1
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Bodt SML, Ge J, Ma W, Rasicci DV, Desetty R, McCammon JA, Yengo CM. Dilated cardiomyopathy mutation in beta-cardiac myosin enhances actin activation of the power stroke and phosphate release. bioRxiv 2023:2023.11.10.566646. [PMID: 38014187 PMCID: PMC10680644 DOI: 10.1101/2023.11.10.566646] [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: 11/29/2023]
Abstract
Inherited mutations in human beta-cardiac myosin (M2β) can lead to severe forms of heart failure. The E525K mutation in M2β is associated with dilated cardiomyopathy (DCM) and was found to stabilize the interacting heads motif (IHM) and autoinhibited super-relaxed (SRX) state in dimeric heavy meromyosin. However, in monomeric M2β subfragment 1 (S1) we found that E525K enhances (3-fold) the maximum steady-state actin-activated ATPase activity ( k cat ) and decreases (6-fold) the actin concentration at which ATPase is one-half maximal ( K ATPase ). We also found a 3 to 4-fold increase in the actin-activated power stroke and phosphate release rate constants at 30 μM actin, which overall enhanced the duty ratio 3-fold. Loaded motility assays revealed that the enhanced intrinsic motor activity translates to increased ensemble force in M2β S1. Glutamate 525, located near the actin binding region in the so-called activation loop, is highly conserved and predicted to form a salt-bridge with another conserved residue (lysine 484) in the relay helix. Enhanced sampling molecular dynamics simulations predict that the charge reversal mutation disrupts the E525-K484 salt-bridge, inducing conformations with a more flexible relay helix and a wide phosphate release tunnel. Our results highlight a highly conserved allosteric pathway associated with actin activation of the power stroke and phosphate release and suggest an important feature of the autoinhibited IHM is to prevent this region of myosin from interacting with actin. The ability of the E525K mutation to stabilize the IHM likely overrides the enhanced intrinsic motor properties, which may be key to triggering DCM pathogenesis. Significance Statement Heart disease can be caused by inherited mutations in beta-cardiac myosin, the molecular motor that powers systolic contraction in the ventricles of the heart. However, it remains unclear how these mutations lead to contractile dysfunction and pathogenic remodeling of the heart. We investigated a unique dilated cardiomyopathy mutation (E525K) that dramatically stabilizes the autoinhibited state while enhancing intrinsic motor function. Thus, we examined how this mutation impacts transient kinetic steps of the ATPase cycle, motile properties, and structural changes associated with the power stroke and phosphate release. Our results provide a kinetic and structural basis for how beta-cardiac myosin mutations may disrupt molecular-level contractile function in complex ways, which may inform the development of targeted therapeutics.
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2
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. J Phys Chem Lett 2023; 14:9926-9934. [PMID: 37903229 PMCID: PMC10641874 DOI: 10.1021/acs.jpclett.3c02524] [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] [Received: 09/10/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/01/2023]
Abstract
All protein simulations are conducted with varying degrees of simplification, oftentimes with unknown ramifications about how these simplifications affect the interpretability of the results. In this work, we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: (1) glycosylated neuraminidase in a whole virion (i.e., crowded membrane) environment, (2) glycosylated neuraminidase in its own lipid bilayer, and (3) unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting the solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large-scale conformational change, while making the protein structure more compact. Understanding these effects informs what factors one must consider in attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - İlker Deveci
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
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3
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Seitz C, Deveci İ, McCammon JA. Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics. bioRxiv 2023:2023.09.10.556910. [PMID: 37745347 PMCID: PMC10515755 DOI: 10.1101/2023.09.10.556910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
All protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.
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Affiliation(s)
- Christian Seitz
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - İlker Deveci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
- Department of Pharmacology, University of California, San Diego, La Jolla, California
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4
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Sztain T, Corpuz JC, Bartholow TG, Hernandez JOS, Jiang Z, Mellor DA, Heberlig GW, La Clair JJ, McCammon JA, Burkart MD. Interface Engineering of Carrier-Protein-Dependent Metabolic Pathways. ACS Chem Biol 2023; 18:2014-2022. [PMID: 37671411 PMCID: PMC10807135 DOI: 10.1021/acschembio.3c00238] [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: 09/07/2023]
Abstract
Carrier-protein-dependent metabolic pathways biosynthesize fatty acids, polyketides, and non-ribosomal peptides, producing metabolites with important pharmaceutical, environmental, and industrial properties. Recent findings demonstrate that these pathways rely on selective communication mechanisms involving protein-protein interactions (PPIs) that guide enzyme reactivity and timing. While rational design of these PPIs could enable pathway design and modification, this goal remains a challenge due to the complex nature of protein interfaces. Computational methods offer an encouraging avenue, though many score functions fail to predict experimental observables, leading to low success rates. Here, we improve upon the Rosetta score function, leveraging experimental data through iterative rounds of computational prediction and mutagenesis, to design a hybrid fatty acid-non-ribosomal peptide initiation pathway. By increasing the weight of the electrostatic score term, the computational protocol proved to be more predictive, requiring fewer rounds of iteration to identify mutants with high in vitro activity. This allowed efficient design of new PPIs between a non-ribosomal peptide synthetase adenylation domain, PltF, and a fatty acid synthase acyl carrier protein, AcpP, as validated by activity and structural studies. This method provides a promising platform for customized pathway design, establishing a standard for carrier-protein-dependent pathway engineering through PPI optimization.
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Affiliation(s)
| | | | - Thomas G. Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Javier O. Sanlley Hernandez
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Desirae A. Mellor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Graham W. Heberlig
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - James J. La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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5
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Hock MT, Teitgen AE, McCabe KJ, Hirakis SP, Huber GA, Regnier M, Amaro RE, McCammon JA, McCulloch AD. Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling. J Appl Phys 2023; 134:074905. [PMID: 37601331 PMCID: PMC10435275 DOI: 10.1063/5.0157935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023]
Abstract
2'-Deoxy-ATP (dATP), a naturally occurring near analog of ATP, is a well-documented myosin activator that has been shown to increase contractile force, improve pump function, and enhance lusitropy in the heart. Calcium transients in cardiomyocytes with elevated levels of dATP show faster calcium decay compared with cardiomyocytes with basal levels of dATP, but the mechanisms behind this are unknown. Here, we design and utilize a multiscale computational modeling framework to test the hypothesis that dATP acts on the sarcoendoplasmic reticulum calcium-ATPase (SERCA) pump to accelerate calcium re-uptake into the sarcoplasmic reticulum during cardiac relaxation. Gaussian accelerated molecular dynamics simulations of human cardiac SERCA2A in the E1 apo, ATP-bound and dATP-bound states showed that dATP forms more stable contacts in the nucleotide binding pocket of SERCA and leads to increased closure of cytosolic domains. These structural changes ultimately lead to changes in calcium binding, which we assessed using Brownian dynamics simulations. We found that dATP increases calcium association rate constants to SERCA and that dATP binds to apo SERCA more rapidly than ATP. Using a compartmental ordinary differential equation model of human cardiomyocyte excitation-contraction coupling, we found that these increased association rate constants contributed to the accelerated rates of calcium transient decay observed experimentally. This study provides clear mechanistic evidence of enhancements in cardiac SERCA2A pump function due to interactions with dATP.
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Affiliation(s)
- Marcus T. Hock
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Abigail E. Teitgen
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Kimberly J. McCabe
- Department of Computational Physiology, Simula Resesarch Laboratory, Oslo 0164, Norway
| | - Sophia P. Hirakis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Gary A. Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington 98109, USA
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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6
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Philpott JM, Freeberg AM, Park J, Lee K, Ricci CG, Hunt SR, Narasimamurthy R, Segal DH, Robles R, Cai Y, Tripathi S, McCammon JA, Virshup DM, Chiu JC, Lee C, Partch CL. PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period. Mol Cell 2023; 83:1677-1692.e8. [PMID: 37207626 DOI: 10.1016/j.molcel.2023.04.019] [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: 06/27/2022] [Revised: 02/16/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
PERIOD (PER) and Casein Kinase 1δ regulate circadian rhythms through a phosphoswitch that controls PER stability and repressive activity in the molecular clock. CK1δ phosphorylation of the familial advanced sleep phase (FASP) serine cluster embedded within the Casein Kinase 1 binding domain (CK1BD) of mammalian PER1/2 inhibits its activity on phosphodegrons to stabilize PER and extend circadian period. Here, we show that the phosphorylated FASP region (pFASP) of PER2 directly interacts with and inhibits CK1δ. Co-crystal structures in conjunction with molecular dynamics simulations reveal how pFASP phosphoserines dock into conserved anion binding sites near the active site of CK1δ. Limiting phosphorylation of the FASP serine cluster reduces product inhibition, decreasing PER2 stability and shortening circadian period in human cells. We found that Drosophila PER also regulates CK1δ via feedback inhibition through the phosphorylated PER-Short domain, revealing a conserved mechanism by which PER phosphorylation near the CK1BD regulates CK1 kinase activity.
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Affiliation(s)
- Jonathan M Philpott
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jiyoung Park
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Kwangjun Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sabrina R Hunt
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rajesh Narasimamurthy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - David H Segal
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rafael Robles
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yao Cai
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Choogon Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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7
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Weng JH, Ma W, Wu J, Sharma PK, Silletti S, McCammon JA, Taylor S. Capturing Differences in the Regulation of LRRK2 Dynamics and Conformational States by Small Molecule Kinase Inhibitors. ACS Chem Biol 2023; 18:810-821. [PMID: 37043829 PMCID: PMC10127209 DOI: 10.1021/acschembio.2c00868] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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] [Received: 11/21/2022] [Accepted: 03/21/2023] [Indexed: 04/14/2023]
Abstract
Mutations in the human leucine rich repeat protein kinase-2 (LRRK2) create risk factors for Parkinson's disease, and pathological functions of LRRK2 are often correlated with aberrant kinase activity. Past research has focused on developing selective LRRK2 kinase inhibitors. In this study, we combined enhanced sampling simulations with HDX-MS to characterize the inhibitor-induced dynamic changes and the allosteric communications within the C-terminal domains of LRRK2, LRRK2RCKW. We find that the binding of MLi-2 (a type I kinase inhibitor) stabilizes a closed kinase conformation and reduces the global dynamics of LRRK2RCKW, leading to a more compact LRRK2RCKW structure. In contrast, the binding of Rebastinib (a type II kinase inhibitor) stabilizes an open kinase conformation, which promotes a more extended LRRK2RCKW structure. By probing the distinct effects of the type I and type II inhibitors, key interdomain interactions are found to regulate the communication between the kinase domain and the GTPase domain. The intermediate states revealed in our simulations facilitate the efforts toward in silico design of allosteric modulators that control LRRK2 conformations and potentially mediate the oligomeric states of LRRK2 and its interactions with other proteins.
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Affiliation(s)
- Jui-Hung Weng
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Wen Ma
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Jian Wu
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Pallavi Kaila Sharma
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
| | - Steve Silletti
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
| | - Susan Taylor
- Department
of Pharmacology, University of California, San Diego, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, California 92093, United States
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8
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Ma W, You S, Regnier M, McCammon JA. Integrating comparative modeling and accelerated simulations reveals conformational and energetic basis of actomyosin force generation. Proc Natl Acad Sci U S A 2023; 120:e2215836120. [PMID: 36802417 PMCID: PMC9992861 DOI: 10.1073/pnas.2215836120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/23/2022] [Accepted: 01/15/2023] [Indexed: 02/23/2023] Open
Abstract
Muscle contraction is performed by arrays of contractile proteins in the sarcomere. Serious heart diseases, such as cardiomyopathy, can often be results of mutations in myosin and actin. Direct characterization of how small changes in the myosin-actin complex impact its force production remains challenging. Molecular dynamics (MD) simulations, although capable of studying protein structure-function relationships, are limited owing to the slow timescale of the myosin cycle as well as a lack of various intermediate structures for the actomyosin complex. Here, employing comparative modeling and enhanced sampling MD simulations, we show how the human cardiac myosin generates force during the mechanochemical cycle. Initial conformational ensembles for different myosin-actin states are learned from multiple structural templates with Rosetta. This enables us to efficiently sample the energy landscape of the system using Gaussian accelerated MD. Key myosin loop residues, whose substitutions are related to cardiomyopathy, are identified to form stable or metastable interactions with the actin surface. We find that the actin-binding cleft closure is allosterically coupled to the myosin motor core transitions and ATP-hydrolysis product release from the active site. Furthermore, a gate between switch I and switch II is suggested to control phosphate release at the prepowerstroke state. Our approach demonstrates the ability to link sequence and structural information to motor functions.
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Affiliation(s)
- Wen Ma
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093
| | - Shengjun You
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD21205
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA98109
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA92093
- Department of Pharmacology, University of California, San Diego, La Jolla, CA92093
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9
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Miao Y, Chang CEA, Zhu W, McCammon JA. Editorial: Mechanisms, thermodynamics and kinetics of ligand binding revealed from molecular simulations and machine learning. Front Mol Biosci 2023; 10:1139471. [PMID: 36733435 PMCID: PMC9887283 DOI: 10.3389/fmolb.2023.1139471] [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] [Received: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States,*Correspondence: Yinglong Miao, ; Chia-En A. Chang, ; Weiliang Zhu, ; J. Andrew McCammon,
| | - Chia-En A. Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States,*Correspondence: Yinglong Miao, ; Chia-En A. Chang, ; Weiliang Zhu, ; J. Andrew McCammon,
| | - Weiliang Zhu
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,*Correspondence: Yinglong Miao, ; Chia-En A. Chang, ; Weiliang Zhu, ; J. Andrew McCammon,
| | - J. Andrew McCammon
- Departments of Chemistry & Biochemistry and Pharmacology, University of California San Diego, San Diego, San Diego, CA, United States,*Correspondence: Yinglong Miao, ; Chia-En A. Chang, ; Weiliang Zhu, ; J. Andrew McCammon,
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10
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Takahashi Y, Bosmans KC, Hsu PK, Paul K, Seitz C, Yeh CY, Wang YS, Yarmolinsky D, Sierla M, Vahisalu T, McCammon JA, Kangasjärvi J, Zhang L, Kollist H, Trac T, Schroeder JI. Stomatal CO 2/bicarbonate sensor consists of two interacting protein kinases, Raf-like HT1 and non-kinase-activity requiring MPK12/MPK4. Sci Adv 2022; 8:eabq6161. [PMID: 36475789 PMCID: PMC9728965 DOI: 10.1126/sciadv.abq6161] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The continuing rise in the atmospheric carbon dioxide (CO2) concentration causes stomatal closing, thus critically affecting transpirational water loss, photosynthesis, and plant growth. However, the primary CO2 sensor remains unknown. Here, we show that elevated CO2 triggers interaction of the MAP kinases MPK4/MPK12 with the HT1 protein kinase, thus inhibiting HT1 kinase activity. At low CO2, HT1 phosphorylates and activates the downstream negatively regulating CBC1 kinase. Physiologically relevant HT1-mediated phosphorylation sites in CBC1 are identified. In a genetic screen, we identify dominant active HT1 mutants that cause insensitivity to elevated CO2. Dominant HT1 mutants abrogate the CO2/bicarbonate-induced MPK4/12-HT1 interaction and HT1 inhibition, which may be explained by a structural AlphaFold2- and Gaussian-accelerated dynamics-generated model. Unexpectedly, MAP kinase activity is not required for CO2 sensor function and CO2-triggered HT1 inhibition and stomatal closing. The presented findings reveal that MPK4/12 and HT1 together constitute the long-sought primary stomatal CO2/bicarbonate sensor upstream of the CBC1 kinase in plants.
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Affiliation(s)
- Yohei Takahashi
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
- Corresponding author. (Y.T.); (J.I.S.)
| | - Krystal C. Bosmans
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Po-Kai Hsu
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Karnelia Paul
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Chung-Yueh Yeh
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Yuh-Shuh Wang
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Dmitry Yarmolinsky
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Maija Sierla
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki FI-00014, Finland
| | - Triin Vahisalu
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki FI-00014, Finland
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jaakko Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki FI-00014, Finland
| | - Li Zhang
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Hannes Kollist
- Institute of Technology, University of Tartu, Nooruse 1, Tartu 50411, Estonia
| | - Thien Trac
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
| | - Julian I. Schroeder
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA 92093-0116, USA
- Corresponding author. (Y.T.); (J.I.S.)
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11
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Corpuz JC, Patel A, Davis TD, Podust LM, McCammon JA, Burkart MD. Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition. ACS Chem Biol 2022; 17:2890-2898. [PMID: 36173802 PMCID: PMC9808923 DOI: 10.1021/acschembio.2c00523] [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: 01/20/2023]
Abstract
Non-ribosomal peptides play a critical role in the clinic as therapeutic agents. To access more chemically diverse therapeutics, non-ribosomal peptide synthetases (NRPSs) have been targeted for engineering through combinatorial biosynthesis; however, this has been met with limited success in part due to the lack of proper protein-protein interactions between non-cognate proteins. Herein, we report our use of chemical biology to enable X-ray crystallography, molecular dynamics (MD) simulations, and biochemical studies to elucidate binding specificities between peptidyl carrier proteins (PCPs) and adenylation (A) domains. Specifically, we determined X-ray crystal structures of a type II PCP crosslinked to its cognate A domain, PigG and PigI, and of PigG crosslinked to a non-cognate PigI homologue, PltF. The crosslinked PCP-A domain structures possess large protein-protein interfaces that predominantly feature hydrophobic interactions, with specific electrostatic interactions that orient the substrate for active site delivery. MD simulations of the PCP-A domain complexes and unbound PCP structures provide a dynamical evaluation of the transient interactions formed at PCP-A domain interfaces, which confirm the previously hypothesized role of a PCP loop as a crucial recognition element. Finally, we demonstrate that the interfacial interactions at the PCP loop 1 region can be modified to control PCP binding specificity through gain-of-function mutations. This work suggests that loop conformational preferences and dynamism account for improved shape complementary in the PCP-A domain interactions. Ultimately, these studies show how crystallographic, biochemical, and computational methods can be used to rationally re-engineer NRPSs for non-cognate interactions.
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Affiliation(s)
- Joshua C. Corpuz
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - Larissa M. Podust
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla CA 92093, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0332, USA
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12
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Ahn SH, Huber GA, McCammon JA. Investigating Intrinsically Disordered Proteins With Brownian Dynamics. Front Mol Biosci 2022; 9:898838. [PMID: 35755809 PMCID: PMC9213797 DOI: 10.3389/fmolb.2022.898838] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) have recently become systems of great interest due to their involvement in modulating many biological processes and their aggregation being implicated in many diseases. Since IDPs do not have a stable, folded structure, however, they cannot be easily studied with experimental techniques. Hence, conducting a computational study of these systems can be helpful and be complementary with experimental work to elucidate their mechanisms. Thus, we have implemented the coarse-grained force field for proteins (COFFDROP) in Browndye 2.0 to study IDPs using Brownian dynamics (BD) simulations, which are often used to study large-scale motions with longer time scales and diffusion-limited molecular associations. Specifically, we have checked our COFFDROP implementation with eight naturally occurring IDPs and have investigated five (Glu-Lys)25 IDP sequence variants. From measuring the hydrodynamic radii of eight naturally occurring IDPs, we found the ideal scaling factor of 0.786 for non-bonded interactions. We have also measured the entanglement indices (average Cα distances to the other chain) between two (Glu-Lys)25 IDP sequence variants, a property related to molecular association. We found that entanglement indices decrease for all possible pairs at excess salt concentration, which is consistent with long-range interactions of these IDP sequence variants getting weaker at increasing salt concentration.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States.,Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, CA, United States.,Department of Pharmacology, University of California, San Diego, San Diego, CA, United States
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13
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Seitz C, Casalino L, McCammon JA, Amaro RE. Whole virion simulations unveiling the hemagglutinin-neuraminidase interplay. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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14
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Hock M, Childers MC, Teitgen AE, Huber G, McCabe KJ, McCammon JA, Regnier M, McCulloch AD. Multiscale simulations of the effects of 2’-deoxy-ATP and a myosin mutation on actomyosin interactions. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Seitz C, Markota V, Sztain-Pedone T, Esler M, Moghadasi A, Kennelly S, Demir O, Aihara H, Harki DA, Harris R, McCammon JA, Amaro RE. Developing inhibitors of the SARS-CoV-2 main protease. Biophys J 2022. [PMCID: PMC8833006 DOI: 10.1016/j.bpj.2021.11.1796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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16
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Laughlin TG, Deep A, Prichard AM, Seitz C, Gu Y, Enustun E, Suslov S, Khanna K, Birkholz EA, Armbruster E, McCammon JA, Amaro RE, Pogliano J, Corbett KD, Villa E. Architecture and self-assembly of the jumbo bacteriophage nuclear shell. Nature 2022; 608:429-435. [PMID: 35922510 PMCID: PMC9365700 DOI: 10.1038/s41586-022-05013-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 01/31/2022] [Accepted: 06/22/2022] [Indexed: 12/26/2022]
Abstract
Bacteria encode myriad defences that target the genomes of infecting bacteriophage, including restriction-modification and CRISPR-Cas systems1. In response, one family of large bacteriophages uses a nucleus-like compartment to protect its replicating genomes by excluding host defence factors2-4. However, the principal composition and structure of this compartment remain unknown. Here we find that the bacteriophage nuclear shell assembles primarily from one protein, which we name chimallin (ChmA). Combining cryo-electron tomography of nuclear shells in bacteriophage-infected cells and cryo-electron microscopy of a minimal chimallin compartment in vitro, we show that chimallin self-assembles as a flexible sheet into closed micrometre-scale compartments. The architecture and assembly dynamics of the chimallin shell suggest mechanisms for its nucleation and growth, and its role as a scaffold for phage-encoded factors mediating macromolecular transport, cytoskeletal interactions, and viral maturation.
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Affiliation(s)
- Thomas G. Laughlin
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Amar Deep
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Amy M. Prichard
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Christian Seitz
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Yajie Gu
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Eray Enustun
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Sergey Suslov
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Kanika Khanna
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA ,grid.47840.3f0000 0001 2181 7878Present Address: Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Erica A. Birkholz
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Emily Armbruster
- grid.266100.30000 0001 2107 4242Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - J. Andrew McCammon
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pharmacology, University of California San Diego, La Jolla, CA USA
| | - Rommie E. Amaro
- grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Joe Pogliano
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Kevin D. Corbett
- grid.266100.30000 0001 2107 4242Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA USA
| | - Elizabeth Villa
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA. .,Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA, USA.
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17
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Ahn SH, Ojha AA, Amaro RE, McCammon JA. Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling. J Chem Theory Comput 2021; 17:7938-7951. [PMID: 34844409 DOI: 10.1021/acs.jctc.1c00770] [Citation(s) in RCA: 8] [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] [Indexed: 11/28/2022]
Abstract
Gaussian-accelerated molecular dynamics (GaMD) is a well-established enhanced sampling method for molecular dynamics simulations that effectively samples the potential energy landscape of the system by adding a boost potential, which smoothens the surface and lowers the energy barriers between states. GaMD is unable to give time-dependent properties such as kinetics directly. On the other hand, the weighted ensemble (WE) method can efficiently sample transitions between states with its many weighted trajectories, which directly yield rates and pathways. However, convergence to equilibrium conditions remains a challenge for the WE method. Hence, we have developed a hybrid method that combines the two methods, wherein GaMD is first used to sample the potential energy landscape of the system and WE is subsequently used to further sample the potential energy landscape and kinetic properties of interest. We show that the hybrid method can sample both thermodynamic and kinetic properties more accurately and quickly compared to using either method alone.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry, University of California San Diego, La Jolla 92093, California, United States
| | - Anupam A Ojha
- Department of Chemistry, University of California San Diego, La Jolla 92093, California, United States
| | - Rommie E Amaro
- Department of Chemistry, University of California San Diego, La Jolla 92093, California, United States
| | - J Andrew McCammon
- Department of Chemistry, University of California San Diego, La Jolla 92093, California, United States.,Department of Pharmacology, University of California San Diego, La Jolla 92093, California, United States
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18
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Ahn SH, Seitz C, Cruzeiro VWD, McCammon JA, Götz AW. Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field. Data Brief 2021; 38:107401. [PMID: 34621930 PMCID: PMC8481974 DOI: 10.1016/j.dib.2021.107401] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/09/2021] [Accepted: 09/17/2021] [Indexed: 11/25/2022] Open
Abstract
Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b558 , heme b595 , and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.
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Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Christian Seitz
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Vinícius Wilian D. Cruzeiro
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, United States
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19
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. Nat Chem 2021; 13:963-968. [PMID: 34413500 PMCID: PMC8488004 DOI: 10.1038/s41557-021-00758-3] [Citation(s) in RCA: 186] [Impact Index Per Article: 62.0] [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: 02/15/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded 'down' to an exposed 'up' state to bind the human angiotensin-converting enzyme 2 receptor and infect cells. While snapshots of the 'up' and 'down' states have been obtained by cryo-electron microscopy and cryo-electron tomagraphy, details of the RBD-opening transition evade experimental characterization. Here over 130 µs of weighted ensemble simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD-opening pathways. Together with ManifoldEM analysis of cryo-electron microscopy data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408 and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein represents a landmark study for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Anthony T Bogetti
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Jory A Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Ryan S McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.,Department of Pharmacology, University of California-San Diego, La Jolla, CA, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Lillian T Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA.
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20
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Abstract
The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site. These simulations sampled comparable dynamics and pocket volumes to conventional brute force simulations carried out on two orders of magnitude greater timescales.
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Affiliation(s)
| | - Rommie Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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21
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Ahn SH, Qin S, Zhang JZ, McCammon JA, Zhang J, Zhou HX. Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation. J Chem Phys 2021; 154:221101. [PMID: 34241191 DOI: 10.1063/5.0049810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Surl-Hee Ahn
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Sanbo Qin
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Jason Z Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California 92093, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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22
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Sztain T, Ahn SH, Bogetti AT, Casalino L, Goldsmith JA, Seitz E, McCool RS, Kearns FL, Acosta-Reyes F, Maji S, Mashayekhi G, McCammon JA, Ourmazd A, Frank J, McLellan JS, Chong LT, Amaro RE. A glycan gate controls opening of the SARS-CoV-2 spike protein. bioRxiv 2021:2021.02.15.431212. [PMID: 33619492 PMCID: PMC7899456 DOI: 10.1101/2021.02.15.431212] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
SARS-CoV-2 infection is controlled by the opening of the spike protein receptor binding domain (RBD), which transitions from a glycan-shielded "down" to an exposed "up" state in order to bind the human ACE2 receptor and infect cells. While snapshots of the "up" and "down" states have been obtained by cryoEM and cryoET, details of the RBD opening transition evade experimental characterization. Here, over 130 μs of weighted ensemble (WE) simulations of the fully glycosylated spike ectodomain allow us to characterize more than 300 continuous, kinetically unbiased RBD opening pathways. Together with ManifoldEM analysis of cryo-EM data and biolayer interferometry experiments, we reveal a gating role for the N-glycan at position N343, which facilitates RBD opening. Residues D405, R408, and D427 also participate. The atomic-level characterization of the glycosylated spike activation mechanism provided herein achieves a new high-water mark for ensemble pathway simulations and offers a foundation for understanding the fundamental mechanisms of SARS-CoV-2 viral entry and infection.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Surl-Hee Ahn
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | | | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Jory A. Goldsmith
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Evan Seitz
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
| | - Ryan S. McCool
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
| | - Francisco Acosta-Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Suvrajit Maji
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
- Department of Pharmacology, UC San Diego, La Jolla, CA 92093
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, 3135 N. Maryland Ave, Milwaukee, WI 53211, USA
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY, 10032, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA 92093
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23
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Rahmani H, Ma W, Hu Z, Daneshparvar N, Taylor DW, McCammon JA, Irving TC, Edwards RJ, Taylor KA. The myosin II coiled-coil domain atomic structure in its native environment. Proc Natl Acad Sci U S A 2021; 118:e2024151118. [PMID: 33782130 PMCID: PMC8040620 DOI: 10.1073/pnas.2024151118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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] [Indexed: 01/09/2023] Open
Abstract
The atomic structure of the complete myosin tail within thick filaments isolated from Lethocerus indicus flight muscle is described and compared to crystal structures of recombinant, human cardiac myosin tail segments. Overall, the agreement is good with three exceptions: the proximal S2, in which the filament has heads attached but the crystal structure doesn't, and skip regions 2 and 4. At the head-tail junction, the tail α-helices are asymmetrically structured encompassing well-defined unfolding of 12 residues for one myosin tail, ∼4 residues of the other, and different degrees of α-helix unwinding for both tail α-helices, thereby providing an atomic resolution description of coiled-coil "uncoiling" at the head-tail junction. Asymmetry is observed in the nonhelical C termini; one C-terminal segment is intercalated between ribbons of myosin tails, the other apparently terminating at Skip 4 of another myosin tail. Between skip residues, crystal and filament structures agree well. Skips 1 and 3 also agree well and show the expected α-helix unwinding and coiled-coil untwisting in response to skip residue insertion. Skips 2 and 4 are different. Skip 2 is accommodated in an unusual manner through an increase in α-helix radius and corresponding reduction in rise/residue. Skip 4 remains helical in one chain, with the other chain unfolded, apparently influenced by the acidic myosin C terminus. The atomic model may shed some light on thick filament mechanosensing and is a step in understanding the complex roles that thick filaments of all species undergo during muscle contraction.
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Affiliation(s)
- Hamidreza Rahmani
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380
- Department of Physics, Florida State University, Tallahassee, FL 32306-4380
| | - Wen Ma
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Zhongjun Hu
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380
| | - Nadia Daneshparvar
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380
- Department of Physics, Florida State University, Tallahassee, FL 32306-4380
| | - Dianne W Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Thomas C Irving
- Department of Biological Sciences, Illinois Institute of Technology, Chicago, IL 60616
| | - Robert J Edwards
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27607
| | - Kenneth A Taylor
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4380;
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24
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Zhang Z, Ricci CG, Fan C, Cheng LT, Li B, McCammon JA. Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding. J Chem Theory Comput 2021; 17:2465-2478. [PMID: 33650860 DOI: 10.1021/acs.jctc.0c01109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We develop a hybrid approach that combines the Monte Carlo (MC) method, a variational implicit-solvent model (VISM), and a binary level-set method for the simulation of biomolecular binding in an aqueous solvent. The solvation free energy for the biomolecular complex is estimated by minimizing the VISM free-energy functional of all possible solute-solvent interfaces that are used as dielectric boundaries. This functional consists of the solute volumetric, solute-solvent interfacial, solute-solvent van der Waals interaction, and electrostatic free energy. A technique of shifting the dielectric boundary is used to accurately predict the electrostatic part of the solvation free energy. Minimizing such a functional in each MC move is made possible by our new and fast binary level-set method. This method is based on the approximation of surface area by the convolution of an indicator function with a compactly supported kernel and is implemented by simple flips of numerical grid cells locally around the solute-solvent interface. We apply our approach to the p53-MDM2 system for which the two molecules are approximated by rigid bodies. Our efficient approach captures some of the poses before the final bound state. All-atom molecular dynamics simulations with most of such poses quickly reach the final bound state. Our work is a new step toward realistic simulations of biomolecular interactions. With further improvement of coarse graining and MC sampling, and combined with other models, our hybrid approach can be used to study the free-energy landscape and kinetic pathways of ligand binding to proteins.
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Affiliation(s)
- Zirui Zhang
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
| | - Chao Fan
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Bo Li
- Department of Mathematics and Quantitative Biology Ph.D. Program, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry and Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0365, United States
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25
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Braza MKE, Seitz C, McCammon JA, Amaro RE, Nellas RB. In Silico Insights on the Allosteric Modulation of the µ-Opioid Receptor and G Protein Complex in the Presence of Agonist Ligand BU72 and Potential Positive Allosteric Modulator BMS-986121. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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26
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Ma W, You S, Regnier M, McCammon JA. Molecular Mechanism of Force Generation by the Actin-Myosin Complex During Cardiac Muscle Contraction. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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27
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McCabe KJ, Aboelkassem Y, Teitgen AE, Huber GA, McCammon JA, Regnier M, McCulloch AD. Predicting the effects of dATP on cardiac contraction using multiscale modeling of the sarcomere. Arch Biochem Biophys 2020; 695:108582. [PMID: 32956632 DOI: 10.1016/j.abb.2020.108582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/30/2020] [Accepted: 09/04/2020] [Indexed: 11/26/2022]
Abstract
2'-deoxy-ATP (dATP) is a naturally occurring small molecule that has shown promise as a therapeutic because it significantly increases cardiac myocyte force development even at low dATP/ATP ratios. To investigate mechanisms by which dATP alters myosin crossbridge dynamics, we used Brownian dynamics simulations to calculate association rates between actin and ADP- or dADP-bound myosin. These rates were then directly incorporated in a mechanistic Monte Carlo Markov Chain model of cooperative sarcomere contraction. A unique combination of increased powerstroke and detachment rates was required to match experimental steady-state and kinetic data for dATP force production in rat cardiac myocytes when the myosin attachment rate in the model was constrained by the results of a Brownian dynamics simulation. Nearest-neighbor cooperativity was seen to contribute to, but not fully explain, the steep relationship between dATP/ATP ratio and steady-state force-development observed at lower dATP concentrations. Dynamic twitch simulations performed using measured calcium transients as inputs showed that the effects of dATP on the crossbridge alone were not sufficient to explain experimentally observed enhancement of relaxation kinetics by dATP treatment. Hence, dATP may also affect calcium handling even at low concentrations. By enabling the effects of dATP on sarcomere mechanics to be predicted, this multi-scale modeling framework may elucidate the molecular mechanisms by which dATP can have therapeutic effects on cardiac contractile dysfunction.
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Affiliation(s)
- Kimberly J McCabe
- Simula Research Laboratory, Department of Computational Physiology, PO Box 134, 1325, Lysaker, Norway.
| | - Yasser Aboelkassem
- San Diego State University, Department of Mechanical Engineering, 5500 Campanile Drive San Diego, CA, 92182, USA
| | - Abigail E Teitgen
- University of California San Diego, Department of Bioengineering, 9500 Gilman Drive MC 0412 La Jolla, CA, 92093, USA
| | - Gary A Huber
- University of California San Diego, Department of Chemistry & Biochemistry, 9500 Gilman Drive, MC 0303 La Jolla, CA, 92093, USA
| | - J Andrew McCammon
- University of California San Diego, Department of Chemistry & Biochemistry, 9500 Gilman Drive, MC 0303 La Jolla, CA, 92093, USA
| | - Michael Regnier
- University of Washington, Department of Bioengineering, Box 355061 Seattle, WA, 98195, USA
| | - Andrew D McCulloch
- University of California San Diego, Department of Bioengineering, 9500 Gilman Drive MC 0412 La Jolla, CA, 92093, USA
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28
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Abstract
The SARS-CoV-2 pandemic has rapidly spread across the globe, posing an urgent health concern. Many quests to computationally identify treatments against the virus rely on in silico small molecule docking to experimentally determined structures of viral proteins. One limit to these approaches is that protein dynamics are often unaccounted for, leading to overlooking transient, druggable conformational states. Using Gaussian accelerated molecular dynamics to enhance sampling of conformational space, we identified cryptic pockets within the SARS-CoV-2 main protease, including some within regions far from the active site and assed their druggability. These pockets can aid in virtual screening efforts to identify a protease inhibitor for the treatment of COVID-19.
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Affiliation(s)
| | | | - J. Andrew McCammon
- Department of Chemistry and Biochemistry
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
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29
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Mindrebo JT, Patel A, Kim WE, Davis TD, Chen A, Bartholow TG, La Clair JJ, McCammon JA, Noel JP, Burkart MD. Gating mechanism of elongating β-ketoacyl-ACP synthases. Nat Commun 2020; 11:1727. [PMID: 32265440 PMCID: PMC7138838 DOI: 10.1038/s41467-020-15455-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 05/08/2019] [Accepted: 03/06/2020] [Indexed: 12/20/2022] Open
Abstract
Carbon-carbon bond forming reactions are essential transformations in natural product biosynthesis. During de novo fatty acid and polyketide biosynthesis, β-ketoacyl-acyl carrier protein (ACP) synthases (KS), catalyze this process via a decarboxylative Claisen-like condensation reaction. KSs must recognize multiple chemically distinct ACPs and choreograph a ping-pong mechanism, often in an iterative fashion. Here, we report crystal structures of substrate mimetic bearing ACPs in complex with the elongating KSs from Escherichia coli, FabF and FabB, in order to better understand the stereochemical features governing substrate discrimination by KSs. Complemented by molecular dynamics (MD) simulations and mutagenesis studies, these structures reveal conformational states accessed during KS catalysis. These data taken together support a gating mechanism that regulates acyl-ACP binding and substrate delivery to the KS active site. Two active site loops undergo large conformational excursions during this dynamic gating mechanism and are likely evolutionarily conserved features in elongating KSs.
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Affiliation(s)
- Jeffrey T Mindrebo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Thomas G Bartholow
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Joseph P Noel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA. .,Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA. .,Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.
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30
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Lee CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, McCammon JA, Ramamoorthi R, Holst M, Rangamani P. 3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput Biol 2020; 16:e1007756. [PMID: 32251448 PMCID: PMC7162555 DOI: 10.1371/journal.pcbi.1007756] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 07/22/2019] [Revised: 04/16/2020] [Accepted: 03/01/2020] [Indexed: 12/17/2022] Open
Abstract
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed geometries. Enabling such simulations requires watertight meshing of electron micrograph images into 3D volume meshes, which can then form the basis of computer simulations of such processes using numerical techniques such as the finite element method. In this paper, we describe the use of our recently rewritten mesh processing software, GAMer 2, to bridge the gap between poorly conditioned meshes generated from segmented micrographs and boundary marked tetrahedral meshes which are compatible with simulation. We demonstrate the application of a workflow using GAMer 2 to a series of electron micrographs of neuronal dendrite morphology explored at three different length scales and show that the resulting meshes are suitable for finite element simulations. This work is an important step towards making physical simulations of biological processes in realistic geometries routine. Innovations in algorithms to reconstruct and simulate cellular length scale phenomena based on emerging structural data will enable realistic physical models and advance discovery at the interface of geometry and cellular processes. We posit that a new frontier at the intersection of computational technologies and single cell biology is now open.
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Affiliation(s)
- Christopher T. Lee
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America
| | - Justin G. Laughlin
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America
| | - Nils Angliviel de La Beaumelle
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, United States of America
| | - Ravi Ramamoorthi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, United States of America
| | - Michael Holst
- Department of Mathematics, University of California, San Diego, La Jolla, California, United States of America
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California, United States of America
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31
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Kajimoto T, Caliman AD, Tobias IS, Okada T, Pilo CA, Van AAN, McCammon JA, Nakamura SI, Newton AC. A new molecular mechanism of evasion of apoptosis revealed by novel C‐kinase activity reporter. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.03250] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Lee CT, Laughlin JG, Moody JB, Amaro RE, McCammon JA, Holst M, Rangamani P. An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries. Biophys J 2020; 118:1003-1008. [PMID: 32032503 PMCID: PMC7063475 DOI: 10.1016/j.bpj.2019.11.3400] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 09/11/2019] [Revised: 11/08/2019] [Accepted: 11/27/2019] [Indexed: 11/16/2022] Open
Abstract
Advances in imaging methods such as electron microscopy, tomography, and other modalities are enabling high-resolution reconstructions of cellular and organelle geometries. Such advances pave the way for using these geometries for biophysical and mathematical modeling once these data can be represented as a geometric mesh, which, when carefully conditioned, enables the discretization and solution of partial differential equations. In this work, we outline the steps for a naïve user to approach the Geometry-preserving Adaptive MeshER software version 2, a mesh generation code written in C++ designed to convert structural data sets to realistic geometric meshes while preserving the underlying shapes. We present two example cases: 1) mesh generation at the subcellular scale as informed by electron tomography and 2) meshing a protein with a structure from x-ray crystallography. We further demonstrate that the meshes generated by the Geometry-preserving Adaptive MeshER software are suitable for use with numerical methods. Together, this collection of libraries and tools simplifies the process of constructing realistic geometric meshes from structural biology data.
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Affiliation(s)
- Christopher T Lee
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California.
| | - Justin G Laughlin
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California
| | - John B Moody
- Department of Mathematics, University of California, San Diego, La Jolla, California
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Michael Holst
- Department of Mathematics, University of California, San Diego, La Jolla, California
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, California.
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33
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Patel A, MIndrebo JT, Kim WE, Chen A, Bartholow TG, Davis TD, La Clair JJ, McCammon JA, Noel JP, Burkart MD. A Computational Perspective on the Gating Mechanism of β-Ketoacyl-ACP Synthases. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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Ma W, Carney S, Chemla YR, Luthey-Schulten Z, McCammon JA. Molecular Mechanism of Conformational Switching that Regulates Helicase Function. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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35
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Abstract
Brownian dynamics (BD) is a technique for carrying out computer simulations of physical systems that are driven by thermal fluctuations. Biological systems at the macromolecular and cellular level, while falling in the gap between well-established atomic-level models and continuum models, are especially suitable for such simulations. We present a brief history, examples of important biological processes that are driven by thermal motion, and those that have been profitably studied by BD. We also present some of the challenges facing developers of algorithms and software, especially in the attempt to simulate larger systems more accurately and for longer times.
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Affiliation(s)
- Gary A Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0340, USA.,Department of Pharmocology, University of California San Diego, La Jolla, CA 92093-0636, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0340, USA.,Department of Pharmocology, University of California San Diego, La Jolla, CA 92093-0636, USA
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36
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Abstract
Acyl carrier proteins (ACP)s transport intermediates through many primary and secondary metabolic pathways. Studying the effect of substrate identity on ACP structure has been hindered by the lability of the thioester bond that attaches acyl substrates to the 4'-phosphopantetheine cofactor of ACP. Here we show that an acyl acyl-carrier protein synthetase (AasS) can be used in real time to shift the hydrolysis equilibrium toward favoring acyl-ACP during solution NMR spectroscopy. Only 0.005 molar equivalents of AasS enables 1 week of stability to palmitoyl-AcpP from Escherichia coli. 2D NMR spectra enabled with this method revealed that the tethered palmitic acid perturbs nearly every secondary structural region of AcpP. This technique will allow previously unachievable structural studies of unstable acyl-ACP species, contributing to the understanding of these complex biosynthetic pathways.
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Affiliation(s)
- Terra Sztain
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
| | - Thomas G Bartholow
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States.,Department of Pharmacology , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0340 , United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093-0358 , United States
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37
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Aboelkassem Y, McCabe KJ, Huber GA, Regnier M, McCammon JA, McCulloch AD. A Stochastic Multiscale Model of Cardiac Thin Filament Activation Using Brownian-Langevin Dynamics. Biophys J 2019; 117:2255-2272. [PMID: 31547973 DOI: 10.1016/j.bpj.2019.08.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/31/2019] [Accepted: 08/02/2019] [Indexed: 11/16/2022] Open
Abstract
We use Brownian-Langevin dynamics principles to derive a coarse-graining multiscale myofilament model that can describe the thin-filament activation process during contraction. The model links atomistic molecular simulations of protein-protein interactions in the thin-filament regulatory unit to sarcomere-level activation dynamics. We first calculate the molecular interaction energy between tropomyosin and actin surface using Brownian dynamics simulations. This energy profile is then generalized to account for the observed tropomyosin transitions between its regulatory stable states. The generalized energy landscape then served as a basis for developing a filament-scale model using Langevin dynamics. This integrated analysis, spanning molecular to thin-filament scales, is capable of tracking the events of the tropomyosin conformational changes as it moves over the actin surface. The tropomyosin coil with flexible overlap regions between adjacent tropomyosins is represented in the model as a system of coupled stochastic ordinary differential equations. The proposed multiscale approach provides a more detailed molecular connection between tropomyosin dynamics, the trompomyosin-actin interaction-energy landscape, and the generated force by the sarcomere.
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Affiliation(s)
- Yasser Aboelkassem
- Department of Bioengineering, University of California San Diego, La Jolla, California.
| | - Kimberly J McCabe
- Department of Bioengineering, University of California San Diego, La Jolla, California
| | - Gary A Huber
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Andrew D McCulloch
- Department of Bioengineering, University of California San Diego, La Jolla, California
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38
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Lee CT, Moody JB, Amaro RE, McCammon JA, Holst MJ. The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. ACM Trans Math Softw 2019; 45:28. [PMID: 31474782 PMCID: PMC6716611 DOI: 10.1145/3321515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/01/2019] [Indexed: 06/10/2023]
Abstract
We introduce CASC: a new, modern, and header-only C++ library which provides a data structure to represent arbitrary dimension abstract simplicial complexes (ASC) with user-defined classes stored directly on the simplices at each dimension. This is accomplished by using the latest C++ language features including variadic template parameters introduced in C++11 and automatic function return type deduction from C++14. Effectively CASC decouples the representation of the topology from the interactions of user data. We present the innovations and design principles of the data structure and related algorithms. This includes a metadata aware decimation algorithm which is general for collapsing simplices of any dimension. We also present an example application of this library to represent an orientable surface mesh.
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Affiliation(s)
- Christopher T Lee
- Department of Chemistry and Biochemistry, University of California San Diego
| | - John B Moody
- ViaSat, Inc. Carlsbad-Bldg 10-2063, 6155 El Camino Real, Carlsbad, CA 92009
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego
| | - Michael J Holst
- Department of Mathematics, University of California San Diego
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39
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Sztain T, Patel A, Lee DJ, Davis TD, McCammon JA, Burkart MD. Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein. Angew Chem Int Ed Engl 2019; 58:10888-10892. [PMID: 31140212 DOI: 10.1002/anie.201903815] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 03/28/2019] [Revised: 05/17/2019] [Indexed: 12/23/2022]
Abstract
At the center of many complex biosynthetic pathways, the acyl carrier protein (ACP) shuttles substrates to appropriate enzymatic partners to produce fatty acids and polyketides. Carrier proteins covalently tether their cargo via a thioester linkage to a phosphopantetheine cofactor. Due to the labile nature of this linkage, chemoenzymatic methods have been developed that involve replacement of the thioester with a more stable amide or ester bond. We explored the importance of the thioester bond to the structure of the carrier protein by using solution NMR spectroscopy and molecular dynamics simulations. Remarkably, the replacement of sulfur with other heteroatoms results in significant structural changes, thus suggesting more rigorous selections of isosteric substitutes is needed.
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Affiliation(s)
- Terra Sztain
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA
| | - Ashay Patel
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA
| | - D John Lee
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA
| | - Tony D Davis
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA
| | - J Andrew McCammon
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA.,Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0340, USA
| | - Michael D Burkart
- Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0358, USA
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40
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Sztain T, Patel A, Lee DJ, Davis TD, McCammon JA, Burkart MD. Modifying the Thioester Linkage Affects the Structure of the Acyl Carrier Protein. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Terra Sztain
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
| | - Ashay Patel
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
| | - D. John Lee
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
| | - Tony D. Davis
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
| | - J. Andrew McCammon
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
- Pharmacology University of California, San Diego 9500 Gilman Drive La Jolla 92093-0340 USA
| | - Michael D. Burkart
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla 92093-0358 USA
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41
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Palermo G, Casalino L, Magistrato A, Andrew McCammon J. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. J Struct Biol 2019; 206:267-279. [PMID: 30880083 PMCID: PMC6637970 DOI: 10.1016/j.jsb.2019.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 12/26/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/06/2023]
Abstract
Noncoding RNA (ncRNA) has a key role in regulating gene expression, mediating fundamental processes and diseases via a variety of yet unknown mechanisms. Here, we review recent applications of conventional and enhanced Molecular Dynamics (MD) simulations methods to address the mechanistic function of large biomolecular systems that are tightly involved in the ncRNA function and that are of key importance in life sciences. This compendium focuses of three biomolecular systems, namely the CRISPR-Cas9 genome editing machinery, group II intron ribozyme and the ribonucleoprotein complex of the spliceosome, which edit and process ncRNA. We show how the application of a novel accelerated MD simulations method has been key in disclosing the conformational transitions underlying RNA binding in the CRISPR-Cas9 complex, suggesting a mechanism for RNA recruitment and clarifying the conformational changes required for attaining genome editing. As well, we discuss the use of mixed quantum-classical MD simulations in deciphering the catalytic mechanism of RNA splicing as operated by group II intron ribozyme, one of the largest ncRNA structures crystallized so far. Finally, we debate the future challenges and opportunities in the field, discussing the recent application of MD simulations for unraveling the functional biophysics of the spliceosome, a multi-mega Dalton complex of proteins and small nuclear RNAs that performs RNA splicing in humans. This showcase of applications highlights the current talent of MD simulations to dissect atomic-level details of complex biomolecular systems instrumental for the design of finely engineered genome editing machines. As well, this review aims at inspiring future investigations of several other ncRNA regulatory systems, such as micro and small interfering RNAs, which achieve their function and specificity using RNA-based recognition and targeting strategies.
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Affiliation(s)
- Giulia Palermo
- Department of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, CA 92521, United States.
| | - Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States
| | - Alessandra Magistrato
- Consiglio Nazionale delle Ricerche-Istituto Officina dei Materiali, Democritos National Simulation Center c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States; Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, United States; National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093, United States
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42
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Ricci C, Chen JS, Miao Y, Jinek M, Doudna JA, McCammon JA, Palermo G. Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent Sci 2019; 5:651-662. [PMID: 31041385 PMCID: PMC6487449 DOI: 10.1021/acscentsci.9b00020] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Indexed: 05/02/2023]
Abstract
CRISPR-Cas9 is the state-of-the-art technology for editing and manipulating nucleic acids. However, the occurrence of off-target mutations can limit its applicability. Here, all-atom enhanced molecular dynamics (MD) simulations-using Gaussian accelerated MD (GaMD)-are used to decipher the mechanism of off-target binding at the molecular level. GaMD reveals that base pair mismatches in the target DNA at distal sites with respect to the protospacer adjacent motif (PAM) can induce an extended opening of the RNA:DNA heteroduplex, which leads to newly formed interactions between the unwound DNA and the L2 loop of the catalytic HNH domain. These conserved interactions constitute a "lock" effectively decreasing the conformational freedom of the HNH domain and hampering its activation for cleavage. Remarkably, depending on their positions at PAM distal sites, DNA mismatches responsible for off-target cleavages are unable to "lock" the HNH domain, thereby leading to the unselective cleavage of DNA sequences. In consistency with the available experimental data, the ability to "lock" the catalytic HNH domain in an inactive "conformational checkpoint" is shown to be a key determinant in the onset of off-target effects. This mechanistic rationale contributes in clarifying a long lasting open issue in the CRISPR-Cas9 function and poses the foundation for designing novel and more specific Cas9 variants, which could be obtained by magnifying the "locking" interactions between HNH and the target DNA in the presence of any incorrect off-target sequence, thus preventing undesired cleavages.
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Affiliation(s)
- Clarisse
G. Ricci
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Janice S. Chen
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - Yinglong Miao
- Center
for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Martin Jinek
- Department
of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jennifer A. Doudna
- Department of Molecular
and Cell Biology, Department of Chemistry, Howard Hughes Medical Institute, Innovative Genomics
Institute, and Molecular Biophysics and Integrated Bioimaging Division, Lawrence
Berkeley National Laboratory, University
of California Berkeley, Berkeley, California 94720, United States
| | - J. Andrew McCammon
- Department
of Pharmacology, Department of Chemistry and Biochemistry, and National Biomedical
Computation Resource, University of California
San Diego, La Jolla, California 92093, United States
| | - Giulia Palermo
- Department
of Bioengineering, Bourns College of Engineering, University of California Riverside, 900 University Avenue, Riverside, California 92521, United States
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43
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Palermo G, Ricci CG, McCammon JA. The invisible dance of CRISPR-Cas9. Simulations unveil the molecular side of the gene-editing revolution. Phys Today 2019; 72:30-36. [PMID: 31511751 PMCID: PMC6738945 DOI: 10.1063/pt.3.4182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since the discovery of the DNA double helix, the main molecular repository of genetic information, scientists have been struggling to find ways to efficiently manipulate genes. The ability to mark, modify, or regulate specific sequences of DNA in a controlled fashion is of key importance because of the ways that gene editing could be used to improve human life. For example, genetic therapies are being developed to permanently cure cancer and other life-threatening diseases.
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44
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Huang YMM, Munguia J, Miao Y, Nizet V, McCammon JA. Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem Biol Drug Des 2019; 93:647-652. [PMID: 30570806 DOI: 10.1111/cbdd.13462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 11/28/2022]
Abstract
To maintain the lipid asymmetry of the cell envelope in Gram-negative bacteria, the MlaC protein serves as a lipid transfer factor and delivers phospholipids from the outer to the inner membrane. A strategy of antibiotic discovery is to design a proper compound that can tightly bind to the MlaC protein and inhibit the MlaC function. In this study, we performed virtual screening on multiple MlaC structures obtained from molecular dynamics simulations to identify potential MlaC binders. Our results suggested that clorobiocin is a compound that could bind to the MlaC protein. Through the comparison of the bound geometry between clorobiocin and novobiocin, we pointed out that the methyl-pyrrole group of the noviose sugar in clorobiocin forms hydrophobic interactions with amino acids in the phospholipid binding pocket, which allows the compound to bind deep in the active site. This also explains why clorobiocin shows a tighter binding affinity than novobiocin. Our study highlights a practical path of antibiotic development against Gram-negative bacteria.
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Affiliation(s)
- Yu-Ming M Huang
- Department of Pharmacology, University of California, San Diego, La Jolla, California
| | - Jason Munguia
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Yinglong Miao
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego, La Jolla, California.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California
| | - J Andrew McCammon
- Department of Pharmacology, University of California, San Diego, La Jolla, California.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
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45
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Dodge GJ, Jaremko KL, Patel A, McCammon JA, Smith JL, Burkart MD. Molecular Dynamics Simulations Reveal the Origins of the Distinct Activities and Substrate Selectivities of E. coli Dehydratases FabA and FabZ. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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46
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Laughlin JG, Lee CT, McCammon JA, Amaro RE, Holst M, Rangamani P. Modeling the Impact of Spine Apparatus on Signaling and Regulation in Realistic Dendritic Spine Geometries. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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47
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Seitz C, Casalino L, Huber G, Konecny R, Huang YM, Amaro R, McCammon JA. How does Glycosylation Affect Drug Binding on Influenza? The Roles of Electrostatics and Sterics Examined through Brownian Dynamics Simulations. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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48
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Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J 2019; 116:205-214. [PMID: 30606449 PMCID: PMC6349996 DOI: 10.1016/j.bpj.2018.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 01/02/2018] [Revised: 06/23/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
The atomic-level mechanisms that coordinate ligand release from protein pockets are only known for a handful of proteins. Here, we report results from accelerated molecular dynamics simulations for benzene dissociation from the buried cavity of the T4 lysozyme Leu99Ala mutant (L99A). In these simulations, benzene is released through a previously characterized, sparsely populated room-temperature excited state of the mutant, explaining the coincidence for experimentally measured benzene off rate and apo protein slow-timescale NMR relaxation rates between ground and excited states. The path observed for benzene egress is a multistep ligand migration from the buried cavity to ultimate release through an opening between the F/G-, H-, and I-helices and requires a number of cooperative multiresidue and secondary-structure rearrangements within the C-terminal domain of L99A. These rearrangements are identical to those observed along the ground state to excited state transitions characterized by molecular dynamic simulations run on the Anton supercomputer. Analyses of the molecular properties of the residues lining the egress path suggest that protein surface electrostatic potential may play a role in the release mechanism. Simulations of wild-type T4 lysozyme also reveal that benzene-egress-associated dynamics in the L99A mutant are potentially exaggerations of the substrate-processivity-related dynamics of the wild type.
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Affiliation(s)
| | | | - Daniel J Mermelstein
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Nathan Mih
- Department of Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California
| | | | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California.
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49
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Kajimoto T, Caliman AD, Tobias IS, Okada T, Pilo CA, Van AAN, Andrew McCammon J, Nakamura SI, Newton AC. Activation of atypical protein kinase C by sphingosine 1-phosphate revealed by an aPKC-specific activity reporter. Sci Signal 2019; 12:eaat6662. [PMID: 30600259 PMCID: PMC6657501 DOI: 10.1126/scisignal.aat6662] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 12/21/2022]
Abstract
Atypical protein kinase C (aPKC) isozymes are unique in the PKC superfamily in that they are not regulated by the lipid second messenger diacylglycerol, which has led to speculation about whether a different second messenger acutely controls their function. Here, using a genetically encoded reporter that we designed, aPKC-specific C kinase activity reporter (aCKAR), we found that the lipid mediator sphingosine 1-phosphate (S1P) promoted the cellular activity of aPKC. Intracellular S1P directly bound to the purified kinase domain of aPKC and relieved autoinhibitory constraints, thereby activating the kinase. In silico studies identified potential binding sites on the kinase domain, one of which was validated biochemically. In HeLa cells, S1P-dependent activation of aPKC suppressed apoptosis. Together, our findings identify a previously undescribed molecular mechanism of aPKC regulation, a molecular target for S1P in cell survival regulation, and a tool to further explore the biochemical and biological functions of aPKC.
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Affiliation(s)
- Taketoshi Kajimoto
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alisha D Caliman
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Irene S Tobias
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Taro Okada
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Caila A Pilo
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - An-Angela N Van
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - J Andrew McCammon
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA
| | - Shun-Ichi Nakamura
- Division of Biochemistry, Department of Biochemistry and Molecular Biology, Graduate School of Medicine, Kobe University, Kobe 650-0017, Japan
| | - Alexandra C Newton
- Department of Pharmacology, University of California at San Diego, La Jolla, CA 92037, USA.
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50
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Kim WE, Patel A, Hur GH, Tufar P, Wuo MG, McCammon JA, Burkart MD. Mechanistic Probes for the Epimerization Domain of Nonribosomal Peptide Synthetases. Chembiochem 2018; 20:147-152. [PMID: 30194895 DOI: 10.1002/cbic.201800439] [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: 07/31/2018] [Indexed: 11/12/2022]
Abstract
Nonribosomal peptide synthetases (NRPSs) are responsible for the synthesis of a variety of bioactive natural products with clinical and economic significance. Interestingly, these large multimodular enzyme machineries incorporate nonproteinogenic d-amino acids through the use of auxiliary epimerization domains, converting l-amino acids into d-amino acids that impart into the resulting natural products unique bioactivity and resistance to proteases. Due to the large and complex nature of NRPSs, several questions remain unanswered about the mechanism of the catalytic domain reactions. We have investigated the use of mechanism-based crosslinkers to probe the mechanism of an epimerization domain in gramicidin S biosynthesis. In addition, MD simulations were performed, showcasing the possible roles of catalytic residues within the epimerization domain.
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Affiliation(s)
- Woojoo E Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Ashay Patel
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Gene H Hur
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Peter Tufar
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael G Wuo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA.,Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0636, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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