1
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Mochi JA, Jani J, Tak K, Pappachan A. Insights into the ATP / GTP selectivity of a GTPase, adenylosuccinate synthetase from Leishmania donovani. Biochem Biophys Res Commun 2024; 715:149975. [PMID: 38676997 DOI: 10.1016/j.bbrc.2024.149975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024]
Abstract
Many GTPases have been shown to utilize ATP too as the phosphoryl donor. Both GTP and ATP are important molecules in the cellular environments and play multiple and discrete functional role within the cells. In our present study, we showed that one of the purine metabolic enzymes Adenylosuccinate synthetase from Leishmania donovani (LdAdSS) which belongs to the BioD-superfamily of GTPases can also carry out the catalysis by hydrolysing ATP instead of its cognate substrate GTP albeit with less efficiency. Biochemical and biophysical studies indicated its ability to bind to ATP too but at a higher concentration of ATP compared to that of GTP. Sequence analysis and molecular dynamic simulations suggested that residues of the switch loop and the G4-G5 (593SAXD596) connected motif of LdAdSS plays a role in determining the nucleotide specificity. Though the crucial interaction between Asp596 and the nucleotide is broken when ATP is bound, interactions between the Ala594 and the adenine ring of ATP could still hold ATP in the GTP binding site. The results of the present study suggested that though LdAdSS is GTP specific, it still shows ATP hydrolysing activity.
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Affiliation(s)
- Jigneshkumar A Mochi
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382030, Gujarat, India
| | - Jaykumar Jani
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382030, Gujarat, India
| | - Kiran Tak
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382030, Gujarat, India; Department of Biology, Indian Institute of Sciences Education and Research (IISER), Bhopal, 462 066, Madhya Pradesh, India
| | - Anju Pappachan
- School of Life Sciences, Central University of Gujarat, Gandhinagar, 382030, Gujarat, India.
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2
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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3
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Wang Y, Unnikrishnan M, Ramsey B, El Andlosy D, Keeley AT, Murphy CJ, Gruebele M. In-Cell Association of a Bioorthogonal Tubulin. Biomacromolecules 2024; 25:1282-1290. [PMID: 38251876 DOI: 10.1021/acs.biomac.3c01253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.
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Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brooke Ramsey
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Driss El Andlosy
- Computer Science and Technologies Department, Parkland Community College, Champaign, Illinois 61821, United States
| | - Alex T Keeley
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Nam K, Arattu Thodika AR, Grundström C, Sauer UH, Wolf-Watz M. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. J Chem Inf Model 2024; 64:150-163. [PMID: 38117131 PMCID: PMC10778088 DOI: 10.1021/acs.jcim.3c01618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy profiles for both enzyme opening and ligand release and compare them with profiles from the apoenzyme. Results reveal a three-step ligand release process, which initiates with the opening of the adenosine triphosphate-binding subdomain (ATP lid), followed by ligand release and concomitant opening of the adenosine monophosphate-binding subdomain (AMP lid). The ligands then transition to nonspecific positions before complete dissociation. In these processes, the first step is energetically driven by ATP lid opening, whereas the second step is driven by ATP release. In contrast, the AMP lid opening and its ligand release make minor contributions to the total free energy for enzyme opening. Regarding the ligand binding mechanism, our results suggest that AMP lid closure occurs via an induced-fit mechanism triggered by AMP binding, whereas ATP lid closure follows conformational selection. This difference in the closure mechanisms provides an explanation with implications for the debate on ligand-driven conformational changes of AK. Additionally, we determine an X-ray structure of an AK variant that exhibits significant rearrangements in the stacking of catalytic arginines, explaining its reduced catalytic activity. In the context of apoenzyme opening, the sequence of events is different. Here, the AMP lid opens first while the ATP lid remains closed, and the free energy associated with ATP lid opening varies with orientation, aligning with the reported AK opening and closing rate heterogeneity. Finally, this study, in conjunction with our previous research, provides a comprehensive view of the intricate interplay between various structural elements, ligands, and catalytic residues that collectively contribute to the robust catalytic power of the enzyme.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Abdul Raafik Arattu Thodika
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | | | - Uwe H. Sauer
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
| | - Magnus Wolf-Watz
- Department
of Chemistry, Umeå University, Umeå 90187, SE, Sweden
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5
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Gade M, Gardner JM, Jain P, Laurino P. Nucleoside-Driven Specificity of DNA Methyltransferase. Chembiochem 2023; 24:e202300094. [PMID: 37548117 DOI: 10.1002/cbic.202300094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
We have studied the adenosine binding specificities of two bacterial DNA methyltransferases, Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While they have similar cofactor binding pocket interactions, experimental data showed different specificity for novel S-nucleobase-l-methionine cofactors (SNMs; N=guanosyl, cytidyl, uridyl). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-l-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data prove catalytically productive methylation by the M.HhaI binding pocket for all the SNMs. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.
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Affiliation(s)
- Madhuri Gade
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Jasmine M Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Prashant Jain
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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6
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Tischlik S, Oelker M, Rogne P, Sauer-Eriksson AE, Drescher M, Wolf-Watz M. Insights into Enzymatic Catalysis from Binding and Hydrolysis of Diadenosine Tetraphosphate by E. coli Adenylate Kinase. Biochemistry 2023; 62:2238-2243. [PMID: 37418448 PMCID: PMC10399197 DOI: 10.1021/acs.biochem.3c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/04/2023] [Indexed: 07/09/2023]
Abstract
Adenylate kinases play a crucial role in cellular energy homeostasis through the interconversion of ATP, AMP, and ADP in all living organisms. Here, we explore how adenylate kinase (AdK) from Escherichia coli interacts with diadenosine tetraphosphate (AP4A), a putative alarmone associated with transcriptional regulation, stress, and DNA damage response. From a combination of EPR and NMR spectroscopy together with X-ray crystallography, we found that AdK interacts with AP4A with two distinct modes that occur on disparate time scales. First, AdK dynamically interconverts between open and closed states with equal weights in the presence of AP4A. On a much slower time scale, AdK hydrolyses AP4A, and we suggest that the dynamically accessed substrate-bound open AdK conformation enables this hydrolytic activity. The partitioning of the enzyme into open and closed states is discussed in relation to a recently proposed linkage between active site dynamics and collective conformational dynamics.
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Affiliation(s)
- Sonja Tischlik
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Melanie Oelker
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Per Rogne
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - A. Elisabeth Sauer-Eriksson
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
- Centre
of Microbial Research (UCMR), Umeå
University, SE-901 87 Umeå, Sweden
| | - Malte Drescher
- Department
of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Magnus Wolf-Watz
- Department
of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
- Centre
of Microbial Research (UCMR), Umeå
University, SE-901 87 Umeå, Sweden
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7
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Pu F, Wang R, Yang X, Hu X, Wang J, Zhang L, Zhao Y, Zhang D, Liu Z, Liu J. Nucleotide and codon usage biases involved in the evolution of African swine fever virus: A comparative genomics analysis. J Basic Microbiol 2023; 63:499-518. [PMID: 36782108 DOI: 10.1002/jobm.202200624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/05/2023] [Accepted: 01/21/2023] [Indexed: 02/15/2023]
Abstract
Since African swine fever virus (ASFV) replication is closely related to its host's machinery, codon usage of viral genome can be subject to selection pressures. A better understanding of codon usage can give new insights into viral evolution. We implemented information entropy and revealed that the nucleotide usage pattern of ASFV is significantly associated with viral isolation factors (region and time), especially the usages of thymine and cytosine. Despite the domination of adenine and thymine in the viral genome, we found that mutation pressure alters the overall codon usage pattern of ASFV, followed by selective forces from natural selection. Moreover, the nucleotide skew index at the gene level indicates that nucleotide usages influencing synonymous codon bias of ASFV are significantly correlated with viral protein hydropathy. Finally, evolutionary plasticity is proved to contribute to the weakness in synonymous codons with A- or T-end serving as optimal codons of ASFV, suggesting that fine-tuning translation selection plays a role in synonymous codon usages of ASFV for adapting host. Taken together, ASFV is subject to evolutionary dynamics on nucleotide selections and synonymous codon usage, and our detailed analysis offers deeper insights into the genetic characteristics of this newly emerging virus around the world.
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Affiliation(s)
- Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | - Xuanye Yang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Xinyan Hu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Jinqian Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Lijuan Zhang
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Zewen Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
| | - Junlin Liu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China.,College of Life Science and Engineering, Northwest Minzu University, Lanzhou, Gansu, China
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8
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Characterizing a novel CMK-EngA fusion protein from Bifidobacterium: Implications for inter-domain regulation. Biochem Biophys Rep 2022; 33:101410. [PMID: 36578527 PMCID: PMC9791819 DOI: 10.1016/j.bbrep.2022.101410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
EngA is an essential and unique bacterial GTPase involved in ribosome biogenesis. The essentiality and species-specific variations among EngA homologues make the protein a potential target for future drug development. In this aspect, it is important to understand the variations of EngA among probiotic organisms and non-probiotic bacteria to understand species specificity. The search for variations among EngA homologues revealed a unique variant, exclusively found in Bifidobacterium and a few Actinobacteria species. Bifidobacterium possesses a multifunctional fusion protein, wherein EngA is fused with an N-terminal CMK (Cytidylate Monophosphate Kinase) domain. The resulting protein is therefore a large (70kDa size) with 3 consecutive P-loops and a 50 amino acid long linker connecting the EngA and CMK domains. EngA is known to regulate ribosome biogenesis via nucleotide-dependent conformational changes. The additional domain may introduce further intricate regulation in ribosome biogenesis or participate in newer biological processes. This study is the first attempt to characterise this novel class of bacterial EngA found in the Genus of Bifidobacteria.
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9
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Park Y, Liao J, Hoang QQ. Roc, the G-domain of the Parkinson's disease-associated protein LRRK2. Trends Biochem Sci 2022; 47:1038-1047. [PMID: 35840518 PMCID: PMC9669111 DOI: 10.1016/j.tibs.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/24/2022]
Abstract
Mutation in leucine-rich repeat (LRR) kinase 2 (LRRK2) is a common cause of Parkinson's disease (PD). Aberrant LRRK2 kinase activity is associated with disease pathogenesis and thus it is an attractive drug target for combating PD. Intense efforts in the past nearly two decades have focused on the development of small-molecule inhibitors of the kinase domain of LRRK2 and have identified potent kinase inhibitors. However, most LRRK2 kinase inhibitors have shown adverse effects; therefore, alternative-mechanism-based strategies are desperately needed. In this review, we discuss the new insights gleaned from recent cryoelectron microscope (cryo-EM) structures of LRRK2 towards understanding the mechanisms of actions of LRRK2 and explore the potential new therapeutic avenues.
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Affiliation(s)
- Yangshin Park
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jingling Liao
- Department of Public Health, Academy of Nutrition and Health, Wuhan University of Science and Technology School of Medicine, 430074 Wuhan, China.
| | - Quyen Q Hoang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Neurology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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10
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Lu J, Scheerer D, Haran G, Li W, Wang W. Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase. J Phys Chem B 2022; 126:8188-8201. [PMID: 36222098 PMCID: PMC9589722 DOI: 10.1021/acs.jpcb.2c05497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The catalytic cycle of the enzyme adenylate kinase involves large conformational motions between open and closed states. A previous single-molecule experiment showed that substrate binding tends to accelerate both the opening and the closing rates and that a single turnover event often involves multiple rounds of conformational switching. In this work, we showed that the repeated conformational transitions of adenylate kinase are essential for the relaxation of incorrectly bound substrates into the catalytically competent conformation by combining all-atom and coarse-grained molecular simulations. In addition, free energy calculations based on all-atom and coarse-grained models demonstrated that the enzyme with incorrectly bound substrates has much a lower free energy barrier for domain opening compared to that with the correct substrate conformation, which may explain the the acceleration of the domain opening rate by substrate binding. The results of this work provide mechanistic understanding to previous experimental observations and shed light onto the interplay between conformational dynamics and enzyme catalysis.
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Affiliation(s)
- Jiajun Lu
- Department
of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China,Wenzhou
Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang325000, China
| | - David Scheerer
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot761001, Israel
| | - Gilad Haran
- Department
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot761001, Israel,
| | - Wenfei Li
- Department
of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China,Wenzhou
Key Laboratory of Biophysics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang325000, China,
| | - Wei Wang
- Department
of Physics, National Laboratory of Solid State Microstructure, Nanjing University, Nanjing210093, China,
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11
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Kenkre V, Spendier K. A theory of coalescence of signaling receptor clusters in immune cells. PHYSICA A 2022; 602:127650. [PMID: 35966144 PMCID: PMC9365117 DOI: 10.1016/j.physa.2022.127650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A theory of coalescence of signal receptor clusters in mast cells is developed in close connection with experiments. It is based on general considerations involving a feedback procedure and a time-dependent capture as part of a reaction-diffusion process. Characteristic features of observations that need to be explained are indicated and it is shown why calculations available in the literature are not satisfactory. While the latter involves static centers at which the reaction part of the phenomenon occurs, by its very nature, coalescence involves dynamically evolving centers. This is so because the process continuously modifies the size of the cluster aggregate which then proceeds to capture more material. We develop a procedure that consists of first solving a static reaction-diffusion problem and then imbuing the center with changing size. The consequence is a dependence of the size of the signal receptor cluster aggregate on time. A preliminary comparison with experiment is shown to reveal a sharp difference between theory and data. The observation indicates that the reaction occurs slowly at first and then picks up rapidly as time proceeds. Parameter modification to fit the observations cannot solve the problem. We use this observation to build into the theory an accumulation rate that is itself dependent on time. A memory representation and its physical basis are explained. The consequence is a theory that can be fit to observations successfully.
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Affiliation(s)
- V.M. Kenkre
- Department of Physics and Astronomy, University of New Mexico, 210 Yale Blvd NE, Albuquerque, 87131, NM, USA
| | - K. Spendier
- Department of Physics and Energy Science and UCCS Center for the Biofrontiers Institute, University of Colorado Colorado Springs, 1420 Austin Bluffs Pkwy, Colorado Springs, 80918, CO, USA
- Corresponding author. (K. Spendier)
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12
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Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint. Int J Mol Sci 2022; 23:ijms23126521. [PMID: 35742970 PMCID: PMC9223553 DOI: 10.3390/ijms23126521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK19-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.
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13
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Jew KM, Le VTB, Amaral K, Ta A, Nguyen May NM, Law M, Adelstein N, Kuhn ML. Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs. Front Microbiol 2022; 12:805181. [PMID: 35173693 PMCID: PMC8843374 DOI: 10.3389/fmicb.2021.805181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
Acetylation is a protein post-translational modification (PTM) that can affect a variety of cellular processes. In bacteria, two PTM Nε-acetylation mechanisms have been identified: non-enzymatic/chemical acetylation via acetyl phosphate or acetyl coenzyme A and enzymatic acetylation via protein acetyltransferases. Prior studies have shown that extensive acetylation of Nε-lysine residues of numerous proteins from a variety of bacteria occurs via non-enzymatic acetylation. In Escherichia coli, new Nε-lysine acetyltransferases (KATs) that enzymatically acetylate other proteins have been identified, thus expanding the repertoire of protein substrates that are potentially regulated by acetylation. Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. Five E. coli KAT substrate proteins that were previously identified as being acetylated by YiaC and had 3D structures in the PDB were selected for further analysis: adenylate kinase (Adk), isocitrate dehydrogenase (Icd), catalase HPII (KatE), methionyl-tRNA formyltransferase (Fmt), and a peroxide stress resistance protein (YaaA). We methodically compared over 350 protein structures of these E. coli enzymes and their homologs; to accurately determine lysine residue conservation requires a strategy that incorporates both flexible structural alignments and visual inspection. Moreover, our results revealed discrepancies in conclusions about lysine residue conservation in homologs when examining linear amino acid sequences compared to 3D structures.
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Affiliation(s)
- Kristen M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Van Thi Bich Le
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Kiana Amaral
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Allysa Ta
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Nina M Nguyen May
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Melissa Law
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Nicole Adelstein
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA, United States
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14
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Drone honey bees are disproportionately sensitive to abiotic stressors despite expressing high levels of stress response proteins. Commun Biol 2022; 5:141. [PMID: 35177754 PMCID: PMC8854713 DOI: 10.1038/s42003-022-03092-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/01/2022] [Indexed: 12/21/2022] Open
Abstract
Drone honey bees (Apis mellifera) are the obligate sexual partners of queens, and the availability of healthy, high-quality drones directly affects a queen’s fertility and productivity. Yet, our understanding of how stressors affect adult drone fertility, survival, and physiology is presently limited. Here, we investigated sex biases in susceptibility to abiotic stressors (cold stress, topical imidacloprid exposure, and topical exposure to a realistic cocktail of pesticides). We found that drones (haploid males) were more sensitive to cold and imidacloprid exposure than workers (sterile, diploid females), but the cocktail was not toxic at the concentrations tested. We corroborated this lack of cocktail toxicity with in-hive exposures via pollen feeding. We then used quantitative proteomics to investigate protein expression profiles in the hemolymph of topically exposed workers and drones, and found that 34 proteins were differentially expressed in exposed drones relative to controls, but none were differentially expressed in exposed workers. Contrary to our hypothesis, we show that drones express surprisingly high baseline levels of putative stress response proteins relative to workers. This suggests that drones’ stress tolerance systems are fundamentally rewired relative to workers, and susceptibility to stress depends on more than simply gene dose or allelic diversity. The effect of stress on honey bee drone survival and physiology are largely unknown, but it is hypothesized that increased stress would reduce their survival. Surprisingly, although drones are more likely to die from some stressors than workers, they exhibit higher baseline stress response proteins.
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15
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Ware TB, Hsu KL. Advances in chemical proteomic evaluation of lipid kinases-DAG kinases as a case study. Curr Opin Chem Biol 2021; 65:101-108. [PMID: 34311404 PMCID: PMC8671151 DOI: 10.1016/j.cbpa.2021.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/24/2021] [Accepted: 06/18/2021] [Indexed: 10/20/2022]
Abstract
Advancements in chemical proteomics and mass spectrometry lipidomics are providing new opportunities to understand lipid kinase activity, specificity, and regulation on a global cellular scale. Here, we describe recent developments in chemical biology of lipid kinases with a focus on those members that phosphorylate diacylglycerols. We further discuss future implications of how these mass spectrometry-based approaches can be adapted for studies of additional lipid kinase members with the aim of bridging the gap between protein and lipid kinase-focused investigations.
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Affiliation(s)
- Timothy B Ware
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, United States; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, United States; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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16
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Li Y, Wang R, Wang H, Pu F, Feng X, Jin L, Ma Z, Ma XX. Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages. Front Cell Infect Microbiol 2021; 11:771010. [PMID: 34804999 PMCID: PMC8602353 DOI: 10.3389/fcimb.2021.771010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.
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Affiliation(s)
- Yicong Li
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Rui Wang
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
| | - Huihui Wang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Feiyang Pu
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xili Feng
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Li Jin
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xiao-Xia Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
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17
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Kotla S, Zhang A, Imanishi M, Ko KA, Lin SH, Gi YJ, Moczygemba M, Isgandarova S, Schadler KL, Chung C, Milgrom SA, Banchs J, Yusuf SW, Amaya DN, Guo H, Thomas TN, Shen YH, Deswal A, Herrmann J, Kleinerman ES, Entman ML, Cooke JP, Schifitto G, Maggirwar SB, McBeath E, Gupte AA, Krishnan S, Patel ZS, Yoon Y, Burks JK, Fujiwara K, Brookes PS, Le NT, Hamilton DJ, Abe JI. Nucleus-mitochondria positive feedback loop formed by ERK5 S496 phosphorylation-mediated poly (ADP-ribose) polymerase activation provokes persistent pro-inflammatory senescent phenotype and accelerates coronary atherosclerosis after chemo-radiation. Redox Biol 2021; 47:102132. [PMID: 34619528 PMCID: PMC8502954 DOI: 10.1016/j.redox.2021.102132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 02/08/2023] Open
Abstract
The incidence of cardiovascular disease (CVD) is higher in cancer survivors than in the general population. Several cancer treatments are recognized as risk factors for CVD, but specific therapies are unavailable. Many cancer treatments activate shared signaling events, which reprogram myeloid cells (MCs) towards persistent senescence-associated secretory phenotype (SASP) and consequently CVD, but the exact mechanisms remain unclear. This study aimed to provide mechanistic insights and potential treatments by investigating how chemo-radiation can induce persistent SASP. We generated ERK5 S496A knock-in mice and determined SASP in myeloid cells (MCs) by evaluating their efferocytotic ability, antioxidation-related molecule expression, telomere length, and inflammatory gene expression. Candidate SASP inducers were identified by high-throughput screening, using the ERK5 transcriptional activity reporter cell system. Various chemotherapy agents and ionizing radiation (IR) up-regulated p90RSK-mediated ERK5 S496 phosphorylation. Doxorubicin and IR caused metabolic changes with nicotinamide adenine dinucleotide depletion and ensuing mitochondrial stunning (reversible mitochondria dysfunction without showing any cell death under ATP depletion) via p90RSK-ERK5 modulation and poly (ADP-ribose) polymerase (PARP) activation, which formed a nucleus-mitochondria positive feedback loop. This feedback loop reprogramed MCs to induce a sustained SASP state, and ultimately primed MCs to be more sensitive to reactive oxygen species. This priming was also detected in circulating monocytes from cancer patients after IR. When PARP activity was transiently inhibited at the time of IR, mitochondrial stunning, priming, macrophage infiltration, and coronary atherosclerosis were all eradicated. The p90RSK-ERK5 module plays a crucial role in SASP-mediated mitochondrial stunning via regulating PARP activation. Our data show for the first time that the nucleus-mitochondria positive feedback loop formed by p90RSK-ERK5 S496 phosphorylation-mediated PARP activation plays a crucial role of persistent SASP state, and also provide preclinical evidence supporting that transient inhibition of PARP activation only at the time of radiation therapy can prevent future CVD in cancer survivors.
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Affiliation(s)
- Sivareddy Kotla
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Aijun Zhang
- Department of Medicine, Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
| | - Masaki Imanishi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyung Ae Ko
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Young Jin Gi
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margie Moczygemba
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Sevinj Isgandarova
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Keri L Schadler
- Department of Pediatric Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah A Milgrom
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Oncology, University of Colorado Cancer Center, Aurora, CO, 80045, USA
| | - Jose Banchs
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Syed Wamique Yusuf
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Diana N Amaya
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huifang Guo
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tamlyn N Thomas
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ying H Shen
- Division of Cardiothoracic Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Anita Deswal
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joerg Herrmann
- Cardio Oncology Clinic, Division of Preventive Cardiology, Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eugenie S Kleinerman
- Department of Pediatric Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark L Entman
- Division of Cardiovascular Sciences, Baylor College of Medicine, Houston, TX, USA
| | - John P Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX, USA
| | | | - Sanjay B Maggirwar
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Elena McBeath
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Anisha A Gupte
- Department of Medicine, Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
| | - Sunil Krishnan
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Oncology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | | | - Yisang Yoon
- Department of Physiology, Medical College of Georgia, Augusta, GA, USA
| | - Jared K Burks
- Department of Leukemia, Division of Center Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keigi Fujiwara
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul S Brookes
- Department of Anesthesiology and Perioperative Medicine, University of Rochester, Rochester, NY, USA
| | - Nhat-Tu Le
- Division of Cardiovascular Sciences, Baylor College of Medicine, Houston, TX, USA
| | - Dale J Hamilton
- Department of Medicine, Center for Bioenergetics, Houston Methodist Research Institute, Houston, TX, USA
| | - Jun-Ichi Abe
- Department of Cardiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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18
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Quantifying the propagation of parametric uncertainty on flux balance analysis. Metab Eng 2021; 69:26-39. [PMID: 34718140 DOI: 10.1016/j.ymben.2021.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022]
Abstract
Flux balance analysis (FBA) and associated techniques operating on stoichiometric genome-scale metabolic models play a central role in quantifying metabolic flows and constraining feasible phenotypes. At the heart of these methods lie two important assumptions: (i) the biomass precursors and energy requirements neither change in response to growth conditions nor environmental/genetic perturbations, and (ii) metabolite production and consumption rates are equal at all times (i.e., steady-state). Despite the stringency of these two assumptions, FBA has been shown to be surprisingly robust at predicting cellular phenotypes. In this paper, we formally assess the impact of these two assumptions on FBA results by quantifying how uncertainty in biomass reaction coefficients, and departures from steady-state due to temporal fluctuations could propagate to FBA results. In the first case, conditional sampling of parameter space is required to re-weigh the biomass reaction so as the molecular weight remains equal to 1 g mmol-1, and in the second case, metabolite (and elemental) pool conservation must be imposed under temporally varying conditions. Results confirm the importance of enforcing the aforementioned constraints and explain the robustness of FBA biomass yield predictions.
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19
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Ojeda-May P, Mushtaq AU, Rogne P, Verma A, Ovchinnikov V, Grundström C, Dulko-Smith B, Sauer UH, Wolf-Watz M, Nam K. Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions. Biochemistry 2021; 60:2246-2258. [PMID: 34250801 PMCID: PMC8297476 DOI: 10.1021/acs.biochem.1c00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes employ a wide range of protein motions to achieve efficient catalysis of
chemical reactions. While the role of collective protein motions in substrate binding,
product release, and regulation of enzymatic activity is generally understood, their
roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations,
enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are
combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the
roles of catalytic residues in catalysis and the conformational change in the enzyme.
This study reveals that the motions in the active site, which occur on a time scale of
picoseconds to nanoseconds, link the catalytic reaction to the slow conformational
dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In
particular, substantial conformational rearrangement occurs in the active site following
the catalytic reaction. This rearrangement not only affects the reaction barrier but
also promotes a more open conformation of the enzyme after the reaction, which then
results in an accelerated opening of the enzyme compared to that of the reactant state.
The results illustrate a linkage between enzymatic catalysis and collective protein
motions, whereby the disparate time scales between the two processes are bridged by a
cascade of intermediate-scale motion of catalytic residues modulating the free energy
landscapes of the catalytic and conformational change processes.
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Affiliation(s)
- Pedro Ojeda-May
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden.,High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | | | - Per Rogne
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Apoorv Verma
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | | | - Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Uwe H Sauer
- Department of Chemistry, Umeå University, Umeå SE-90187, Sweden
| | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
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20
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Xu R, Yang Y, Zheng X. Unique structural features of the adenylate kinase hCINAP/AK6 and its multifaceted functions in carcinogenesis and tumor progression. FEBS Lett 2021; 595:2071-2084. [PMID: 34245011 DOI: 10.1002/1873-3468.14158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/30/2022]
Abstract
Human coilin-interacting nuclear ATPase protein (hCINAP), also known as adenylate kinase 6 (AK6), is an atypical adenylate kinase with critical roles in many biological processes, including gene transcription, ribosome synthesis, cell metabolism, cell proliferation and apoptosis, DNA damage responses, and genome stability. Furthermore, hCINAP/AK6 dysfunction is associated with cancer and various inflammatory diseases. In this review, we summarize the structural features and biological roles of hCINAP in several important signaling pathways, as well as its connection with tumor onset and progression.
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Affiliation(s)
- Ruidan Xu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Yongfeng Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
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21
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Kocic G, Gajic M, Tomovic K, Hadzi-Djokic J, Anderluh M, Smelcerovic A. Purine adducts as a presumable missing link for aristolochic acid nephropathy-related cellular energy crisis, potential anti-fibrotic prevention and treatment. Br J Pharmacol 2021; 178:4411-4427. [PMID: 34235731 DOI: 10.1111/bph.15618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
Aristolochic acid nephropathy is a progressive exposome-induced disease characterized by tubular atrophy and fibrosis culminating in end-stage renal disease and malignancies. The molecular mechanisms of the energy crisis as a putative cause of fibrosis have not yet been elucidated. In light of the fact that aristolochic acid forms DNA and RNA adducts by covalent binding of aristolochic acid metabolites to exocyclic amino groups of (deoxy)adenosine and (deoxy)guanosine, we hypothesize here that similar aristolochic acid adducts may exist with other purine-containing molecules. We also provide new insights into the aristolochic acid-induced energy crisis and presumably a link between already known mechanisms. In addition, an overview of potential targets in fibrosis treatment is provided, which is followed by recommendations on possible preventive measures that could be taken to at least postpone or partially alleviate aristolochic acid nephropathy.
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Affiliation(s)
- Gordana Kocic
- Department of Biochemistry, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Mihajlo Gajic
- Department of Pharmacy, Faculty of Medicine, University of Nis, Nis, Serbia
| | - Katarina Tomovic
- Department of Pharmacy, Faculty of Medicine, University of Nis, Nis, Serbia
| | | | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Andrija Smelcerovic
- Department of Chemistry, Faculty of Medicine, University of Nis, Nis, Serbia
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22
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Updegrove TB, Harke J, Anantharaman V, Yang J, Gopalan N, Wu D, Piszczek G, Stevenson DM, Amador-Noguez D, Wang JD, Aravind L, Ramamurthi KS. Reformulation of an extant ATPase active site to mimic ancestral GTPase activity reveals a nucleotide base requirement for function. eLife 2021; 10:65845. [PMID: 33704064 PMCID: PMC7952092 DOI: 10.7554/elife.65845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/05/2021] [Indexed: 12/23/2022] Open
Abstract
Hydrolysis of nucleoside triphosphates releases similar amounts of energy. However, ATP hydrolysis is typically used for energy-intensive reactions, whereas GTP hydrolysis typically functions as a switch. SpoIVA is a bacterial cytoskeletal protein that hydrolyzes ATP to polymerize irreversibly during Bacillus subtilis sporulation. SpoIVA evolved from a TRAFAC class of P-loop GTPases, but the evolutionary pressure that drove this change in nucleotide specificity is unclear. We therefore reengineered the nucleotide-binding pocket of SpoIVA to mimic its ancestral GTPase activity. SpoIVAGTPase functioned properly as a GTPase but failed to polymerize because it did not form an NDP-bound intermediate that we report is required for polymerization. Further, incubation of SpoIVAGTPase with limiting ATP did not promote efficient polymerization. This approach revealed that the nucleotide base, in addition to the energy released from hydrolysis, can be critical in specific biological functions. We also present data suggesting that increased levels of ATP relative to GTP at the end of sporulation was the evolutionary pressure that drove the change in nucleotide preference in SpoIVA.
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Affiliation(s)
- Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Jailynn Harke
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jin Yang
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - Nikhil Gopalan
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, United States
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | | | - Jue D Wang
- Department of Bacteriology, University of Wisconsin, Madison, United States
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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23
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Rogne P, Dulko-Smith B, Goodman J, Rosselin M, Grundström C, Hedberg C, Nam K, Sauer-Eriksson AE, Wolf-Watz M. Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3. Biochemistry 2020; 59:3570-3581. [PMID: 32822537 DOI: 10.1021/acs.biochem.0c00549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly.
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Affiliation(s)
- Per Rogne
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Alington, Arlington, Texas 76019-0065, United States
| | - Jack Goodman
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Marie Rosselin
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Alington, Arlington, Texas 76019-0065, United States
| | | | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
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24
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Ionescu MI. Molecular docking investigation of the amantadine binding to the enzymes upregulated or downregulated in Parkinson's disease. ADMET AND DMPK 2020; 8:149-175. [PMID: 35300368 PMCID: PMC8915579 DOI: 10.5599/admet.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/01/2020] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disease. Levodopa in combination with amantadine has a demonstrated efficacy in motility impairment. An extensive investigation of some enzymes described to be upregulated or downregulated in PD was made - adenylate kinase (AK), adenine phosphoribosyltransferase (APRT), ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1), nucleoside-diphosphate kinase 3 (NDK3), purine nucleoside phosphorylase 1 (PNP1), and ecto-5'-nucleotidase (NT5E). Also, creatine kinase (CK) was included in the study because it is one of the main enzymes involved in the regulation of the nucleotide ratio in energy metabolism. To date, there is no proven link between amantadine treatment of PD and these enzymes. Because there are many AKs isoforms modified in PD, the AK was the first investigated. The molecular docking experiments allow the analysis of the selective binding of amantadine - unionized (with -NH2 group) and ionized form (with -NH3 + group) - to the AKs' isoforms implicated in PD. Using available X-ray 3D structures of human AKs in closed-conformation, it was demonstrated that there are notable differences between the interactions of the two forms of amantadine for the zebrafish AK1 (5XZ2), human AK2 (2C9Y), human AK5 (2BWJ), and AK from B.stearothermophilus. The cytosolic human AK1 and human AK2 mostly interact with ionized amantadine by AMP binding residues. The human AK5 interaction with ionized amantadine does not involve the residues from the catalytic site. Among other enzymes tested in the present study, APRT revealed the best results in respect of binding amantadine ionized form. The results offer a new perspective for further investigation of the connections between amantadine treatment of PD and some enzymes involved in purine metabolism.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 6 Louis Pasteur, 400349, Cluj-Napoca, Romania, .,Department of Microbiology, County Emergency Clinical Hospital, 400006, Cluj-Napoca, Romania
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25
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Hossain MS, Rahaman SA, Hatai J, Saha M, Bandyopadhyay S. Switching the recognition ability of a photoswitchable receptor towards phosphorylated anions. Chem Commun (Camb) 2020; 56:4172-4175. [PMID: 32167107 DOI: 10.1039/d0cc00926a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
An azobenzene based photoswitchable macrocyclic receptor displays different binding affinities in its E and Z forms towards various phosphorylated coenzymes under physiological conditions with remarkable selectivity for ATP in the E-form and selectivity towards GTP in the photoisomerized Z-form. Linear discriminant analysis clearly separated the analytes using the E-form. An application of this method enabled monitoring the progress of enzymatic phosphorylation using a tyrosine kinase enzyme.
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Affiliation(s)
- Munshi Sahid Hossain
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Sk Atiur Rahaman
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Joydev Hatai
- Institute of Organic Chemistry, University of Duisburg-Essen, Universitatsstraße 745141, Essen, Germany.
| | - Monochura Saha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
| | - Subhajit Bandyopadhyay
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, West Bengal 741246, India.
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26
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Abstract
How proteins evolved to recognize and bind their ligands is a key mystery in protein function evolution. To explore this mystery, we study how proteins bind adenine, an ancient fragment. We characterize physicochemical patterns of protein–adenine interactions and link these to proteins’ evolutionary origins. In conflict with previous findings, we see that all of adenine’s hydrogen donors and acceptors have been used to bind proteins, and that adenine binding is likely to have emerged multiple times in evolution. To identify adenine-binding sites of shared origin, we use “themes”: short amino acid segments suggested to constitute evolutionary building blocks. We detect specific themes that are engaged in adenine binding; the detection of these in a protein’s sequence might reveal its function. Proteins’ interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein–adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein–adenine interactions in the Watson–Crick edge of adenine and shows that all of adenine’s edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments (“themes”) that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
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27
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Abstract
Adenylate kinase is a small, usually monomeric, enzyme found in every living thing due to its crucial role in energetic metabolism. This paper outlines the most relevant data about adenylate kinases isoforms, and the connection between dysregulation or mutation of human adenylate kinase and medical conditions. The following datadases were consulted: National Centre for Biotechnology Information, Protein Data Bank, and Mouse Genomic Informatics. The SmartBLAST tool, EMBOSS Needle Program, and Clustal Omega Program were used to analyze the best protein match, and to perform pairwise sequence alignment and multiple sequence alignment. Human adenylate kinase genes are located on different chromosomes, six of them being on the chromosomes 1 and 9. The adenylate kinases' intracellular localization and organ distribution explain their dysregulation in many diseases. The cytosolic isoenzyme 1 and the mitochondrial isoenzyme 2 are the main adenylate kinases that are integrated in the vast network of inflammatory modulators. The cytosolic isoenzyme 5 is correlated with limbic encephalitis and Leu673Pro mutation of the isoenzyme 7 leads to primary male infertility due to impairment of the ciliary function. The impairment of the mitochondrial isoenzymes 2 and 4 is demonstrated in neuroblastoma or glioma. The adenylate kinases are disease modifier that can assess the risk of diseases where oxidative stress plays a crucial role in pathogenesis like metabolic syndrome or neurodegenerative diseases. Because adenylate kinases has ATP as substrate, they are integrated in the global network of energetic process of any organism therefore are valid target for new pharmaceutical compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Faculty of Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, 6 Louis Pasteur, Cluj-Napoca, 400349, Romania. .,County Emergency Clinical Hospital, Cluj-Napoca, Romania.
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28
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Chen P, Jiao X, Zhang Y, Wu L, Tang DJ, Li P, Chen X, Chao D, Tang JL, Ming Z. The crystal structure of the phytopathogenic bacterial sensor PcrK reveals different cytokinin recognition mechanism from the plant sensor AHK4. J Struct Biol 2019; 208:69-76. [PMID: 31419523 DOI: 10.1016/j.jsb.2019.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
Plant cytokinins (CKs) are essential for many central cellular processes and play important roles in the interaction between bacteria and plants. Perception of CK is executed by the CHASE domain in the histidine kinase sensors of a class of two-component regulatory systems. Despite advances in understanding the structural basis for CK perception by the sensor AHK4 in Arabidopsis, the molecular mechanism of CK binding by other sensors is unclear. Here, we report the crystal structure of the CHASE domain in the histidine kinase PcrK of the bacterial plant pathogen Xanthomonas campestris pathovar campestris, which senses plant CK, determined at 2.55 Å resolution. The structure reveals that the PcrK has an AHK4-like overall topology and assembles into a homodimer. Strikingly, detailed structural analysis unveils two unique features of the PcrK ligand binding pocket: the size of the pocket is restricted for CK binding, and the PcrK applies a positively charged arginine but not a negatively charged aspartate to recognize the ligand. We propose a model to explain how the PcrK accommodates CK-sized compounds through conformational changes, providing a potential mechanistic framework for understanding ligand recognition by the PcrK.
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Affiliation(s)
- Peng Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xi Jiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yukun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Dong-Jie Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Peifang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xiaoxuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Dong Chao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China.
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29
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Rogne P, Andersson D, Grundström C, Sauer-Eriksson E, Linusson A, Wolf-Watz M. Nucleation of an Activating Conformational Change by a Cation-π Interaction. Biochemistry 2019; 58:3408-3412. [PMID: 31339702 DOI: 10.1021/acs.biochem.9b00538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a key molecule in biology, adenosine triphosphate (ATP) has numerous crucial functions in, for instance, energetics, post-translational modifications, nucleotide biosynthesis, and cofactor metabolism. Here, we have discovered an intricate interplay between the enzyme adenylate kinase and its substrate ATP. The side chain of an arginine residue was found to be an efficient sensor of the aromatic moiety of ATP through the formation of a strong cation-π interaction. In addition to recognition, the interaction was found to have dual functionality. First, it nucleates the activating conformational transition of the ATP binding domain and also affects the specificity in the distant AMP binding domain. In light of the functional consequences resulting from the cation-π interaction, it is possible that the mode of ATP recognition may be a useful tool in enzyme design.
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Affiliation(s)
- Per Rogne
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - David Andersson
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | | | | | - Anna Linusson
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
| | - Magnus Wolf-Watz
- Department of Chemistry , Umeå University , SE-901 87 Umeå , Sweden
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30
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Song K, Wang Y, Li Y, Ding C, Cai R, Tao G, Zhao P, Xia Q, He H. A Convenient, Rapid, Sensitive, and Reliable Spectrophotometric Assay for Adenylate Kinase Activity. Molecules 2019; 24:molecules24040663. [PMID: 30781833 PMCID: PMC6412689 DOI: 10.3390/molecules24040663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/09/2019] [Accepted: 02/12/2019] [Indexed: 11/16/2022] Open
Abstract
Enzymatic activity assays are essential and critical for the study of enzyme kinetics. Adenylate kinase (Adk) plays a fundamental role in cellular energy and nucleotide homeostasis. To date, assays based on different principles have been used for the determination of Adk activity. Here, we show a spectrophotometric analysis technique to determine Adk activity with bromothymol blue as a pH indicator. We analyzed the effects of substrates and the pH indicator on the assay using orthogonal design and then established the most optimal assay for Adk activity. Subsequently, we evaluated the thermostability of Adk and the inhibitory effect of KCl on Adk activity with this assay. Our results show that this assay is simple, rapid, and precise. It shows great potential as an alternative to the conventional Adk activity assay. Our results also suggest that orthogonal design is an effective approach, which is very suitable for the optimization of complex enzyme reaction conditions.
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Affiliation(s)
- Kai Song
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Yejing Wang
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
| | - Yu Li
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Chaoxiang Ding
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Rui Cai
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
| | - Gang Tao
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
| | - Huawei He
- Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Beibei, Chongqing 400715, China.
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31
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Żaczek S, Kowalska J, Dybala-Defratyka A. Ligand-Driven Conformational Dynamics Influences Selectivity of UbiX. Chembiochem 2018; 19:2403-2409. [PMID: 30136768 DOI: 10.1002/cbic.201800389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 12/31/2022]
Abstract
Up until now, it has remained elusive as to why the flavin prenyltransferase UbiX requires dimethylallyl monophosphate (DMAP) as one of its cosubstrates instead of dimethylallyl pyrophosphate (DMAPP), even though the former is not used in metabolic pathways, while the latter is a common isoprenoid precursor. Herein, mainly on the basis of molecular dynamics (MD) simulations, we demonstrate that the selectivity of UbiX may be governed by its conformational dynamics. The hydrogen-bonding network of UbiX does not facilitate a proper encompassing of DMAPP. This induces significant conformational changes of the enzyme that result mostly in unreactive trajectories, whereas DMAP remains at a catalytically competent position throughout the performed simulations. Within the presented study, we provide a justification for the atypical selectivity of UbiX.
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Affiliation(s)
- Szymon Żaczek
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Justyna Kowalska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
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32
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Kokkonen P, Bednar D, Dockalova V, Prokop Z, Damborsky J. Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site. J Biol Chem 2018; 293:11505-11512. [PMID: 29858243 PMCID: PMC6065182 DOI: 10.1074/jbc.ra117.000328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and is likely the route for bulky substrates. These results provide insights into the structure-dynamics function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to 1,2-dichloroethane introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Veronika Dockalova
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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33
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Ionescu MI, Oniga O. Molecular Docking Evaluation of ( E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors. Molecules 2018; 23:molecules23051076. [PMID: 29751552 PMCID: PMC6102543 DOI: 10.3390/molecules23051076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Multi-drug resistant microorganism infections with emerging problems that require not only a prevention strategy, but also the development of new inhibitory compounds. Six previously synthesized 5-arylidene-2-thioxothiazolidin-4-one derivatives 1a–f, were screened for inhibitory activity on adenylate kinases of different origins by molecular docking. The compounds 1c and 1d were the most efficient inhibitors of bacterial and some archean adenylate kinases. Hydrogen bond interactions were observed with the residues belonging to the ATP binding site. Moreover human adenylate kinases are poor targets, suggesting that this selectivity offers promising prospectives for refining the structure of our compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania.
- Department of Microbiology, County Emergency Clinical Hospital, 400006 Cluj-Napoca, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania.
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