1
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Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [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] [Indexed: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
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Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
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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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Kim J, Moon S, Romo TD, Yang Y, Bae E, Phillips GN. Conformational dynamics of adenylate kinase in crystals. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014702. [PMID: 38389978 PMCID: PMC10883716 DOI: 10.1063/4.0000205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
Adenylate kinase is a ubiquitous enzyme in living systems and undergoes dramatic conformational changes during its catalytic cycle. For these reasons, it is widely studied by genetic, biochemical, and biophysical methods, both experimental and theoretical. We have determined the basic crystal structures of three differently liganded states of adenylate kinase from Methanotorrus igneus, a hyperthermophilic organism whose adenylate kinase is a homotrimeric oligomer. The multiple copies of each protomer in the asymmetric unit of the crystal provide a unique opportunity to study the variation in the structure and were further analyzed using advanced crystallographic refinement methods and analysis tools to reveal conformational heterogeneity and, thus, implied dynamic behaviors in the catalytic cycle.
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Affiliation(s)
- Junhyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Tod D Romo
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Yifei Yang
- Departments of BioSciences, Rice University, Houston, Texas 77005, USA
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4
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Scheerer D, Adkar BV, Bhattacharyya S, Levy D, Iljina M, Riven I, Dym O, Haran G, Shakhnovich EI. Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase. Proc Natl Acad Sci U S A 2023; 120:e2219855120. [PMID: 37094144 PMCID: PMC10160949 DOI: 10.1073/pnas.2219855120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/22/2023] [Indexed: 04/26/2023] Open
Abstract
Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity.
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Affiliation(s)
- David Scheerer
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Bharat V Adkar
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | | | - Dorit Levy
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Marija Iljina
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Inbal Riven
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Orly Dym
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 761001, Israel
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
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5
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Xia A, Guo X, Chai Y, Zhang W, Huang Y, Zhu X, Zhu X, Liao Q. Green light enhanced the photostability and catalytic performance of fatty acid photodecarboxylase. Chem Commun (Camb) 2023; 59:6674-6677. [PMID: 37096404 DOI: 10.1039/d3cc00995e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Green light was documented to improve the photostability of fatty acid photodecarboxylase from Chlorella variabilis (CvFAP). Compared to blue light, green light increased the pentadecane yield by 27.6% and improved the residual activity of CvFAP to 5.9-fold after the preillumination. Kinetics and thermodynamics indicated that blue light facilitated a high CvFAP activity.
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Affiliation(s)
- Ao Xia
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Xiaobo Guo
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Yingxin Chai
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Yun Huang
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Xianqing Zhu
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Xun Zhu
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
| | - Qiang Liao
- Key Laboratory of Low-grade Energy Utilization Technologies and Systems, Chongqing University, Ministry of Education, Chongqing 400044, China.
- Institute of Engineering Thermophysics, School of Energy and Power Engineering, Chongqing University, Chongqing 400044, China
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6
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Verma A, Åberg-Zingmark E, Sparrman T, Mushtaq AU, Rogne P, Grundström C, Berntsson R, Sauer UH, Backman L, Nam K, Sauer-Eriksson E, Wolf-Watz M. Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases. SCIENCE ADVANCES 2022; 8:eabm4089. [PMID: 36332013 PMCID: PMC9635829 DOI: 10.1126/sciadv.abm4089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
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Affiliation(s)
- Apoorv Verma
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Tobias Sparrman
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Per Rogne
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | | | - Ronnie Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Uwe H. Sauer
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019, USA
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7
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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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8
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Zhang Y, Chen M, Lu J, Li W, Wolynes PG, Wang W. Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. J Phys Chem B 2022; 126:6792-6801. [PMID: 36044985 PMCID: PMC9483917 DOI: 10.1021/acs.jpcb.2c03832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
Substrate inhibition, whereby enzymatic activity decreases
with
excess substrate after reaching a maximum turnover rate, is among
the most elusive phenomena in enzymatic catalysis. Here, based on
a dynamic energy landscape model, we investigate the underlying mechanism
by performing molecular simulations and frustration analysis for a
model enzyme adenylate kinase (AdK), which catalyzes the phosphoryl
transfer reaction ATP + AMP ⇋ ADP + ADP. Intriguingly, these
reveal a kinetic repartitioning mechanism of substrate inhibition,
whereby excess substrate AMP suppresses the population of an energetically
frustrated, but kinetically activated, catalytic pathway going through
a substrate (ATP)-product (ADP) cobound complex with steric incompatibility.
Such a frustrated pathway plays a crucial role in facilitating the
bottleneck product ADP release, and its suppression by excess substrate
AMP leads to a slow down of product release and overall turnover.
The simulation results directly demonstrate that substrate inhibition
arises from the rate-limiting product-release step, instead of the
steps for populating the catalytically competent complex as often
suggested in previous works. Furthermore, there is a tight interplay
between the enzyme conformational equilibrium and the extent of substrate
inhibition. Mutations biasing to more closed conformations tend to
enhance substrate inhibition. We also characterized the key features
of single-molecule enzyme kinetics with substrate inhibition effect.
We propose that the above molecular mechanism of substrate inhibition
may be relevant to other multisubstrate enzymes in which product release
is the bottleneck step.
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Affiliation(s)
- Yangyang Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Mingchen Chen
- Department of Research and Development, neoX Biotech, Beijing 102206, China.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jiajun Lu
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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9
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Chen D, Li Y, Li X, Savidge T, Qian Y, Fan X. Factors determining the enzyme catalytic power caused by noncovalent interactions: Charge alterations in enzyme active sites. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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10
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Orädd F, Ravishankar H, Goodman J, Rogne P, Backman L, Duelli A, Nors Pedersen M, Levantino M, Wulff M, Wolf-Watz M, Andersson M. Tracking the ATP-binding response in adenylate kinase in real time. SCIENCE ADVANCES 2021; 7:eabi5514. [PMID: 34788091 PMCID: PMC8597995 DOI: 10.1126/sciadv.abi5514] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/27/2021] [Indexed: 05/25/2023]
Abstract
The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a “cracking mechanism” proposed to underlie global structural transformation, such as allostery, in proteins.
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Affiliation(s)
- Fredrik Orädd
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Harsha Ravishankar
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Jack Goodman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Per Rogne
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Lars Backman
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Annette Duelli
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Martin Nors Pedersen
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Matteo Levantino
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Michael Wulff
- ESRF—The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble, Cedex 9, France
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linnaeus Väg 10, 901 87 Umeå, Sweden
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11
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Stuber K, Schneider T, Werner J, Kovermann M, Marx A, Scheffner M. Structural and functional consequences of NEDD8 phosphorylation. Nat Commun 2021; 12:5939. [PMID: 34642328 PMCID: PMC9020517 DOI: 10.1038/s41467-021-26189-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 09/21/2021] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin (Ub) and Ub-like proteins (Ubls) such as NEDD8 are best known for their function as covalent modifiers of other proteins but they are also themselves subject to post-translational modifications including phosphorylation. While functions of phosphorylated Ub (pUb) have been characterized, the consequences of Ubl phosphorylation remain unclear. Here we report that NEDD8 can be phosphorylated at S65 - the same site as Ub - and that S65 phosphorylation affects the structural dynamics of NEDD8 and Ub in a similar manner. While both pUb and phosphorylated NEDD8 (pNEDD8) can allosterically activate the Ub ligase Parkin, they have different protein interactomes that in turn are distinct from those of unmodified Ub and NEDD8. Among the preferential pNEDD8 interactors are HSP70 family members and we show that pNEDD8 stimulates HSP70 ATPase activity more pronouncedly than unmodified NEDD8. Our findings highlight the general importance of Ub/NEDD8 phosphorylation and support the notion that the function of pUb/pNEDD8 does not require their covalent attachment to other proteins. Both ubiquitin and NEDD8 can be phosphorylated, but the biological role of NEDD8 phosphorylation remains unclear. Here, the authors identify similarities and differences of ubiquitin and NEDD8 phosphorylation, showing that phosphorylated NEDD8 has a distinct interactome and regulates HSP70 proteins.
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Affiliation(s)
- Katrin Stuber
- Dept. of Biology, University of Konstanz, Konstanz, Germany.,Dept. of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Tobias Schneider
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Jill Werner
- Dept. of Biology, University of Konstanz, Konstanz, Germany.,Dept. of Chemistry, University of Konstanz, Konstanz, Germany
| | - Michael Kovermann
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Andreas Marx
- Dept. of Chemistry, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Martin Scheffner
- Dept. of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
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12
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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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13
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Yuan Y, Zhu Q, Song R, Ma J, Dong H. A Two-Ended Data-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein. J Chem Theory Comput 2020; 16:4631-4640. [PMID: 32320614 DOI: 10.1021/acs.jctc.9b01184] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational transitions of protein between different states are often associated with their biological functions. These dynamic processes, however, are usually not easy to be well characterized by experimental measurements, mainly because of inadequate temporal and spatial resolution. Meantime, sampling of configuration space with molecular dynamics (MD) simulations is still a challenge. Here we proposed a robust two-ended data-driven accelerated (teDA2) conformational sampling method, which drives the structural change in an adaptively updated feature space without introducing a bias potential. teDA2 was applied to explore adenylate kinase (ADK), a model with well characterized "open" and "closed" states. A single conformational transition event of ADK could be achieved within only a few or tens of nanoseconds sampled with teDA2. By analyzing hundreds of transition events, we reproduced different mechanisms and the associated pathways for domain motion of ADK reported in the literature. The multiroute characteristic of ADK was confirmed by the fact that some metastable states identified with teDA2 resemble available crystal structures determined at different conditions. This feature was further validated with Markov state modeling with independent MD simulations. Therefore, our work provides strong evidence for the conformational plasticity of protein, which is mainly due to the inherent degree of flexibility. As a reliable and efficient enhanced sampling protocol, teDA2 could be used to study the dynamics between functional states of various biomolecular machines.
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Affiliation(s)
- Yigao Yuan
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China
| | - Qiang Zhu
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China.,Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing China
| | - Ruiheng Song
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 210023 Nanjing China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, 210023 Nanjing, China.,Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
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14
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Fucci IJ, Sinha K, Rule GS. Stabilization of Active Site Dynamics Leads to Increased Activity with 3'-Azido-3'-deoxythymidine Monophosphate for F105Y Mutant Human Thymidylate Kinase. ACS OMEGA 2020; 5:2355-2367. [PMID: 32064397 PMCID: PMC7017412 DOI: 10.1021/acsomega.9b03766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/10/2020] [Indexed: 05/04/2023]
Abstract
Thymidylate kinases are essential enzymes with roles in DNA synthesis and repair and have been the target of drug development for antimalarials, antifungals, HIV treatment, and cancer therapeutics. Human thymidylate kinase (hTMPK) conversion of the anti-HIV prodrug 3'-azido-3'-deoxythymidine (AZT or zidovudine) monophosphate to diphosphate is the rate-limiting step in the activation of AZT. A point mutant (F105Y) has been previously reported with significantly increased activity for the monophosphate form of the drug [3'-azidothymidine-5'-monophosphate (AZTMP)]. Using solution nuclear magnetic resonance (NMR) techniques, we show that while the wild-type (WT) and F105Y hTMPK adopt the same structure in solution, significant changes in dynamics may explain their different activities toward TMP and AZTMP. 13C spin-relaxation measurements show that there is little change in dynamics on the ps to ns time scale. In contrast, methyl 1H relaxation dispersion shows that AZTMP alters adenosine nucleotide handling in the WT protein but not in the mutant. Additionally, the F105Y mutant has reduced conformational flexibility, leading to an increase in affinity for the product ADP and a slower rate of phosphorylation of TMP. The dynamics at the catalytic center for F105Y bound to AZTMP are tuned to the same frequency as WT bound to TMP, which may explain the mutant's catalytic efficiency toward the prodrug.
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15
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Conformational and functional characterization of artificially conjugated non-canonical ubiquitin dimers. Sci Rep 2019; 9:19991. [PMID: 31882959 PMCID: PMC6934565 DOI: 10.1038/s41598-019-56458-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/03/2019] [Indexed: 11/30/2022] Open
Abstract
Ubiquitylation is an eminent posttranslational modification referring to the covalent attachment of single ubiquitin molecules or polyubiquitin chains to a target protein dictating the fate of such labeled polypeptide chains. Here, we have biochemically produced artificially Lys11-, and Lys27-, and Lys63-linked ubiquitin dimers based on click-chemistry generating milligram quantities in high purity. We show that the artificial linkage used for the conjugation of two ubiquitin moieties represents a fully reliable surrogate of the natural isopeptide bond by acquiring highly resolved nuclear magnetic resonance (NMR) spectroscopic data including ligand binding studies. Extensive coarse grained and atomistic molecular dynamics (MD) simulations allow to extract structures representing the ensemble of domain-domain conformations used to verify the experimental data. Advantageously, this methodology does not require individual isotopic labeling of both ubiquitin moieties as NMR data have been acquired on the isotopically labeled proximal moiety and complementary MD simulations have been used to fully interpret the experimental data in terms of domain-domain conformation. This combined approach intertwining NMR spectroscopy with MD simulations makes it possible to describe the conformational space non-canonically Lys11-, and Lys27-linked ubiquitin dimers occupy in a solution averaged ensemble by taking atomically resolved information representing all residues in ubiquitin dimers into account.
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16
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Wiedenbeck E, Kovermann M, Gebauer D, Cölfen H. Flüssige metastabile Vorstufen von Ibuprofen als Zwischenprodukt der Nukleation in wässriger Lösung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910986] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Eduard Wiedenbeck
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Michael Kovermann
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
| | - Denis Gebauer
- Leibniz University of Hannover, Institut für Anorganische Chemie Callinstraße 9 30167 Hannover Deutschland
| | - Helmut Cölfen
- Physical ChemistryUniversity of Konstanz Universitätsstraße 10 78457 Konstanz Deutschland
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17
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Wiedenbeck E, Kovermann M, Gebauer D, Cölfen H. Liquid Metastable Precursors of Ibuprofen as Aqueous Nucleation Intermediates. Angew Chem Int Ed Engl 2019; 58:19103-19109. [PMID: 31556970 PMCID: PMC6972611 DOI: 10.1002/anie.201910986] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 01/25/2023]
Abstract
The nucleation mechanism of crystals of small organic molecules, postulated based on computer simulations, still lacks experimental evidence. In this study we designed an experimental approach to monitor the early stages of the crystallization of ibuprofen as a model system for small organic molecules. Ibuprofen undergoes liquid–liquid phase separation prior to nucleation. The binodal and spinodal limits of the corresponding liquid–liquid miscibility gap were analyzed and confirmed. An increase in viscosity sustains the kinetic stability of the dense liquid intermediate. Since the distances between ibuprofen molecules within the dense liquid phase are similar to those in the crystal forms, this dense liquid phase is identified as a precursor phase in the nucleation of ibuprofen, in which densification is followed by generation of structural order. This discovery may make it possible to enrich poorly soluble pharmaceuticals beyond classical solubility limitations in aqueous environments.
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Affiliation(s)
- Eduard Wiedenbeck
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Michael Kovermann
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Denis Gebauer
- Leibniz University of Hannover, Institute of Inorganic Chemistry, Callinstraße 9, 30167, Hannover, Germany
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
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18
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Li W, Wang J, Zhang J, Takada S, Wang W. Overcoming the Bottleneck of the Enzymatic Cycle by Steric Frustration. PHYSICAL REVIEW LETTERS 2019; 122:238102. [PMID: 31298900 DOI: 10.1103/physrevlett.122.238102] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/10/2019] [Indexed: 06/10/2023]
Abstract
The enormous catalytic power of natural enzymes relies on the ability to overcome the bottleneck event in the enzymatic cycle, yet the underlying physical mechanisms are not fully understood. Here, by performing molecular simulations of the whole enzymatic cycle for a model multisubstrate enzyme with a dynamic energy landscape model, we show that multisubstrate enzymes can utilize steric frustration to facilitate the rate-limiting product-release step. During the enzymatic cycles, the bottleneck product is actively squeezed out by the binding of a new substrate at the neighboring site through the population of a substrate-product cobound complex, in which the binding pockets are frustrated due to steric incompatibility. Such steric frustration thereby enables an active mechanism of product release driven by substrate-binding energy, facilitating the enzymatic cycle.
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Affiliation(s)
- Wenfei Li
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Wei Wang
- Department of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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19
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Yamamoto T, Yamagaki T, Satake H. Development of Software for the In-Depth Analysis of Protein Dynamics as Determined by MALDI Mass Spectrometry-Based Hydrogen/Deuterium Exchange. ACTA ACUST UNITED AC 2019; 8:S0082. [PMID: 33299732 PMCID: PMC7709884 DOI: 10.5702/massspectrometry.s0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/13/2019] [Indexed: 11/23/2022]
Abstract
Hydrogen/deuterium exchange (HDX) coupled with pepsin digestion is useful for rapidly analyzing the kinetic properties of small amounts of protein. However, the analysis of HDX by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is time-consuming due to a lack of dedicated software. Currently available software programs mainly calculate average mass shifts, even though the isotopic distribution width contains information regarding multiple protein conformations. Moreover, HDX reaction samples are typically composed of peptides that contain various numbers of deuterium atoms, which also hinders the rapid and comprehensive analysis of protein dynamics. We report here on the development of a software program "Scipas DX" that can be used to automatically analyze the hydrogen-deuterium isotopic distribution in peaks in HDX spectra and calculate the average number of atoms exchanged, the average deuteration ratio, the abundance ratio for exchanged atoms, and their fitted spectra with a high degree of accuracy within a few minutes. Analysis of the abundance ratio for exchanged atoms of a model protein, adenylate kinase 1, using Scipas DX indicate that the local structure at residues 83-106 and 107-117 are in a slow equilibrium, suggesting that these regions adopt multiple conformations that are involved in the stability and in switching between the active and inactive forms. Furthermore, precise HDX kinetics of the average deuteration ratio both confirmed the known induced conformations of two regions (residues 46-75 and 131-165) that are responsible for ligand binding and verified the novel structural dynamics of residues 107-117 and 166-196 following ligand binding to ligand-binding pockets 1 and 2, respectively. Collectively, these results highlight the usefulness and versatility of Scipas DX in MALDI-MS HDX-based analyses of protein dynamics.
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Affiliation(s)
- Tatsuya Yamamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
| | - Tohru Yamagaki
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto 619-0284, Japan
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20
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Wu M, Lu HP. Oscillating Piconewton Force Manipulation on Single-Molecule Enzymatic Conformational and Reaction Dynamics. J Phys Chem B 2018; 122:12312-12321. [PMID: 30481025 DOI: 10.1021/acs.jpcb.8b08980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oscillation force has been demonstrated in theoretical studies as a critical role in unraveling the comprehensive enzymatic dynamics and addressing its regulation on enzyme activity. Utilizing the imposed external mechanical oscillation force by our newly developed magnetic tweezers coupled with a single-molecule photon-stamping imaging spectroscopic microscope, we experimentally studied a millisecond-scale oscillation force manipulation on single horseradish peroxidase enzymatic conformational and reaction dynamics. We have studied the enzymatic reaction dynamics and found that the enzyme activity changes under the real-time oscillatory force manipulation. Moreover, the oscillation force shows the capability of manipulating the enzyme active-site conformational state as well as the nascent-formed product's interaction with the active site of the enzyme, which impacts on the product release pathways. Specifically, we have identified that there are two product releasing pathways, the solvation-mediated diffusion releasing pathway and the spilling-out releasing pathway. We have observed that the spilling-out pathway can be significantly perturbed by the oscillatory force manipulation. Our correlated interpretation of enzymatic conformational and reaction dynamics provides a new insight into the comprehensive understanding of the complex conformational dynamics evolved in an enzymatic reaction. Technically, we have also demonstrated a novel approach capable of unfolding an enzyme under an enzymatic reaction condition in real time and, furthermore, by using an oscillatory mechanical weak piconewton force to manipulate enzyme conformations, and the enzyme thermal fluctuation is fully maintained. The real-time in situ fluorescence probe at the enzymatic active site reports the active-site conformational dynamics through each enzymatic reaction turnovers.
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Affiliation(s)
- Meiling Wu
- Department of Chemistry, Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - H Peter Lu
- Department of Chemistry, Center for Photochemical Sciences , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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21
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A Luminal Loop of Wilson Disease Protein Binds Copper and Is Required for Protein Activity. Biophys J 2018; 115:1007-1018. [PMID: 30173886 PMCID: PMC6139820 DOI: 10.1016/j.bpj.2018.07.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 11/22/2022] Open
Abstract
The copper-transporting ATPase ATP7B is essential for loading of copper ions to copper-dependent enzymes in the secretory pathway; its inactivation results in Wilson disease. In contrast to copper-ion uptake by the cytoplasmic domains, ATP7B-mediated copper-ion release in the Golgi has not been explored yet. We demonstrate here that a luminal loop in ATP7B, rich in histidine/methionine residues, binds reduced copper (Cu(I)) ions, and identified copper-binding residues play an essential role in ATP7B-mediated metal ion release. NMR experiments on short-peptide models demonstrate that three methionine and two histidine residues are specifically involved in Cu(I) ion binding; with these residues replaced by alanines, no Cu(I) ion interaction is detected. Although more than one Cu(I) ion can interact with the wild-type peptide, removing either all histidine or all methionine residues reduces the stoichiometry to one Cu(I) ion binding per peptide. Using a yeast complementation assay, we show that for efficient copper transport by full-length ATP7B, the complete set of histidine and methionine residues in the lumen loop are required. The replacement of histidine/methionine residues by alanines does not perturb overall ATP7B structure, as the localization of ATP7B variants in yeast cells matches that of the wild-type protein. Thus, in similarity to ATP7A, ATP7B also appears to have a luminal “exit” copper ion site.
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22
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Hu R, Rodrigues JV, Pradeep Waduge J, Yamazaki H, Cressiot B, Chishti Y, Makowski L, Yu D, Shakhnovich E, Zhao Q, Wanunu M. Differential Enzyme Flexibility Probed Using Solid-State Nanopores. ACS NANO 2018; 12:4494-4502. [PMID: 29630824 PMCID: PMC9016714 DOI: 10.1021/acsnano.8b00734] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enzymes and motor proteins are dynamic macromolecules that coexist in a number of conformations of similar energies. Protein function is usually accompanied by a change in structure and flexibility, often induced upon binding to ligands. However, while measuring protein flexibility changes between active and resting states is of therapeutic significance, it remains a challenge. Recently, our group has demonstrated that breadth of signal amplitudes in measured electrical signatures as an ensemble of individual protein molecules is driven through solid-state nanopores and correlates with protein conformational dynamics. Here, we extend our study to resolve subtle flexibility variation in dihydrofolate reductase mutants from unlabeled single molecules in solution. We first demonstrate using a canonical protein system, adenylate kinase, that both size and flexibility changes can be observed upon binding to a substrate that locks the protein in a closed conformation. Next, we investigate the influence of voltage bias and pore geometry on the measured electrical pulse statistics during protein transport. Finally, using the optimal experimental conditions, we systematically study a series of wild-type and mutant dihydrofolate reductase proteins, finding a good correlation between nanopore-measured protein conformational dynamics and equilibrium bulk fluorescence probe measurements. Our results unequivocally demonstrate that nanopore-based measurements reliably probe conformational diversity in native protein ensembles.
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Affiliation(s)
- Rui Hu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - João V. Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J Pradeep Waduge
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Hirohito Yamazaki
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Benjamin Cressiot
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Yasmin Chishti
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Dapeng Yu
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory, School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Beijing 100084, People’s Republic of China
- Corresponding Authors:.,
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Corresponding Authors:.,
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23
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Molecular mechanism of ATP versus GTP selectivity of adenylate kinase. Proc Natl Acad Sci U S A 2018; 115:3012-3017. [PMID: 29507216 DOI: 10.1073/pnas.1721508115] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure-function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.
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24
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Mazal H, Aviram H, Riven I, Haran G. Effect of ligand binding on a protein with a complex folding landscape. Phys Chem Chem Phys 2018; 20:3054-3062. [PMID: 28721412 DOI: 10.1039/c7cp03327c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ligand binding to a protein can stabilize it significantly against unfolding. The variation of the folding free energy, ΔΔG0, due to ligand binding can be derived from a simple reaction scheme involving exclusive binding to the native state. One obtains the following expression: , where Kd is the ligand dissociation constant and L is its concentration, R is the universal gas constant and T is the temperature. This expression has been shown to correctly describe experimental results on multiple proteins. In the current work we studied the effect of ligand binding on the stability of the multi-domain protein adenylate kinase from E. coli (AKE). Unfolding experiments were conducted using single-molecule FRET spectroscopy, which allowed us to directly obtain the fraction of unfolded protein in a model-free way from FRET efficiency histograms. Surprisingly, it was found that the effect of two inhibitors (Ap5A and AMPPNP) and a substrate (AMP) on the stability of AKE was much smaller than expected based on Kd values obtained independently using microscale thermophoresis. To shed light on this issue, we measured the Kd for Ap5A over a range of chemical denaturant concentrations where the protein is still folded. It was found that Kd increases dramatically over this range, likely due to the population of folding intermediates, whose binding to the ligand is much weaker than that of the native state. We propose that binding to folding intermediates may dominate the effect of ligands on the stability of multi-domain proteins, and could therefore have a strong impact on protein homeostasis in vivo.
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Affiliation(s)
- Hisham Mazal
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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25
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Zheng Y, Cui Q. Multiple Pathways and Time Scales for Conformational Transitions in apo-Adenylate Kinase. J Chem Theory Comput 2018; 14:1716-1726. [PMID: 29378407 DOI: 10.1021/acs.jctc.7b01064] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The open/close transition in adenylate kinase (AK) is regarded as a representative example for large-scale conformational transition in proteins, yet its mechanism remains unclear despite numerous experimental and computational studies. Using extensive (∼50 μs) explicit solvent atomistic simulations and Markov state analysis, we shed new lights on the mechanism of this transition in the apo form of AK. The closed basin of apo AK features an open NMP domain while the LID domain closes and rotates toward it. Therefore, although the computed structural properties of the closed ensemble are consistent with previously reported FRET and PRE measurements, our simulations suggest that NMP closure is likely to follow AMP binding, in contrast to the previous interpretation of FRET and PRE data that the apo state was able to sample the fully closed conformation for "ligand selection". The closed state ensemble is found to be kinetically heterogeneous; multiple pathways and time scales are associated with the open/close transition, providing new clues to the disparate time scales observed in different experiments. Besides interdomain interactions, a novel mutual information analysis identifies specific intradomain interactions that correlate strongly to transition kinetics, supporting observations from previous chimera experiments. While our results underscore the role of internal domain properties in determining the kinetics of open/close transition in apo AK, no evidence is observed for any significant degree of local unfolding during the transition. These observations about AK have general implications to our view of conformational states, transition pathways, and time scales of conformational changes in proteins. The key features and time scales of observed transition pathways are robust and similar from simulations using two popular fixed charge force fields.
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Affiliation(s)
- Yuqing Zheng
- Graduate Program in Biophysics and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
| | - Qiang Cui
- Graduate Program in Biophysics and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States
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26
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Fast CS, Vahidi S, Konermann L. Changes in Enzyme Structural Dynamics Studied by Hydrogen Exchange-Mass Spectrometry: Ligand Binding Effects or Catalytically Relevant Motions? Anal Chem 2017; 89:13326-13333. [DOI: 10.1021/acs.analchem.7b03506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Courtney S. Fast
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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27
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Rogne P, Wolf-Watz M. Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States. Biophys J 2017; 111:1385-1395. [PMID: 27705762 DOI: 10.1016/j.bpj.2016.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/22/2016] [Accepted: 08/26/2016] [Indexed: 11/29/2022] Open
Abstract
Proteins are often functionally dependent on conformational changes that allow them to sample structural states that are sparsely populated in the absence of a substrate or binding partner. The distribution of such structural microstates is governed by their relative stability, and the kinetics of their interconversion is governed by the magnitude of associated activation barriers. Here, we have explored the interplay among structure, stability, and function of a selected enzyme, adenylate kinase (Adk), by monitoring changes in its enzymatic activity in response to additions of urea. For this purpose we used a 31P NMR assay that was found useful for heterogeneous sample compositions such as presence of urea. It was found that Adk is activated at low urea concentrations whereas higher urea concentrations unfolds and thereby deactivates the enzyme. From a quantitative analysis of chemical shifts, it was found that urea redistributes preexisting structural microstates, stabilizing a substrate-bound open state at the expense of a substrate-bound closed state. Adk is rate-limited by slow opening of substrate binding domains and the urea-dependent redistribution of structural states is consistent with a model where the increased activity results from an increased rate-constant for domain opening. In addition, we also detected a strong correlation between the catalytic free energy and free energy of substrate (ATP) binding, which is also consistent with the catalytic model for Adk. From a general perspective, it appears that urea can be used to modulate conformational equilibria of folded proteins toward more expanded states for cases where a sizeable difference in solvent-accessible surface area exists between the states involved. This effect complements the action of osmolytes, such as trimethylamine N-oxide, that favor more compact protein states.
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Affiliation(s)
- Per Rogne
- Department of Chemistry, Umeå University, Umeå, Sweden
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28
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Halder R, Manna RN, Chakraborty S, Jana B. Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π–Cation Interaction. J Phys Chem B 2017; 121:5699-5708. [DOI: 10.1021/acs.jpcb.7b01736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sandipan Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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29
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Structural basis for ligand binding to an enzyme by a conformational selection pathway. Proc Natl Acad Sci U S A 2017; 114:6298-6303. [PMID: 28559350 DOI: 10.1073/pnas.1700919114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Proteins can bind target molecules through either induced fit or conformational selection pathways. In the conformational selection model, a protein samples a scarcely populated high-energy state that resembles a target-bound conformation. In enzymatic catalysis, such high-energy states have been identified as crucial entities for activity and the dynamic interconversion between ground states and high-energy states can constitute the rate-limiting step for catalytic turnover. The transient nature of these states has precluded direct observation of their properties. Here, we present a molecular description of a high-energy enzyme state in a conformational selection pathway by an experimental strategy centered on NMR spectroscopy, protein engineering, and X-ray crystallography. Through the introduction of a disulfide bond, we succeeded in arresting the enzyme adenylate kinase in a closed high-energy conformation that is on-pathway for catalysis. A 1.9-Å X-ray structure of the arrested enzyme in complex with a transition state analog shows that catalytic sidechains are properly aligned for catalysis. We discovered that the structural sampling of the substrate free enzyme corresponds to the complete amplitude that is associated with formation of the closed and catalytically active state. In addition, we found that the trapped high-energy state displayed improved ligand binding affinity, compared with the wild-type enzyme, demonstrating that substrate binding to the high-energy state is not occluded by steric hindrance. Finally, we show that quenching of fast time scale motions observed upon ligand binding to adenylate kinase is dominated by enzyme-substrate interactions and not by intramolecular interactions resulting from the conformational change.
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30
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Weininger U, Modig K, Geitner AJ, Schmidpeter PAM, Koch JR, Akke M. Dynamics of Aromatic Side Chains in the Active Site of FKBP12. Biochemistry 2016; 56:334-343. [DOI: 10.1021/acs.biochem.6b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ulrich Weininger
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
- Institute
of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
| | - Anne-Juliane Geitner
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Philipp A. M. Schmidpeter
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Johanna R. Koch
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Mikael Akke
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
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31
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Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016; 56:1002-1006. [DOI: 10.1002/anie.201609830] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/09/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Xin-Hua Gu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Da-Chuan Guo
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Jin Wang
- Department of Physics and Astronomy and Department of Chemistry; State University of New York at Stony Brook; Stony Brook New York 11794 USA
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
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32
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Gong Z, Gu XH, Guo DC, Wang J, Tang C. Protein Structural Ensembles Visualized by Solvent Paramagnetic Relaxation Enhancement. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Xin-Hua Gu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Da-Chuan Guo
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
| | - Jin Wang
- Department of Physics and Astronomy and Department of Chemistry; State University of New York at Stony Brook; Stony Brook New York 11794 USA
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems; State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics; National Center for Magnetic Resonance in Wuhan; Collaborative Innovation Center of Chemistry for Life Sciences; Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences; Wuhan Hubei Province 430071 China
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33
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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34
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Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M. Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis. PLoS One 2016; 11:e0163115. [PMID: 27642758 PMCID: PMC5028032 DOI: 10.1371/journal.pone.0163115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 09/03/2016] [Indexed: 01/08/2023] Open
Abstract
Enzymes have evolved with highly specific values of their catalytic parameters kcat and KM. This poses fundamental biological questions about the selection pressures responsible for evolutionary tuning of these parameters. Here we are address these questions for the enzyme adenylate kinase (Adk) in eukaryotic yeast cells. A plasmid shuffling system was developed to allow quantification of relative fitness (calculated from growth rates) of yeast in response to perturbations of Adk activity introduced through mutations. Biophysical characterization verified that all variants studied were properly folded and that the mutations did not cause any substantial differences to thermal stability. We found that cytosolic Adk is essential for yeast viability in our strain background and that viability could not be restored with a catalytically dead, although properly folded Adk variant. There exist a massive overcapacity of Adk catalytic activity and only 12% of the wild type kcat is required for optimal growth at the stress condition 20°C. In summary, the approach developed here has provided new insights into the evolutionary tuning of kcat for Adk in a eukaryotic organism. The developed methodology may also become useful for uncovering new aspects of active site dynamics and also in enzyme design since a large library of enzyme variants can be screened rapidly by identifying viable colonies.
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Affiliation(s)
- Hasan Tükenmez
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | | | | | - Anders Byström
- Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
| | - Magnus Wolf-Watz
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
- * E-mail: (MWW); (AB)
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35
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Shao Q. Enhanced conformational sampling technique provides an energy landscape view of large-scale protein conformational transitions. Phys Chem Chem Phys 2016; 18:29170-29182. [DOI: 10.1039/c6cp05634b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel in silico approach (NMA–ITS) is introduced to rapidly and effectively sample the configuration space and give quantitative data for exploring the conformational changes of proteins.
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Affiliation(s)
- Qiang Shao
- Drug Discovery and Design Center
- CAS Key Laboratory of Receptor Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai
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