xinzhe Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Rita dos Santos Natividade
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
| | - Jonathan J. Knowlton
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Cryo-Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX77030
| | - Gwen M. Taylor
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Rodolfo A. Moreno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
| | - Patrick Wörz
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Zachery R. Lonergan
- Cryo-Electron Microscopy and Tomography Core, Baylor College of Medicine, Houston, TX77030
| | - Pavithra Aravamudhan
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Camila Guzman-Cardozo
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Sukhleen Kour
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
| | - Udai Bhan Pandey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN37232
- Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, PA15261
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, 1348Louvain-la-Neuve, Belgium
- Children’s Neuroscience Institute, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
- Walloon Excellence in Life Sciences and Biotechnology, 1300Wavre, Belgium
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX77030
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX77030
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX77030
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, D-72076Tübingen, Germany
| | - Terence S. Dermody
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA15224
- Institute of Infection, Inflammation, and Immunity, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, PA15224
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA15219
| |
Collapse
|
11
|
Lu S, Montoya M, Hu L, Neetu N, Sankaran B, Prasad BVV, Palzkill T. Mutagenesis and structural analysis reveal the CTX-M β-lactamase active site is optimized for cephalosporin catalysis and drug resistance. J Biol Chem 2023; 299:104630. [PMID: 36963495 PMCID: PMC10139949 DOI: 10.1016/j.jbc.2023.104630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 03/26/2023] Open
Abstract
CTX-M β-lactamases are a widespread source of resistance to β-lactam antibiotics in Gram-negative bacteria. These enzymes readily hydrolyze penicillins and cephalosporins, including oxyimino-cephalosporins such as cefotaxime. To investigate the preference of CTX-M enzymes for cephalosporins, we examined eleven active-site residues in the CTX-M-14 β-lactamase model system by alanine mutagenesis to assess the contribution of the residues to catalysis and specificity for the hydrolysis of the penicillin, ampicillin, and the cephalosporins cephalothin and cefotaxime. Key active site residues for class A β-lactamases, including Lys73, Ser130, Asn132, Lys234, Thr216, and Thr235, contribute significantly to substrate binding and catalysis of penicillin and cephalosporin substrates in that alanine substitutions decrease both kcat and kcat/KM. A second group of residues, including Asn104, Tyr105, Asn106, Thr215, and Thr216, contribute only to substrate binding, with the substitutions decreasing only kcat/KM. Importantly, calculating the average effect of a substitution across the 11 active-site residues shows that the most significant impact is on cefotaxime hydrolysis while ampicillin hydrolysis is least affected, suggesting the active site is highly optimized for cefotaxime catalysis. Furthermore, we determined X-ray crystal structures for the apo-enzymes of the mutants N106A, S130A, N132A, N170A, T215A, and T235A. Surprisingly, in the structures of some mutants, particularly N106A and T235A, the changes in structure propagate from the site of substitution to other regions of the active site, suggesting that the impact of substitutions is due to more widespread changes in structure and illustrating the interconnected nature of the active site.
Collapse
Affiliation(s)
- Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Miranda Montoya
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Neetu Neetu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
| |
Collapse
|
12
|
Ayyar BV, Ettayebi K, Salmen W, Karandikar UC, Neill FH, Tenge VR, Crawford SE, Bieberich E, Prasad BVV, Atmar RL, Estes MK. CLIC and membrane wound repair pathways enable pandemic norovirus entry and infection. Nat Commun 2023; 14:1148. [PMID: 36854760 PMCID: PMC9974061 DOI: 10.1038/s41467-023-36398-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Globally, most cases of gastroenteritis are caused by pandemic GII.4 human norovirus (HuNoV) strains with no approved therapies or vaccines available. The cellular pathways that these strains exploit for cell entry and internalization are unknown. Here, using nontransformed human jejunal enteroids (HIEs) that recapitulate the physiology of the gastrointestinal tract, we show that infectious GII.4 virions and virus-like particles are endocytosed using a unique combination of endosomal acidification-dependent clathrin-independent carriers (CLIC), acid sphingomyelinase (ASM)-mediated lysosomal exocytosis, and membrane wound repair pathways. We found that besides the known interaction of the viral capsid Protruding (P) domain with host glycans, the Shell (S) domain interacts with both galectin-3 (gal-3) and apoptosis-linked gene 2-interacting protein X (ALIX), to orchestrate GII.4 cell entry. Recognition of the viral and cellular determinants regulating HuNoV entry provides insight into the infection process of a non-enveloped virus highlighting unique pathways and targets for developing effective therapeutics.
Collapse
Affiliation(s)
- B Vijayalakshmi Ayyar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Wilhelm Salmen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Umesh C Karandikar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Victoria R Tenge
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky, Lexington, KY 40506 and VAMC, Lexington, KY, 40502, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
13
|
Judge A, Hu L, Sankaran B, Van Riper J, Venkataram Prasad BV, Palzkill T. Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase. Commun Biol 2023; 6:35. [PMID: 36635385 PMCID: PMC9837174 DOI: 10.1038/s42003-023-04422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.
Collapse
Affiliation(s)
- Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Van Riper
- Graduate Program in Chemical, Physical, and Structural Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
14
|
Lu S, Hu L, Lin H, Judge A, Rivera P, Palaniappan M, Sankaran B, Wang J, Prasad BVV, Palzkill T. An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes. Nat Commun 2022; 13:6726. [PMID: 36344533 PMCID: PMC9640584 DOI: 10.1038/s41467-022-34564-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 10/27/2022] [Indexed: 11/09/2022] Open
Abstract
β-lactamases inactivate β-lactam antibiotics leading to drug resistance. Consequently, inhibitors of β-lactamases can combat this resistance, and the β-lactamase inhibitory protein (BLIP) is a naturally occurring inhibitor. The widespread CTX-M-14 and CTX-M-15 β-lactamases have an 83% sequence identity. In this study, we show that BLIP weakly inhibits CTX-M-14 but potently inhibits CTX-M-15. The structure of the BLIP/CTX-M-15 complex reveals that binding is associated with a conformational change of an active site loop of β-lactamase. Surprisingly, the loop structure in the complex is similar to that in a drug-resistant variant (N106S) of CTX-M-14. We hypothesized that the pre-established favorable loop conformation of the N106S mutant would facilitate binding. The N106S substitution results in a ~100- and 10-fold increase in BLIP inhibition potency for CTX-M-14 and CTX-M-15, respectively. Thus, this indicates that an active site loop in β-lactamase toggles between conformations that control antibiotic hydrolysis and inhibitor susceptibility. These findings highlight the role of accessible active site conformations in controlling enzyme activity and inhibitor susceptibility as well as the influence of mutations in selectively stabilizing discrete conformations.
Collapse
Affiliation(s)
- Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hanfeng Lin
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Paola Rivera
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
15
|
Hu L, Salmen W, Sankaran B, Lasanajak Y, Smith DF, Crawford SE, Estes MK, Prasad BVV. Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography. Commun Biol 2022; 5:419. [PMID: 35513489 PMCID: PMC9072675 DOI: 10.1038/s42003-022-03357-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 04/12/2022] [Indexed: 02/08/2023] Open
Abstract
The VP8* domain of spike protein VP4 in group A and C rotaviruses, which cause epidemic gastroenteritis in children, exhibits a conserved galectin-like fold for recognizing glycans during cell entry. In group B rotavirus, which causes significant diarrheal outbreaks in adults, the VP8* domain (VP8*B) surprisingly lacks sequence similarity with VP8* of group A or group C rotavirus. Here, by using the recently developed AlphaFold2 for ab initio structure prediction and validating the predicted model by determining a 1.3-Å crystal structure, we show that VP8*B exhibits a novel fold distinct from the galectin fold. This fold with a β-sheet clasping an α-helix represents a new fold for glycan recognition based on glycan array screening, which shows that VP8*B recognizes glycans containing N-acetyllactosamine moiety. Although uncommon, our study illustrates how evolution can incorporate structurally distinct folds with similar functionality in a homologous protein within the same virus genus.
Collapse
Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Wilhelm Salmen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Yi Lasanajak
- Emory Glycomics and Molecular Interactions Core (EGMIC), Emory University School of Medicine, Atlanta, GA, USA
| | - David F Smith
- Emory Glycomics and Molecular Interactions Core (EGMIC), Emory University School of Medicine, Atlanta, GA, USA
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
16
|
Choi KJ, Quan MD, Qi C, Lee JH, Tsoi PS, Zahabiyon M, Bajic A, Hu L, Prasad BVV, Liao SCJ, Li W, Ferreon ACM, Ferreon JC. NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. Nat Cell Biol 2022; 24:737-747. [PMID: 35484250 PMCID: PMC9106587 DOI: 10.1038/s41556-022-00896-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/16/2022] [Indexed: 12/12/2022]
Abstract
Human NANOG expression resets stem cells to ground-state pluripotency. Here we identify the unique features of human NANOG that relate to its dose-sensitive function as a master transcription factor. NANOG is largely disordered, with a C-terminal prion-like domain that phase-transitions to gel-like condensates. Full-length NANOG readily forms higher-order oligomers at low nanomolar concentrations, orders of magnitude lower than typical amyloids. Using single-molecule Förster resonance energy transfer and fluorescence cross-correlation techniques, we show that NANOG oligomerization is essential for bridging DNA elements in vitro. Using chromatin immunoprecipitation sequencing and Hi-C 3.0 in cells, we validate that NANOG prion-like domain assembly is essential for specific DNA recognition and distant chromatin interactions. Our results provide a physical basis for the indispensable role of NANOG in shaping the pluripotent genome. NANOG's unique ability to form prion-like assemblies could provide a cooperative and concerted DNA bridging mechanism that is essential for chromatin reorganization and dose-sensitive activation of ground-state pluripotency.
Collapse
Affiliation(s)
- Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - My Diem Quan
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Chuangye Qi
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Joo-Hyung Lee
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine and Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA. .,Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center and UTHealth, Houston, TX, USA.
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
17
|
Hu L, Salmen W, Chen R, Zhou Y, Neill F, Crowe JE, Atmar RL, Estes MK, Prasad BVV. Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity. Nat Commun 2022; 13:1241. [PMID: 35273142 PMCID: PMC8913647 DOI: 10.1038/s41467-022-28757-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/08/2022] [Indexed: 12/30/2022] Open
Abstract
Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being used in vaccine development. The atomic structure of the GII.4 capsid in the native T = 3 state has not been determined. Here we present the GII.4 VLP structure with T = 3 symmetry determined using X-ray crystallography and cryo-EM at 3.0 Å and 3.8 Å resolution, respectively, which reveals unanticipated novel features. A novel aspect in the crystal structure determined without imposing icosahedral symmetry is the remarkable adaptability of the capsid protein VP1 driven by the flexible hinge between the shell and the protruding domains. In both crystal and cryo-EM structures, VP1 adopts a stable conformation with the protruding domain resting on the shell domain, in contrast to the 'rising' conformation observed in recent cryo-EM structures of other GII.4 VLPs. Our studies further revealed that the resting state of VP1 dimer is stabilized by a divalent ion, and chelation using EDTA increases capsid diameter, exposing new hydrophobic and antigenic sites and suggesting a transition to the rising conformation. These novel insights into GII.4 capsid structure, stability, and antigen presentation may be useful for ongoing vaccine development.
Collapse
Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Rong Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yi Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Frederick Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
18
|
Alvarado G, Salmen W, Ettayebi K, Hu L, Sankaran B, Estes MK, Venkataram Prasad BV, Crowe JE. Author Correction: Broadly cross-reactive human antibodies that inhibit genogroup I and II noroviruses. Nat Commun 2021; 12:6090. [PMID: 34650069 PMCID: PMC8516901 DOI: 10.1038/s41467-021-26418-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gabriela Alvarado
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Department of Medicine-Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. .,The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA. .,The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
19
|
Zhao B, Hu L, Song Y, Patil K, Ramani S, Atmar RL, Estes MK, Prasad BVV. Norovirus Protease Structure and Antivirals Development. Viruses 2021; 13:v13102069. [PMID: 34696498 PMCID: PMC8537771 DOI: 10.3390/v13102069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 11/30/2022] Open
Abstract
Human norovirus (HuNoV) infection is a global health and economic burden. Currently, there are no licensed HuNoV vaccines or antiviral drugs available. The protease encoded by the HuNoV genome plays a critical role in virus replication by cleaving the polyprotein and is an excellent target for developing small-molecule inhibitors. The current strategy for developing HuNoV protease inhibitors is by targeting the enzyme’s active site and designing inhibitors that bind to the substrate-binding pockets located near the active site. However, subtle differential conformational flexibility in response to the different substrates in the polyprotein and structural differences in the active site and substrate-binding pockets across different genogroups, hamper the development of effective broad-spectrum inhibitors. A comparative analysis of the available HuNoV protease structures may provide valuable insight for identifying novel strategies for the design and development of such inhibitors. The goal of this review is to provide such analysis together with an overview of the current status of the design and development of HuNoV protease inhibitors.
Collapse
Affiliation(s)
- Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (B.Z.); (K.P.); (S.R.); (R.L.A.); (M.K.E.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
- Correspondence: ; Tel.: +1-713-798-5686
| |
Collapse
|
20
|
Tenge VR, Hu L, Prasad BVV, Larson G, Atmar RL, Estes MK, Ramani S. Glycan Recognition in Human Norovirus Infections. Viruses 2021; 13:2066. [PMID: 34696500 PMCID: PMC8537403 DOI: 10.3390/v13102066] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/11/2022] Open
Abstract
Recognition of cell-surface glycans is an important step in the attachment of several viruses to susceptible host cells. The molecular basis of glycan interactions and their functional consequences are well studied for human norovirus (HuNoV), an important gastrointestinal pathogen. Histo-blood group antigens (HBGAs), a family of fucosylated carbohydrate structures that are present on the cell surface, are utilized by HuNoVs to initially bind to cells. In this review, we describe the discovery of HBGAs as genetic susceptibility factors for HuNoV infection and review biochemical and structural studies investigating HuNoV binding to different HBGA glycans. Recently, human intestinal enteroids (HIEs) were developed as a laboratory cultivation system for HuNoV. We review how the use of this novel culture system has confirmed that fucosylated HBGAs are necessary and sufficient for infection by several HuNoV strains, describe mechanisms of antibody-mediated neutralization of infection that involve blocking of HuNoV binding to HBGAs, and discuss the potential for using the HIE model to answer unresolved questions on viral interactions with HBGAs and other glycans.
Collapse
Affiliation(s)
- Victoria R. Tenge
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (B.V.V.P.); (R.L.A.); (M.K.E.)
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (B.V.V.P.); (R.L.A.); (M.K.E.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Göran Larson
- Department of Laboratory Medicine, University of Gothenburg, SE 413 45 Gothenburg, Sweden;
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (B.V.V.P.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (B.V.V.P.); (R.L.A.); (M.K.E.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (B.V.V.P.); (R.L.A.); (M.K.E.)
| |
Collapse
|
21
|
Ding N, Zhao B, Ban X, Li C, Venkataram Prasad BV, Gu Z, Li Z. Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40 T. Front Microbiol 2021; 12:708480. [PMID: 34335544 PMCID: PMC8317173 DOI: 10.3389/fmicb.2021.708480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Marine extremophiles produce cold-adapted and/or salt-tolerant enzymes to survive in harsh conditions. These enzymes are naturally evolved with unique structural features that confer a high level of flexibility, solubility and substrate-binding ability compared to mesophilic and thermostable homologs. Here, we identified and characterized an amylase, SdG5A, from the marine bacterium Saccharophagus degradans 2-40 T . We expressed the protein in Bacillus subtilis and found that the purified SdG5A enabled highly specific production of maltopentaose, an important health-promoting food and nutrition component. Notably, SdG5A exhibited outstanding cold adaptation and salt tolerance, retaining approximately 30 and 70% of its maximum activity at 4°C and in 3 M NaCl, respectively. It converted 68 and 83% of starch into maltooligosaccharides at 4 and 25°C, respectively, within 24 h, with 79% of the yield being the maltopentaose. By analyzing the structure of SdG5A, we found that the C-terminal carbohydrate-binding module (CBM) coupled with an extended linker, displayed a relatively high negative charge density and superior conformational flexibility compared to the whole protein and the catalytic domain. Consistent with our bioinformatics analysis, truncation of the linker-CBM region resulted in a significant loss in activities at low temperature and high salt concentration. This highlights the linker-CBM acting as the critical component for the protein to carry out its activity in biologically unfavorable condition. Together, our study indicated that these unique properties of SdG5A have great potential for both basic research and industrial applications in food, biology, and medical and pharmaceutical fields.
Collapse
Affiliation(s)
- Ning Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Xiaofeng Ban
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Caiming Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States
| | - Zhengbiao Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| | - Zhaofeng Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Collaborative Innovation Center for Food Safety and Quality Control, Jiangnan University, Wuxi, China
| |
Collapse
|
22
|
Liu Z, Zhao F, Zhao B, Yang J, Ferrara J, Sankaran B, Venkataram Prasad BV, Kundu BB, Phillips GN, Gao Y, Hu L, Zhu T, Gao X. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat Commun 2021; 12:4158. [PMID: 34230497 PMCID: PMC8260726 DOI: 10.1038/s41467-021-24421-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.
Collapse
Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Biki Bapi Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
| |
Collapse
|
23
|
Karki M, Jangid R, Anish R, Seervai RN, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges CH, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. Abstract 2042: A cytoskeletal function for PBRM1: reading methylated microtubules to maintain genomic stability. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The chromatin modifier SETD2 often mutated in clear cell renal cell carcinoma (ccRCC), was recently shown to be a dual-function methyltransferase that “writes” methyl marks on both chromatin and microtubules, revealing α-tubulin methylation as a new posttranslational modification of the mitotic spindle. Here, we report that the polybromo protein PBRM1, the 2nd most mutated gene in ccRCC, is a “reader” for this SETD2-dependent methyl mark on α-tubulin. PBRM1 is a component of the PBAF (Polybromo BRG1 associated factor) chromatin remodeler complex. Our western and immunocytochemistry data in multiple kidney-derived cell lines, including HEK293T, HKC and 786-O, revealed that PBRM1 binds to methylated α-tubulin and localizes to the mitotic spindle and spindle pole during cell division. PBRM1 has six bromo domains, two bromo-associated homology (BAH) domains and one HMG domain. While PBRM1 is known to bind acetylated histones via its bromo domains, our GST pull down assays showed that PBRM1 binds methylated α-tubulin via its two BAH domains. Additional western and immunocytochemical experiments following knockout or re-expression of PBRM1 revealed that PBRM1 recruits other PBAF components to the mitotic spindle to maintain genomic stability. Two clinically established ccRCC mutations (P1048R and C1233W) in PBRM1 BAH domains result in loss of microtubule binding, mislocalization of PBAF, and the inability of PBRM1 to maintain genomic stability, as assessed by increased lagging chromosomes, chromosome bridges, multipolar spindles and micronuclei count. A third pathogenic ccRCC mutation (T1202K) in the PBRM1 BAH domain did not affect microtubule binding and consequently was not associated with mitotic spindle defects or genomic instability. Mass spectrometry and RNASeq confirmed BAH domain mutant PBRM1 still assembled a transcriptionally competent PBAF complex, clearly distinguishing the cytoskeletal from the chromatin impact of these mutations. These data reveal a previously unknown function of PBRM1 beyond reading acetylated histones, and expand the repertoire of chromatin remodelers acting on the cytoskeleton to maintain genomic stability.
Citation Format: Menuka Karki, Rahul Jangid, Ramakrishnan Anish, Riyad N. Seervai, Jean-Philippe Bertocchio, Takashi Hotta, Pavlos Msaouel, Sung Y. Jung, Sandra L. Grimm, Cristian Coarfa, Bernard E. Weissman, Ryoma Ohi, Kristen J. Verhey, Courtney H. Hodges, Ruhee Dere, In Young Park, B. V. Venkataram Prasad, W. Kimryn Rathmell, Cheryl L. Walker, Durga N. Tripathi. A cytoskeletal function for PBRM1: reading methylated microtubules to maintain genomic stability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2042.
Collapse
Affiliation(s)
| | | | | | | | | | - Takashi Hotta
- 3University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | | | | | - Ryoma Ohi
- 3University of Michigan Medical School, Ann Arbor, MI
| | | | | | - Ruhee Dere
- 1Baylor College of Medicine, Houston, TX
| | | | | | | | | | | |
Collapse
|
24
|
Tenge VR, Murakami K, Salmen W, Lin SC, Crawford SE, Neill FH, Prasad BVV, Atmar RL, Estes MK. Bile Goes Viral. Viruses 2021; 13:998. [PMID: 34071855 PMCID: PMC8227374 DOI: 10.3390/v13060998] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Laboratory cultivation of viruses is critical for determining requirements for viral replication, developing detection methods, identifying drug targets, and developing antivirals. Several viruses have a history of recalcitrance towards robust replication in laboratory cell lines, including human noroviruses and hepatitis B and C viruses. These viruses have tropism for tissue components of the enterohepatic circulation system: the intestine and liver, respectively. The purpose of this review is to discuss how key enterohepatic signaling molecules, bile acids (BAs), and BA receptors are involved in the replication of these viruses and how manipulation of these factors was useful in the development and/or optimization of culture systems for these viruses. BAs have replication-promoting activities through several key mechanisms: (1) affecting cellular uptake, membrane lipid composition, and endocytic acidification; (2) directly interacting with viral capsids to influence binding to cells; and (3) modulating the innate immune response. Additionally, expression of the Na+-taurocholate cotransporting polypeptide BA receptor in continuous liver cell lines is critical for hepatitis B virus entry and robust replication in laboratory culture. Viruses are capable of hijacking normal cellular functions, and understanding the role of BAs and BA receptors, components of the enterohepatic system, is valuable for expanding our knowledge on the mechanisms of norovirus and hepatitis B and C virus replication.
Collapse
Affiliation(s)
- Victoria R. Tenge
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan;
| | - Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shih-Ching Lin
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
| | - Frederick H. Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA; (V.R.T.); (W.S.); (S.-C.L.); (S.E.C.); (F.H.N.); (B.V.V.P.); (R.L.A.)
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
25
|
Furey IM, Mehta SC, Sankaran B, Hu L, Prasad BVV, Palzkill T. Local interactions with the Glu166 base and the conformation of an active site loop play key roles in carbapenem hydrolysis by the KPC-2 β-lactamase. J Biol Chem 2021; 296:100799. [PMID: 34022225 PMCID: PMC8189571 DOI: 10.1016/j.jbc.2021.100799] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/17/2021] [Indexed: 01/05/2023] Open
Abstract
The Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a common source of antibiotic resistance in Gram-negative bacterial infections. KPC-2 is a class A β-lactamase that exhibits a broad substrate profile and hydrolyzes most β-lactam antibiotics including carbapenems owing to rapid deacylation of the covalent acyl-enzyme intermediate. However, the features that allow KPC-2 to deacylate substrates more rapidly than non-carbapenemase enzymes are not clear. The active-site residues in KPC-2 are largely conserved in sequence and structure compared with non-carbapenemases, suggesting that subtle alterations may collectively facilitate hydrolysis of carbapenems. We utilized a nonbiased genetic approach to identify mutants deficient in carbapenem hydrolysis but competent for ampicillin hydrolysis. Subsequent pre–steady-state enzyme kinetics analyses showed that the substitutions slow the rate of deacylation of carbapenems. Structure determination via X-ray diffraction indicated that a F72Y mutant forms a hydrogen bond between the tyrosine hydroxyl group and Glu166, which may lower basicity and impair the activation of the catalytic water for deacylation, whereas several mutants impact the structure of the Q214-R220 active site loop. A T215P substitution lowers the deacylation rate and drastically alters the conformation of the loop, thereby disrupting interactions between the enzyme and the carbapenem acyl-enzyme intermediate. Thus, the environment of the Glu166 general base and the precise placement and conformational stability of the Q214-R220 loop are critical for efficient deacylation of carbapenems by the KPC-2 enzyme. Therefore, the design of carbapenem antibiotics that interact with Glu166 or alter the Q214-R220 loop conformation may disrupt enzyme function and overcome resistance.
Collapse
Affiliation(s)
- Ian M Furey
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston Texas, USA.
| |
Collapse
|
26
|
Karki M, Jangid RK, Anish R, Seervai RNH, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges HC, Burggren W, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. A cytoskeletal function for PBRM1 reading methylated microtubules. Sci Adv 2021; 7:7/14/eabf2866. [PMID: 33811077 DOI: 10.1126/sciadv.abf2866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic effectors "read" marks "written" on chromatin to regulate function and fidelity of the genome. Here, we show that this coordinated read-write activity of the epigenetic machinery extends to the cytoskeleton, with PBRM1 in the PBAF chromatin remodeling complex reading microtubule methyl marks written by the SETD2 histone methyltransferase. PBRM1 binds SETD2 methyl marks via BAH domains, recruiting PBAF components to the mitotic spindle. This read-write activity was required for normal mitosis: Loss of SETD2 methylation or pathogenic BAH domain mutations disrupt PBRM1 microtubule binding and PBAF recruitment and cause genomic instability. These data reveal PBRM1 functions beyond chromatin remodeling with domains that allow it to integrate chromatin and cytoskeletal activity via its acetyl-binding BD and methyl-binding BAH domains, respectively. Conserved coordinated activity of the epigenetic machinery on the cytoskeleton opens a previously unknown window into how chromatin remodeler defects can drive disease via both epigenetic and cytoskeletal dysfunction.
Collapse
Affiliation(s)
- Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Riyad N H Seervai
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Philippe Bertocchio
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pavlos Msaouel
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - H Courtney Hodges
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
27
|
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are an important source of resistance to these last resort β-lactam antibiotics. OXA-48 is a member of a group of CHDLs named OXA-48-like enzymes. On the basis of sequence similarity, OXA-163 can be classified as an OXA-48-like enzyme, but it has altered substrate specificity. Compared to OXA-48, it shows impaired activity for carbapenems but displays an enhanced hydrolysis of oxyimino-cephalosporins. Here, we address the mechanistic and structural basis for carbapenem hydrolysis by OXA-48-like enzymes. Pre-steady-state kinetic analysis indicates that the rate-limiting step for OXA-48 and OXA-163 hydrolysis of carbapenems is deacylation and that the greatly reduced carbapenemase activity of OXA-163 compared to that of OXA-48 is due entirely to a slower deacylation reaction. Furthermore, our structural data indicate that the positioning of the β5-β6 loop is necessary for carbapenem hydrolysis by OXA-48. A major difference between the OXA-48 and OXA-163 complexes with carbapenems is that the 214-RIEP-217 deletion in OXA-163 creates a large opening in the active site that is absent in the OXA-48/carbapenem structures. We propose that the larger active site results in less constraint on the conformation of the 6α-hydroxyethyl group in the acyl-enzyme. The acyl-enzyme intermediate assumes multiple conformations, most of which are incompatible with rapid deacylation. Consistent with this hypothesis, molecular dynamics simulations indicate that the most stable complex is formed between OXA-48 and imipenem, which correlates with the OXA-48 hydrolysis of imipenem being the fastest observed. Furthermore, the OXA-163 complexes with imipenem and meropenem are the least stable and show significant conformational fluctuations, which correlates with the slow hydrolysis of these substrates.
Collapse
Affiliation(s)
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States,
| | - Feng Wang
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75205, United States
| | | | | |
Collapse
|
28
|
Soeung V, Lu S, Hu L, Judge A, Sankaran B, Prasad BVV, Palzkill T. A drug-resistant β-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency. J Biol Chem 2020; 295:18239-18255. [PMID: 33109613 DOI: 10.1074/jbc.ra120.016103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 11/06/2022] Open
Abstract
Lys234 is one of the residues present in class A β-lactamases that is under selective pressure due to antibiotic use. Located adjacent to proton shuttle residue Ser130, it is suggested to play a role in proton transfer during catalysis of the antibiotics. The mechanism underpinning how substitutions in this position modulate inhibitor efficiency and substrate specificity leading to drug resistance is unclear. The K234R substitution identified in several inhibitor-resistant β-lactamase variants is associated with decreased potency of the inhibitor clavulanic acid, which is used in combination with amoxicillin to overcome β-lactamase-mediated antibiotic resistance. Here we show that for CTX-M-14 β-lactamase, whereas Lys234 is required for hydrolysis of cephalosporins such as cefotaxime, either lysine or arginine is sufficient for hydrolysis of ampicillin. Further, by determining the acylation and deacylation rates for cefotaxime hydrolysis, we show that both rates are fast, and neither is rate-limiting. The K234R substitution causes a 1500-fold decrease in the cefotaxime acylation rate but a 5-fold increase in kcat for ampicillin, suggesting that the K234R enzyme is a good penicillinase but a poor cephalosporinase due to slow acylation. Structural results suggest that the slow acylation by the K234R enzyme is due to a conformational change in Ser130, and this change also leads to decreased inhibition potency of clavulanic acid. Because other inhibitor resistance mutations also act through changes at Ser130 and such changes drastically reduce cephalosporin but not penicillin hydrolysis, we suggest that clavulanic acid paired with an oxyimino-cephalosporin rather than penicillin would impede the evolution of resistance.
Collapse
Affiliation(s)
- Victoria Soeung
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
| |
Collapse
|
29
|
Brown CA, Hu L, Sun Z, Patel MP, Singh S, Porter JR, Sankaran B, Prasad BVV, Bowman GR, Palzkill T. Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance. J Biol Chem 2020; 295:7376-7390. [PMID: 32299911 PMCID: PMC7247304 DOI: 10.1074/jbc.ra119.012489] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 04/14/2020] [Indexed: 11/06/2022] Open
Abstract
CTX-M β-lactamases are widespread in Gram-negative bacterial pathogens and provide resistance to the cephalosporin cefotaxime but not to the related antibiotic ceftazidime. Nevertheless, variants have emerged that confer resistance to ceftazidime. Two natural mutations, causing P167S and D240G substitutions in the CTX-M enzyme, result in 10-fold increased hydrolysis of ceftazidime. Although the combination of these mutations would be predicted to increase ceftazidime hydrolysis further, the P167S/D240G combination has not been observed in a naturally occurring CTX-M variant. Here, using recombinantly expressed enzymes, minimum inhibitory concentration measurements, steady-state enzyme kinetics, and X-ray crystallography, we show that the P167S/D240G double mutant enzyme exhibits decreased ceftazidime hydrolysis, lower thermostability, and decreased protein expression levels compared with each of the single mutants, indicating negative epistasis. X-ray structures of mutant enzymes with covalently trapped ceftazidime suggested that a change of an active-site Ω-loop to an open conformation accommodates ceftazidime leading to enhanced catalysis. 10-μs molecular dynamics simulations further correlated Ω-loop opening with catalytic activity. We observed that the WT and P167S/D240G variant with acylated ceftazidime both favor a closed conformation not conducive for catalysis. In contrast, the single substitutions dramatically increased the probability of open conformations. We conclude that the antagonism is due to restricting the conformation of the Ω-loop. These results reveal the importance of conformational heterogeneity of active-site loops in controlling catalytic activity and directing evolutionary trajectories.
Collapse
Affiliation(s)
- Cameron A Brown
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Zhizeng Sun
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Meha P Patel
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sukrit Singh
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Justin R Porter
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Gregory R Bowman
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.
| |
Collapse
|
30
|
Wang L, Qian H, Nian Y, Han Y, Ren Z, Zhang H, Hu L, Prasad BVV, Laganowsky A, Yan N, Zhou M. Structure and mechanism of human diacylglycerol O-acyltransferase 1. Nature 2020; 581:329-332. [PMID: 32433610 PMCID: PMC7255049 DOI: 10.1038/s41586-020-2280-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 03/17/2020] [Indexed: 12/27/2022]
Abstract
Diacylglycerol O-acyltransferase-1 (DGAT1) synthesizes triacylglycerides and is required for dietary fat absorption and fat storage in humans1. DGAT1 belongs to the superfamily of membrane-bound O-acyltransferases (MBOAT) that are found in all kingdoms of life and involved in acylation of lipids and proteins2,3. It remains unclear how human DGAT1 (hDGAT1) or other mammalian members of the MBOAT family recognize their substrates and catalyze their reactions. The absence of three-dimensional structures also hampers rational targeting of hDGAT1 for therapeutic purposes. Here we present the structure of hDGAT1 in complex with a substrate oleoyl Coenzyme A solved by cryo-electron microscopy. Each hDGAT1 protomer has nine transmembrane helices and eight of which form a conserved structural fold that we define as the MBOAT fold. The MBOAT fold in hDGAT1 carves out a hollow chamber in the membrane that encloses highly conserved catalytic residues. The chamber has separate entrances for the two substrates fatty acyl Coenzyme A and diacylglycerol. hDGAT1 can exist as either a homodimer or homotetramer and the two forms have similar enzymatic activity. The N-terminus of hDGAT1 interacts with the neighboring protomer and these interactions are required for the enzymatic activity.
Collapse
Affiliation(s)
- Lie Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hongwu Qian
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yin Nian
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yimo Han
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.,Department of Material Science and Nanoengineering, Rice University, Houston, TX, USA
| | - Zhenning Ren
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hanzhi Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Ming Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
31
|
Kumar D, Yu X, Crawford SE, Moreno R, Jakana J, Sankaran B, Anish R, Kaundal S, Hu L, Estes MK, Wang Z, Prasad BVV. 2.7 Å cryo-EM structure of rotavirus core protein VP3, a unique capping machine with a helicase activity. Sci Adv 2020; 6:eaay6410. [PMID: 32494598 PMCID: PMC7159914 DOI: 10.1126/sciadv.aay6410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/22/2020] [Indexed: 05/08/2023]
Abstract
In many viruses, including rotavirus (RV), the major pathogen of infantile gastroenteritis, capping of viral messenger RNAs is a pivotal step for efficient translation of the viral genome. In RV, VP3 caps the nascent transcripts synthesized from the genomic dsRNA segments by the RV polymerase VP1 within the particle core. Here, from cryo-electron microscopy, x-ray crystallography, and biochemical analyses, we show that VP3 forms a stable tetrameric assembly with each subunit having a modular domain organization, which uniquely integrates five distinct enzymatic steps required for capping the transcripts. In addition to the previously known guanylyl- and methyltransferase activities, we show that VP3 exhibits hitherto unsuspected RNA triphosphatase activity necessary for initiating transcript capping and RNA helicase activity likely required for separating the RNA duplex formed transiently during endogenous transcription. From our studies, we propose a new mechanism for how VP3 inside the virion core caps the nascent transcripts exiting from the polymerase.
Collapse
Affiliation(s)
- Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinzhe Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sue E. Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rodolfo Moreno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joanita Jakana
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- CryoEM Core, Baylor College of Medicine, Houston, TX 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Soni Kaundal
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- CryoEM Core, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author. (B.V.V.P.); (Z.W.)
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Corresponding author. (B.V.V.P.); (Z.W.)
| |
Collapse
|
32
|
Patel MP, Hu L, Brown CA, Sun Z, Adamski CJ, Stojanoski V, Sankaran B, Prasad BVV, Palzkill T. Synergistic effects of functionally distinct substitutions in β-lactamase variants shed light on the evolution of bacterial drug resistance. J Biol Chem 2018; 293:17971-17984. [PMID: 30275013 DOI: 10.1074/jbc.ra118.003792] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/26/2018] [Indexed: 11/06/2022] Open
Abstract
The CTX-M β-lactamases have emerged as the most widespread extended-spectrum β-lactamases (ESBLs) in Gram-negative bacteria. These enzymes rapidly hydrolyze cefotaxime, but not the related cephalosporin, ceftazidime. ESBL variants have evolved, however, that provide enhanced ceftazidime resistance. We show here that a natural variant at a nonactive site, i.e. second-shell residue N106S, enhances enzyme stability but reduces catalytic efficiency for cefotaxime and ceftazidime and decreases resistance levels. However, when the N106S variant was combined with an active-site variant, D240G, that enhances enzyme catalytic efficiency, but decreases stability, the resultant double mutant exhibited higher resistance levels than predicted on the basis of the phenotypes of each variant. We found that this epistasis is due to compensatory effects, whereby increased stability provided by N106S overrides its cost of decreased catalytic activity. X-ray structures of the variant enzymes in complex with cefotaxime revealed conformational changes in the active-site loop spanning residues 103-106 that were caused by the N106S substitution and relieve steric strain to stabilize the enzyme, but also alter contacts with cefotaxime and thereby reduce catalytic activity. We noted that the 103-106 loop conformation in the N106S-containing variants is different from that of WT CTX-M but nearly identical to that of the non-ESBL, TEM-1 β-lactamase, having a serine at the 106 position. Therefore, residue 106 may serve as a "switch" that toggles the conformations of the 103-106 loop. When it is serine, the loop is in the non-ESBL, TEM-like conformation, and when it is asparagine, the loop is in a CTX-M-like, cefotaximase-favorable conformation.
Collapse
Affiliation(s)
- Meha P Patel
- From the Interdepartmental Graduate Program in Translational Biology and Molecular Medicine; Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Liya Hu
- Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Cameron A Brown
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Zhizeng Sun
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Carolyn J Adamski
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Vlatko Stojanoski
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | | | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030; Verna Marrs McLean Department of Biochemistry and Molecular Biology.
| |
Collapse
|
33
|
Hu L, Sankaran B, Laucirica DR, Patil K, Salmen W, Ferreon ACM, Tsoi PS, Lasanajak Y, Smith DF, Ramani S, Atmar RL, Estes MK, Ferreon JC, Prasad BVV. Glycan recognition in globally dominant human rotaviruses. Nat Commun 2018; 9:2631. [PMID: 29980685 PMCID: PMC6035239 DOI: 10.1038/s41467-018-05098-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/11/2018] [Indexed: 01/01/2023] Open
Abstract
Rotaviruses (RVs) cause life-threatening diarrhea in infants and children worldwide. Recent biochemical and epidemiological studies underscore the importance of histo-blood group antigens (HBGA) as both cell attachment and susceptibility factors for the globally dominant P[4], P[6], and P[8] genotypes of human RVs. How these genotypes interact with HBGA is not known. Here, our crystal structures of P[4] and a neonate-specific P[6] VP8*s alone and in complex with H-type I HBGA reveal a unique glycan binding site that is conserved in the globally dominant genotypes and allows for the binding of ABH HBGAs, consistent with their prevalence. Remarkably, the VP8* of P[6] RVs isolated from neonates displays subtle structural changes in this binding site that may restrict its ability to bind branched glycans. This provides a structural basis for the age-restricted tropism of some P[6] RVs as developmentally regulated unbranched glycans are more abundant in the neonatal gut. Human rotaviruses (RV) bind to histo-blood group antigens (HBGA) for attachment, but how different viral genotypes interact with HBGA isn’t known. Here, Hu et al. report crystal structures of a prevalent and a neonate-specific RV in complex with HBGA and provide insights into glycan recognition and age-restricted tropism of RVs.
Collapse
Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Daniel R Laucirica
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wilhelm Salmen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Phoebe S Tsoi
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi Lasanajak
- Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - David F Smith
- Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Josephine C Ferreon
- Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
34
|
Patel MP, Hu L, Stojanoski V, Sankaran B, Prasad BVV, Palzkill T. The Drug-Resistant Variant P167S Expands the Substrate Profile of CTX-M β-Lactamases for Oxyimino-Cephalosporin Antibiotics by Enlarging the Active Site upon Acylation. Biochemistry 2017; 56:3443-3453. [PMID: 28613873 DOI: 10.1021/acs.biochem.7b00176] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
CTX-M β-lactamases provide resistance against the β-lactam antibiotic, cefotaxime, but not a related antibiotic, ceftazidime. β-Lactamases that carry the P167S substitution, however, provide ceftazidime resistance. In this study, CTX-M-14 was used as a model to study the structural changes caused by the P167S mutation that accelerate ceftazidime turnover. X-ray crystallography was used to determine the structures of the P167S apoenzyme along with the structures of the S70G/P167S, E166A/P167S, and E166A mutant enzymes complexed with ceftazidime as well as the E166A/P167S apoenzyme. The S70G and E166A mutations allow capture of the enzyme-substrate complex and the acylated form of ceftazidime, respectively. The results showed a large conformational change in the Ω-loop of the ceftazidime acyl-enzyme complex of the P167S mutant but not in the enzyme-substrate complex, suggesting the change occurs upon acylation. The change results in a larger active site that prevents steric clash between the aminothiazole ring of ceftazidime and the Asn170 residue in the Ω-loop, allowing accommodation of ceftazidime for hydrolysis. In addition, the conformational change was not observed in the E166A/P167S apoenzyme, suggesting the presence of acylated ceftazidime influences the conformational change. Finally, the E166A acyl-enzyme structure with ceftazidime did not exhibit the altered conformation, indicating the P167S substitution is required for the change. Taken together, the results reveal that the P167S substitution and the presence of acylated ceftazidime both drive the structure toward a conformational change in the Ω-loop and that in CTX-M P167S enzymes found in drug-resistant bacteria this will lead to an increased level of ceftazidime hydrolysis.
Collapse
Affiliation(s)
| | | | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | | |
Collapse
|
35
|
Shanker S, Hu L, Ramani S, Atmar RL, Estes MK, Venkataram Prasad BV. Structural features of glycan recognition among viral pathogens. Curr Opin Struct Biol 2017; 44:211-218. [PMID: 28591681 DOI: 10.1016/j.sbi.2017.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/12/2017] [Accepted: 05/15/2017] [Indexed: 10/19/2022]
Abstract
Recognition and binding to host glycans present on cellular surfaces is an initial and critical step in viral entry. Diverse families of host glycans such as histo-blood group antigens, sialoglycans and glycosaminoglycans are recognized by viruses. Glycan binding determines virus-host specificity, tissue tropism, pathogenesis and potential for interspecies transmission. Viruses including noroviruses, rotaviruses, enteroviruses, influenza, and papillomaviruses have evolved novel strategies to bind specific glycans often in a strain-specific manner. Structural studies have been instrumental in elucidating the molecular determinants of these virus-glycan interactions, aiding in developing vaccines and antivirals targeting this key interaction. Our review focuses on these key structural aspects of virus-glycan interactions, particularly highlighting the different strain-specific strategies employed by viruses to bind host glycans.
Collapse
Affiliation(s)
- Sreejesh Shanker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology.
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | | | - Robert L Atmar
- Department of Molecular Virology and Microbiology; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary K Estes
- Department of Molecular Virology and Microbiology; Department of Medicine, Baylor College of Medicine, Houston, TX 77030, United States
| | | |
Collapse
|
36
|
Stojanoski V, Sankaran B, Prasad BVV, Poirel L, Nordmann P, Palzkill T. Structure of the catalytic domain of the colistin resistance enzyme MCR-1. BMC Biol 2016; 14:81. [PMID: 27655155 PMCID: PMC5031297 DOI: 10.1186/s12915-016-0303-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/31/2016] [Indexed: 11/18/2022] Open
Abstract
Background Due to the paucity of novel antibiotics, colistin has become a last resort antibiotic for treating multidrug resistant bacteria. Colistin acts by binding the lipid A component of lipopolysaccharides and subsequently disrupting the bacterial membrane. The recently identified plasmid-encoded MCR-1 enzyme is the first transmissible colistin resistance determinant and is a cause for concern for the spread of this resistance trait. MCR-1 is a phosphoethanolamine transferase that catalyzes the addition of phosphoethanolamine to lipid A to decrease colistin affinity. Results The structure of the catalytic domain of MCR-1 at 1.32 Å reveals the active site is similar to that of related phosphoethanolamine transferases. Conclusions The putative nucleophile for catalysis, threonine 285, is phosphorylated in cMCR-1 and a zinc is present at a conserved site in addition to three zincs more peripherally located in the active site. As noted for catalytic domains of other phosphoethanolamine transferases, binding sites for the lipid A and phosphatidylethanolamine substrates are not apparent in the cMCR-1 structure, suggesting that they are present in the membrane domain. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0303-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vlatko Stojanoski
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurent Poirel
- Department of Medicine, Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit and European INSERM Laboratory, IAME, University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- Department of Medicine, Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit and European INSERM Laboratory, IAME, University of Fribourg, Fribourg, Switzerland.,University of Lausanne, University Hospital Center, Lausanne, Switzerland
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
37
|
Sapparapu G, Czakó R, Alvarado G, Shanker S, Prasad BVV, Atmar RL, Estes MK, Crowe JE. Frequent Use of the IgA Isotype in Human B Cells Encoding Potent Norovirus-Specific Monoclonal Antibodies That Block HBGA Binding. PLoS Pathog 2016; 12:e1005719. [PMID: 27355511 PMCID: PMC4927092 DOI: 10.1371/journal.ppat.1005719] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 06/02/2016] [Indexed: 11/18/2022] Open
Abstract
Noroviruses (NoV) are the most common cause of non-bacterial acute gastroenteritis and cause local outbreaks of illness, especially in confined situations. Despite being identified four decades ago, the correlates of protection against norovirus gastroenteritis are still being elucidated. Recent studies have shown an association of protection with NoV-specific serum histo-blood group antigen-blocking antibody and with serum IgA in patients vaccinated with NoV VLPs. Here, we describe the isolation and characterization of human monoclonal IgG and IgA antibodies against a GI.I NoV, Norwalk virus (NV). A higher proportion of the IgA antibodies blocked NV VLP binding to glycans than did IgG antibodies. We generated isotype-switched variants of IgG and IgA antibodies to study the effects of the constant domain on blocking and binding activities. The IgA form of antibodies appears to be more potent than the IgG form in blocking norovirus binding to histo-blood group antigens. These studies suggest a unique role for IgA antibodies in protection from NoV infections by blocking attachment to cell receptors.
Collapse
Affiliation(s)
- Gopal Sapparapu
- Department of Pediatrics, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Vaccine Center, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
| | - Rita Czakó
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gabriela Alvarado
- Department of Pathology, Microbiology and Immunology, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
| | - Sreejesh Shanker
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - B. V. Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - James E. Crowe
- Department of Pediatrics, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Vaccine Center, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology and Immunology, Vanderbilt Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
38
|
Park GW, Collins N, Barclay L, Hu L, Prasad BVV, Lopman BA, Vinjé J. Strain-Specific Virolysis Patterns of Human Noroviruses in Response to Alcohols. PLoS One 2016; 11:e0157787. [PMID: 27337036 PMCID: PMC4919085 DOI: 10.1371/journal.pone.0157787] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/03/2016] [Indexed: 12/13/2022] Open
Abstract
Alcohol-based hand sanitizers are widely used to disinfect hands to prevent the spread of pathogens including noroviruses. Alcohols inactivate norovirus by destruction of the viral capsid, resulting in the leakage of viral RNA (virolysis). Since conflicting results have been reported on the susceptibility of human noroviruses against alcohols, we exposed a panel of 30 human norovirus strains (14 GI and 16 GII strains) to different concentrations (50%, 70%, 90%) of ethanol and isopropanol and tested the viral RNA titer by RT-qPCR. Viral RNA titers of 10 (71.4%), 14 (100%), 3 (21.4%) and 7 (50%) of the 14 GI strains were reduced by > 1 log10 RNA copies/ml after exposure to 70% and 90% ethanol, and 70% and 90% isopropanol, respectively. RNA titers of 6 of the 7 non-GII 4 strains remained unaffected after alcohol exposure. Compared to GII strains, GI strains were more susceptible to ethanol than to isopropanol. At 90%, both alcohols reduced RNA titers of 8 of the 9 GII.4 strains by ≥ 1 log10 RNA copies/ml. After exposure to 70% ethanol, RNA titers of GII.4 Den Haag and Sydney strains decreased by ≥ 1.9 log10, whereas RNA reductions for GII.4 New Orleans strains were < 0.5 log10. To explain these differences, we sequenced the complete capsid gene of the 9 GII.4 strains and identified 17 amino acid substitutions in the P2 region among the 3 GII.4 variant viruses. When comparing with an additional set of 200 GII.4 VP1 sequences, only S310 and P396 were present in all GII.4 New Orleans viruses but not in the ethanol-sensitive GII.4 Sydney and GII.4 Den Haag viruses Our data demonstrate that alcohol susceptibility patterns between different norovirus genotypes vary widely and that virolysis data for a single strain or genotype are not representative for all noroviruses.
Collapse
Affiliation(s)
- Geun Woo Park
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Nikail Collins
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Atlanta Research and Education Foundation (AREF), Atlanta, GA, United States of America
| | - Leslie Barclay
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Liya Hu
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - B. V. Venkataram Prasad
- Verna Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, United States of America
| | - Benjamin A. Lopman
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| |
Collapse
|
39
|
Stojanoski V, Adamski CJ, Hu L, Mehta SC, Sankaran B, Zwart P, Prasad BVV, Palzkill T. Removal of the Side Chain at the Active-Site Serine by a Glycine Substitution Increases the Stability of a Wide Range of Serine β-Lactamases by Relieving Steric Strain. Biochemistry 2016; 55:2479-90. [PMID: 27073009 DOI: 10.1021/acs.biochem.6b00056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serine β-lactamases are bacterial enzymes that hydrolyze β-lactam antibiotics. They utilize an active-site serine residue as a nucleophile, forming an acyl-enzyme intermediate during hydrolysis. In this study, thermal denaturation experiments as well as X-ray crystallography were performed to test the effect of substitution of the catalytic serine with glycine on protein stability in serine β-lactamases. Six different enzymes comprising representatives from each of the three classes of serine β-lactamases were examined, including TEM-1, CTX-M-14, and KPC-2 of class A, P99 of class C, and OXA-48 and OXA-163 of class D. For each enzyme, the wild type and a serine-to-glycine mutant were evaluated for stability. The glycine mutants all exhibited enhanced thermostability compared to that of the wild type. In contrast, alanine substitutions of the catalytic serine in TEM-1, OXA-48, and OXA-163 did not alter stability, suggesting removal of the Cβ atom is key to the stability increase associated with the glycine mutants. The X-ray crystal structures of P99 S64G, OXA-48 S70G and S70A, and OXA-163 S70G suggest that removal of the side chain of the catalytic serine releases steric strain to improve enzyme stability. Additionally, analysis of the torsion angles at the nucleophile position indicates that the glycine mutants exhibit improved distance and angular parameters of the intrahelical hydrogen bond network compared to those of the wild-type enzymes, which is also consistent with increased stability. The increased stability of the mutants indicates that the enzyme pays a price in stability for the presence of a side chain at the catalytic serine position but that the cost is necessary in that removal of the serine drastically impairs function. These findings support the stability-function hypothesis, which states that active-site residues are optimized for substrate binding and catalysis but that the requirements for catalysis are often not consistent with the requirements for optimal stability.
Collapse
Affiliation(s)
| | | | | | | | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Advanced Light Source, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Peter Zwart
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Advanced Light Source, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | | |
Collapse
|
40
|
Mani N, Bhandari S, Moreno R, Hu L, Prasad BVV, Suguna K. Multiple oligomeric structures of a bacterial small heat shock protein. Sci Rep 2016; 6:24019. [PMID: 27053150 PMCID: PMC4823740 DOI: 10.1038/srep24019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
Small heat shock proteins are ubiquitous molecular chaperones that form the first line of defence against the detrimental effects of cellular stress. Under conditions of stress they undergo drastic conformational rearrangements in order to bind to misfolded substrate proteins and prevent cellular protein aggregation. Owing to the dynamic nature of small heat shock protein oligomers, elucidating the structural basis of chaperone action and oligomerization still remains a challenge. In order to understand the organization of sHSP oligomers, we have determined crystal structures of a small heat shock protein from Salmonella typhimurium in a dimeric form and two higher oligomeric forms: an 18-mer and a 24-mer. Though the core dimer structure is conserved in all the forms, structural heterogeneity arises due to variation in the terminal regions.
Collapse
Affiliation(s)
- Nandini Mani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Spraha Bhandari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rodolfo Moreno
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Kaza Suguna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| |
Collapse
|
41
|
Hu L, Ramani S, Czako R, Sankaran B, Yu Y, Smith DF, Cummings RD, Estes MK, Venkataram Prasad BV. Structural basis of glycan specificity in neonate-specific bovine-human reassortant rotavirus. Nat Commun 2015; 6:8346. [PMID: 26420502 PMCID: PMC4589887 DOI: 10.1038/ncomms9346] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/07/2015] [Indexed: 12/21/2022] Open
Abstract
Strain-dependent variation of glycan recognition during initial cell attachment of viruses is a critical determinant of host specificity, tissue-tropism and zoonosis. Rotaviruses (RVs), which cause life-threatening gastroenteritis in infants and children, display significant genotype-dependent variations in glycan recognition resulting from sequence alterations in the VP8* domain of the spike protein VP4. The structural basis of this genotype-dependent glycan specificity, particularly in human RVs, remains poorly understood. Here, from crystallographic studies, we show how genotypic variations configure a novel binding site in the VP8* of a neonate-specific bovine-human reassortant to uniquely recognize either type I or type II precursor glycans, and to restrict type II glycan binding in the bovine counterpart. Such a distinct glycan-binding site that allows differential recognition of the precursor glycans, which are developmentally regulated in the neonate gut and abundant in bovine and human milk provides a basis for age-restricted tropism and zoonotic transmission of G10P[11] rotaviruses.
Collapse
Affiliation(s)
- Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rita Czako
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Ying Yu
- Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - David F Smith
- Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Richard D Cummings
- Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
| |
Collapse
|
42
|
Stojanoski V, Chow DC, Fryszczyn B, Hu L, Nordmann P, Poirel L, Sankaran B, Prasad BVV, Palzkill T. Structural Basis for Different Substrate Profiles of Two Closely Related Class D β-Lactamases and Their Inhibition by Halogens. Biochemistry 2015; 54:3370-80. [PMID: 25938261 DOI: 10.1021/acs.biochem.5b00298] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OXA-163 and OXA-48 are closely related class D β-lactamases that exhibit different substrate profiles. OXA-163 hydrolyzes oxyimino-cephalosporins, particularly ceftazidime, while OXA-48 prefers carbapenem substrates. OXA-163 differs from OXA-48 by one substitution (S212D) in the active-site β5 strand and a four-amino acid deletion (214-RIEP-217) in the loop connecting the β5 and β6 strands. Although the structure of OXA-48 has been determined, the structure of OXA-163 is unknown. To further understand the basis for their different substrate specificities, we performed enzyme kinetic analysis, inhibition assays, X-ray crystallography, and molecular modeling. The results confirm the carbapenemase nature of OXA-48 and the ability of OXA-163 to hydrolyze the oxyimino-cephalosporin ceftazidime. The crystal structure of OXA-163 determined at 1.72 Å resolution reveals an expanded active site compared to that of OXA-48, which allows the bulky substrate ceftazidime to be accommodated. The structural differences with OXA-48, which cannot hydrolyze ceftazidime, provide a rationale for the change in substrate specificity between the enzymes. OXA-163 also crystallized under another condition that included iodide. The crystal structure determined at 2.87 Å resolution revealed iodide in the active site accompanied by several significant conformational changes, including a distortion of the β5 strand, decarboxylation of Lys73, and distortion of the substrate-binding site. Further studies showed that both OXA-163 and OXA-48 are inhibited in the presence of iodide. In addition, OXA-10, which is not a member of the OXA-48-like family, is also inhibited by iodide. These findings provide a molecular basis for the hydrolysis of ceftazidime by OXA-163 and, more broadly, show how minor sequence changes can profoundly alter the active-site configuration and thereby affect the substrate profile of an enzyme.
Collapse
Affiliation(s)
| | | | | | | | - Patrice Nordmann
- §Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit, Department of Medicine, Faculty of Science, University of Fribourg, 1700 Fribourg, Switzerland
| | - Laurent Poirel
- §Medical and Molecular Microbiology "Emerging Antibiotic Resistance" Unit, Department of Medicine, Faculty of Science, University of Fribourg, 1700 Fribourg, Switzerland
| | - Banumathi Sankaran
- ∥Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | |
Collapse
|
43
|
Stojanoski V, Chow DC, Hu L, Sankaran B, Gilbert HF, Prasad BVV, Palzkill T. A triple mutant in the Ω-loop of TEM-1 β-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis. J Biol Chem 2015; 290:10382-94. [PMID: 25713062 DOI: 10.1074/jbc.m114.633438] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 11/06/2022] Open
Abstract
β-Lactamases are bacterial enzymes that hydrolyze β-lactam antibiotics. TEM-1 is a prevalent plasmid-encoded β-lactamase in Gram-negative bacteria that efficiently catalyzes the hydrolysis of penicillins and early cephalosporins but not oxyimino-cephalosporins. A previous random mutagenesis study identified a W165Y/E166Y/P167G triple mutant that displays greatly altered substrate specificity with increased activity for the oxyimino-cephalosporin, ceftazidime, and decreased activity toward all other β-lactams tested. Surprisingly, this mutant lacks the conserved Glu-166 residue critical for enzyme function. Ceftazidime contains a large, bulky side chain that does not fit optimally in the wild-type TEM-1 active site. Therefore, it was hypothesized that the substitutions in the mutant expand the binding site in the enzyme. To investigate structural changes and address whether there is an enlargement in the active site, the crystal structure of the triple mutant was solved to 1.44 Å. The structure reveals a large conformational change of the active site Ω-loop structure to create additional space for the ceftazidime side chain. The position of the hydroxyl group of Tyr-166 and an observed shift in the pH profile of the triple mutant suggests that Tyr-166 participates in the hydrolytic mechanism of the enzyme. These findings indicate that the highly conserved Glu-166 residue can be substituted in the mechanism of serine β-lactamases. The results reveal that the robustness of the overall β-lactamase fold coupled with the plasticity of an active site loop facilitates the evolution of enzyme specificity and mechanism.
Collapse
Affiliation(s)
- Vlatko Stojanoski
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and the Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Dar-Chone Chow
- the Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 and
| | - Liya Hu
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - Banumathi Sankaran
- the Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Hiram F Gilbert
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - B V Venkataram Prasad
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and
| | - Timothy Palzkill
- From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology and the Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 and
| |
Collapse
|
44
|
Adamski C, Cardenas AM, Brown NG, Horton LB, Sankaran B, Prasad BVV, Gilbert H, Palzkill T. Molecular basis for the catalytic specificity of the CTX-M extended-spectrum β-lactamases. Biochemistry 2015; 54:447-57. [PMID: 25489790 PMCID: PMC4303298 DOI: 10.1021/bi501195g] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/23/2014] [Indexed: 11/29/2022]
Abstract
Extended-spectrum β-lactamases (ESBLs) pose a threat to public health because of their ability to confer resistance to extended-spectrum cephalosporins such as cefotaxime. The CTX-M β-lactamases are the most widespread ESBL enzymes among antibiotic resistant bacteria. Many of the active site residues are conserved between the CTX-M family and non-ESBL β-lactamases such as TEM-1, but the residues Ser237 and Arg276 are specific to the CTX-M family, suggesting that they may help to define the increased specificity for cefotaxime hydrolysis. To test this hypothesis, site-directed mutagenesis of these positions was performed in the CTX-M-14 β-lactamase. Substitutions of Ser237 and Arg276 with their TEM-1 counterparts, Ala237 and Asn276, had a modest effect on cefotaxime hydrolysis, as did removal of the Arg276 side chain in an R276A mutant. The S237A:R276N and S237A:R276A double mutants, however, exhibited 29- and 14-fold losses in catalytic efficiency for cefotaxime hydrolysis, respectively, while the catalytic efficiency for benzylpenicillin hydrolysis was unchanged. Therefore, together, the Ser237 and Arg276 residues are important contributors to the cefotaximase substrate profile of the enzyme. High-resolution crystal structures of the CTX-M-14 S70G, S70G:S237A, and S70G:S237A:R276A variants alone and in complex with cefotaxime show that residues Ser237 and Arg276 in the wild-type enzyme promote the expansion of the active site to accommodate cefotaxime and favor a conformation of cefotaxime that allows optimal contacts between the enzyme and substrate. The conservation of these residues, linked to their effects on structure and catalysis, imply that their coevolution is an important specificity determinant in the CTX-M family.
Collapse
Affiliation(s)
- Carolyn
J. Adamski
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Ana Maria Cardenas
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Nicholas G. Brown
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Lori B. Horton
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - B. V. Venkataram Prasad
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Hiram
F. Gilbert
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| | - Timothy Palzkill
- Verna and Marrs McLean
Department of Biochemistry and Molecular Biology, Department of Molecular
Virology and Microbiology, Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United
States
| |
Collapse
|
45
|
Venkataram Prasad BV, Shanker S, Hu L, Choi JM, Crawford SE, Ramani S, Czako R, Atmar RL, Estes MK. Structural basis of glycan interaction in gastroenteric viral pathogens. Curr Opin Virol 2014; 7:119-27. [PMID: 25073118 DOI: 10.1016/j.coviro.2014.05.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/12/2023]
Abstract
A critical event in the life cycle of a virus is its initial attachment to host cells. This involves recognition by the viruses of specific receptors on the cell surface, including glycans. Viruses typically exhibit strain-dependent variations in recognizing specific glycan receptors, a feature that contributes significantly to cell tropism, host specificity, host adaptation and interspecies transmission. Examples include influenza viruses, noroviruses, rotaviruses, and parvoviruses. Both rotaviruses and noroviruses are well known gastroenteric pathogens that are of significant global health concern. While rotaviruses, in the family Reoviridae, are the major causative agents of life-threatening diarrhea in children, noroviruses, which belong to the Caliciviridae family, cause epidemic and sporadic cases of acute gastroenteritis across all age groups. Both exhibit enormous genotypic and serotypic diversity. Consistent with this diversity each exhibits strain-dependent variations in the types of glycans they recognize for cell attachment. This chapter reviews the current status of the structural biology of such strain-dependent glycan specificities in these two families of viruses.
Collapse
Affiliation(s)
- B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States.
| | - Sreejesh Shanker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Jae-Mun Choi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Rita Czako
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, United States
| |
Collapse
|
46
|
Yu Y, Lasanajak Y, Song X, Hu L, Ramani S, Mickum ML, Ashline DJ, Prasad BVV, Estes MK, Reinhold VN, Cummings RD, Smith DF. Human milk contains novel glycans that are potential decoy receptors for neonatal rotaviruses. Mol Cell Proteomics 2014; 13:2944-60. [PMID: 25048705 DOI: 10.1074/mcp.m114.039875] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Human milk contains a rich set of soluble, reducing glycans whose functions and bioactivities are not well understood. Because human milk glycans (HMGs) have been implicated as receptors for various pathogens, we explored the functional glycome of human milk using shotgun glycomics. The free glycans from pooled milk samples of donors with mixed Lewis and Secretor phenotypes were labeled with a fluorescent tag and separated via multidimensional HPLC to generate a tagged glycan library containing 247 HMG targets that were printed to generate the HMG shotgun glycan microarray (SGM). To investigate the potential role of HMGs as decoy receptors for rotavirus (RV), a leading cause of severe gastroenteritis in children, we interrogated the HMG SGM with recombinant forms of VP8* domains of the RV outer capsid spike protein VP4 from human neonatal strains N155(G10P[11]) and RV3(G3P[6]) and a bovine strain, B223(G10P[11]). Glycans that were bound by RV attachment proteins were selected for detailed structural analyses using metadata-assisted glycan sequencing, which compiles data on each glycan based on its binding by antibodies and lectins before and after exo- and endo-glycosidase digestion of the SGM, coupled with independent MS(n) analyses. These complementary structural approaches resulted in the identification of 32 glycans based on RV VP8* binding, many of which are novel HMGs, whose detailed structural assignments by MS(n) are described in a companion report. Although sialic acid has been thought to be important as a surface receptor for RVs, our studies indicated that sialic acid is not required for binding of glycans to individual VP8* domains. Remarkably, each VP8* recognized specific glycan determinants within a unique subset of related glycan structures where specificity differences arise from subtle differences in glycan structures.
Collapse
Affiliation(s)
- Ying Yu
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Yi Lasanajak
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Xuezheng Song
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Liya Hu
- §Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sasirekha Ramani
- ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Megan L Mickum
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - David J Ashline
- ‖Glycomics Center, University of New Hampshire, Durham, New Hampshire 03824
| | - B V Venkataram Prasad
- §Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030; ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Mary K Estes
- ¶Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030
| | - Vernon N Reinhold
- ‖Glycomics Center, University of New Hampshire, Durham, New Hampshire 03824
| | - Richard D Cummings
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - David F Smith
- From the ‡Department of Biochemistry and the National Center for Functional Glycomics, Emory University School of Medicine, Atlanta, Georgia 30322;
| |
Collapse
|
47
|
Zheng B, Yao Y, Liu Z, Deng L, Anglin JL, Jiang H, Prasad BVV, Song Y. Crystallographic Investigation and Selective Inhibition of Mutant Isocitrate Dehydrogenase. ACS Med Chem Lett 2013; 4:542-546. [PMID: 23795241 DOI: 10.1021/ml400036z] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Mutations in isocitrate dehydrogenase (IDH), a key enzyme in the tricarboxylic acid cycle, have recently been found in ~75% glioma and ~20% acute myeloid leukemia. Different from the wild-type enzyme, mutant IDH1 catalyzes the reduction of α-ketoglutaric acid to D-2-hydroxyglutaric acid. Strong evidence has shown mutant IDH1 represents a novel target for this type of cancer. We found two 1-hydroxypyridin-2-one compounds that are potent inhibitors of R132H and R132C IDH1 mutants with Ki values as low as 120 nM. These compounds exhibit >60-fold selectivity against wild-type IDH1 and can inhibit the production of D-2-hydroxyglutaric acid in IDH1 mutated cells, representing novel chemical probes for cancer biology studies. We also report the first inhibitor-bound crystal structures of IDH1(R132H), showing these inhibitors have H-bond, electrostatic and hydrophobic interactions with the mutant enzyme. Comparison with the substrate-bound IDH1 structures revealed the structural basis for the high enzyme selectivity of these compounds.
Collapse
Affiliation(s)
- Baisong Zheng
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Yuan Yao
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Zhen Liu
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Lisheng Deng
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Justin L. Anglin
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Hong Jiang
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - B. V. Venkataram Prasad
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| | - Yongcheng Song
- Department of Pharmacology, ‡Verna and Marrs McLean Department
of Biochemistry and Molecular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
77030, United States
| |
Collapse
|
48
|
Vongpunsawad S, Venkataram Prasad BV, Estes MK. Norwalk Virus Minor Capsid Protein VP2 Associates within the VP1 Shell Domain. J Virol 2013; 87:4818-25. [PMID: 23408637 PMCID: PMC3624303 DOI: 10.1128/jvi.03508-12] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/08/2013] [Indexed: 11/20/2022] Open
Abstract
The major capsid protein of norovirus VP1 assembles to form an icosahedral viral particle. Despite evidence that the Norwalk virus (NV) minor structural protein VP2 is present in infectious virions, the available crystallographic and electron cryomicroscopy structures of NV have not revealed the location of VP2. In this study, we determined that VP1 associates with VP2 at the interior surface of the capsid, specifically with the shell (S) domain of VP1. We mapped the interaction site to amino acid 52 of VP1, an isoleucine located within a sequence motif IDPWI in the S domain that is highly conserved across norovirus genogroups. Mutation of this isoleucine abrogated VP2 incorporation into virus-like particles without affecting the ability for VP1 to dimerize and form particles. The highly basic nature of VP2 and its location interior to the viral particle are consistent with its potential role in assisting capsid assembly and genome encapsidation.
Collapse
Affiliation(s)
| | - B. V. Venkataram Prasad
- Department of Molecular Virology and Microbiology
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | | |
Collapse
|
49
|
Deng L, Muhaxhiri Z, Estes MK, Palzkill T, Prasad BVV, Song Y. Synthesis, Activity and Structure-Activity Relationship of Noroviral Protease Inhibitors. Medchemcomm 2013; 4. [PMID: 24244836 DOI: 10.1039/c3md00219e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The protease of norovirus, an important human pathogen, is essential for the viral replication and, therefore, represents a potential drug target. A series of tripeptide-based inhibitors of the protease were designed, synthesized and tested, among which several potent inhibitors were identified with Ki values as low as 75 nM. The structure-activity relationships of these inhibitors are discussed.
Collapse
Affiliation(s)
- Lisheng Deng
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, United States
| | | | | | | | | | | |
Collapse
|
50
|
Yao Y, Chen P, Diao J, Cheng G, Deng L, Anglin JL, Prasad BVV, Song Y. Correction to Selective Inhibitors of Histone Methyltransferase DOT1L: Design, Synthesis, and Crystallographic Studies. J Am Chem Soc 2012. [DOI: 10.1021/ja309785w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|