1
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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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2
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Dulko-Smith B, Ojeda-May P, Ådén J, Wolf-Watz M, Nam K. Mechanistic Basis for a Connection between the Catalytic Step and Slow Opening Dynamics of Adenylate Kinase. J Chem Inf Model 2023; 63:1556-1569. [PMID: 36802243 DOI: 10.1021/acs.jcim.2c01629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Escherichia coli adenylate kinase (AdK) is a small, monomeric enzyme that synchronizes the catalytic step with the enzyme's conformational dynamics to optimize a phosphoryl transfer reaction and the subsequent release of the product. Guided by experimental measurements of low catalytic activity in seven single-point mutation AdK variants (K13Q, R36A, R88A, R123A, R156K, R167A, and D158A), we utilized classical mechanical simulations to probe mutant dynamics linked to product release, and quantum mechanical and molecular mechanical calculations to compute a free energy barrier for the catalytic event. The goal was to establish a mechanistic connection between the two activities. Our calculations of the free energy barriers in AdK variants were in line with those from experiments, and conformational dynamics consistently demonstrated an enhanced tendency toward enzyme opening. This indicates that the catalytic residues in the wild-type AdK serve a dual role in this enzyme's function─one to lower the energy barrier for the phosphoryl transfer reaction and another to delay enzyme opening, maintaining it in a catalytically active, closed conformation for long enough to enable the subsequent chemical step. Our study also discovers that while each catalytic residue individually contributes to facilitating the catalysis, R36, R123, R156, R167, and D158 are organized in a tightly coordinated interaction network and collectively modulate AdK's conformational transitions. Unlike the existing notion of product release being rate-limiting, our results suggest a mechanistic interconnection between the chemical step and the enzyme's conformational dynamics acting as the bottleneck of the catalytic process. Our results also suggest that the enzyme's active site has evolved to optimize the chemical reaction step while slowing down the overall opening dynamics of the enzyme.
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Affiliation(s)
- Beata Dulko-Smith
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Pedro Ojeda-May
- High Performance Computing Centre North (HPC2N), Umeå University, Umeå SE-90187, Sweden
| | - Jörgen Ådén
- 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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3
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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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4
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Miller MD, Phillips GN. Moving beyond static snapshots: Protein dynamics and the Protein Data Bank. J Biol Chem 2021; 296:100749. [PMID: 33961840 PMCID: PMC8164045 DOI: 10.1016/j.jbc.2021.100749] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 01/02/2023] Open
Abstract
Proteins are the molecular machines of living systems. Their dynamics are an intrinsic part of their evolutionary selection in carrying out their biological functions. Although the dynamics are more difficult to observe than a static, average structure, we are beginning to observe these dynamics and form sound mechanistic connections between structure, dynamics, and function. This progress is highlighted in case studies from myoglobin and adenylate kinase to the ribosome and molecular motors where these molecules are being probed with a multitude of techniques across many timescales. New approaches to time-resolved crystallography are allowing simple “movies” to be taken of proteins in action, and new methods of mapping the variations in cryo-electron microscopy are emerging to reveal a more complete description of life’s machines. The results of these new methods are aided in their dissemination by continual improvements in curation and distribution by the Protein Data Bank and their partners around the world.
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Affiliation(s)
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA; Department of Chemistry, Rice University, Houston, Texas, USA.
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5
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Yang L, Sun X, Ye Y, Lu Y, Zuo J, Liu W, Elcock A, Zhu S. p38α Mitogen-Activated Protein Kinase Is a Druggable Target in Pancreatic Adenocarcinoma. Front Oncol 2019; 9:1294. [PMID: 31828036 PMCID: PMC6890821 DOI: 10.3389/fonc.2019.01294] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/07/2019] [Indexed: 12/11/2022] Open
Abstract
p38 mitogen-activated protein kinases are signaling molecules with major involvement in cancer. A detailed mechanistic understanding of how p38 MAPK family members function is urgently warranted for cancer targeted therapy. The conformational dynamics of the most common member of p38 MAPK family, p38α, are crucial for its function but poorly understood. Here we found that, unlike in other cancer types, p38α is significantly activated in pancreatic adenocarcinoma samples, suggesting its potential for anti-pancreatic cancer therapy. Using a state of the art supercomputer, Anton, long-timescale (39 μs) unbiased molecular dynamics simulations of p38α show that apo p38α has high structural flexibility in six regions, and reveal potential catalysis mechanism involving a “butterfly” motion. Moreover, in vitro studies show the low-selectivity of the current p38α inhibitors in both human and mouse pancreatic cancer cell lines, while computational solvent mapping identified 17 novel pockets for drug design. Taken together, our study reveals the conformational dynamics and potentially druggable pockets of p38α, which may potentiate p38α-targeting drug development and benefit pancreatic cancer patients.
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Affiliation(s)
- Ling Yang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaoting Sun
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Ye
- Department of Oral Implantology, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School and Hospital of Stomatology, Tongji University, Shanghai, China
| | - Yongtian Lu
- Department of ENT, Second People's Hospital of Shenzhen, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ji Zuo
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Wen Liu
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Adrian Elcock
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States
| | - Shun Zhu
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
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6
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Ye C, Ding C, Ma R, Wang J, Zhang Z. Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase. Proteins 2019; 87:337-347. [PMID: 30615212 DOI: 10.1002/prot.25655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/01/2019] [Accepted: 01/02/2019] [Indexed: 12/29/2022]
Abstract
Adenylate kinase is a monomeric phosphotransferase with important biological function in regulating concentration of adenosine triphosphate (ATP) in cells, by transferring the terminal phosphate group from ATP to adenosine monophosphate (AMP) and forming two adenosine diphosphate (ADP) molecules. During this reaction, the kinase may undergo a large conformational transition, forming different states with its substrates. Although many structures of the protein are available, atomic details of the whole process remain unclear. In this article, we use both conventional molecular dynamics (MD) simulation and an enhanced sampling technique called parallel cascade selection MD simulation to explore different conformational states of the Escherichia coli adenylate kinase. Based on the simulation results, we propose a possible entrance/release order of substrates during the catalytic cycle. The substrate-free protein prefers an open conformation, but changes to a closed state once ATP·Mg enters into its binding pocket first and then AMP does. After the reaction of ATP transferring the terminal phosphate group to AMP, ADP·Mg and ADP are released sequentially, and finally the whole catalyze cycle is completed. Detailed contact and distance analysis reveals that the entrance/release order of substrates may be largely controlled by electrostatic interactions between the protein and the substrates.
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Affiliation(s)
- Chun Ye
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China.,Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Chengtao Ding
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongsheng Ma
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
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7
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Saavedra HG, Wrabl JO, Anderson JA, Li J, Hilser VJ. Dynamic allostery can drive cold adaptation in enzymes. Nature 2018; 558:324-328. [PMID: 29875414 PMCID: PMC6033628 DOI: 10.1038/s41586-018-0183-2] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 05/01/2018] [Indexed: 11/19/2022]
Abstract
Adaptation of organisms to environmental niches is a hallmark of evolution. One prevalent example is that of thermal adaptation, wherein two descendants evolve at different temperature extremes1,2. Underlying the physiological differences between such organisms are changes in enzymes catalyzing essential reactions3, with orthologues from each organism undergoing adaptive mutations that preserve similar catalytic rates at their respective physiological temperatures 4,5. The sequence changes responsible for these adaptive differences, however, are often at surface exposed sites distant from the substrate binding site, leaving the active site of the enzyme structurally unperturbed6,7. How such changes are allosterically propagated to the active site, to modulate activity, is not known. Here we show that entropy-tuning changes can be engineered into distal sites of Escherichia coli adenylate kinase (AK) to quantitatively assess the role of dynamics in determining affinity, turnover, and the role in driving adaptation. The results not only reveal a dynamics-based allosteric tuning mechanism, but also uncover a spatial separation of the control of key enzymatic parameters. Fluctuations in one mobile domain (i.e. the LID) control substrate affinity, while dynamic attenuation in the other (i.e. the AMPbd) affects rate-limiting conformational changes governing enzyme turnover. Dynamics-based regulation may thus represent an elegant, widespread, and previously unrealized evolutionary adaptation mechanism that fine-tunes biological function without altering the ground state structure. Furthermore, because rigid-body conformational changes in both domains were thought to be rate limiting for turnover8,9, these adaptation studies reveal a new paradigm for understanding the relationship between dynamics and turnover in AK.
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Affiliation(s)
- Harry G Saavedra
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jeremy A Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jing Li
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA. .,T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.
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8
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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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9
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Wang Y, Makowski L. Fine structure of conformational ensembles in adenylate kinase. Proteins 2017; 86:332-343. [DOI: 10.1002/prot.25443] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 10/12/2017] [Accepted: 11/03/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Yujing Wang
- Department of BioengineeringNortheastern UniversityBoston Massachusetts
| | - Lee Makowski
- Department of BioengineeringNortheastern UniversityBoston Massachusetts
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10
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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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11
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Li D, Liu MS, Ji B. Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case. Biophys J 2016; 109:647-60. [PMID: 26244746 DOI: 10.1016/j.bpj.2015.06.059] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/19/2015] [Accepted: 06/29/2015] [Indexed: 12/22/2022] Open
Abstract
Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.
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Affiliation(s)
- Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing, China.
| | - Ming S Liu
- CSIRO - Digital Productivity Flagship, Clayton South, Victoria, Australia; Monash Institute of Medical Research, Clayton, Victoria, Australia.
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing, China.
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12
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Pham GH, Rana ASJB, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Sci 2016; 25:456-71. [PMID: 26506216 DOI: 10.1002/pro.2834] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
Abstract
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
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Affiliation(s)
- Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Ambar S J B Rana
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - E Nihal Korkmaz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Vivian H Trang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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13
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Unan H, Yildirim A, Tekpinar M. Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field. J Comput Aided Mol Des 2015; 29:655-65. [DOI: 10.1007/s10822-015-9849-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 05/22/2015] [Indexed: 11/29/2022]
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14
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Wen B, Peng J, Zuo X, Gong Q, Zhang Z. Characterization of protein flexibility using small-angle x-ray scattering and amplified collective motion simulations. Biophys J 2015; 107:956-64. [PMID: 25140431 DOI: 10.1016/j.bpj.2014.07.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/08/2014] [Accepted: 07/01/2014] [Indexed: 01/12/2023] Open
Abstract
Large-scale flexibility within a multidomain protein often plays an important role in its biological function. Despite its inherent low resolution, small-angle x-ray scattering (SAXS) is well suited to investigate protein flexibility and determine, with the help of computational modeling, what kinds of protein conformations would coexist in solution. In this article, we develop a tool that combines SAXS data with a previously developed sampling technique called amplified collective motions (ACM) to elucidate structures of highly dynamic multidomain proteins in solution. We demonstrate the use of this tool in two proteins, bacteriophage T4 lysozyme and tandem WW domains of the formin-binding protein 21. The ACM simulations can sample the conformational space of proteins much more extensively than standard molecular dynamics (MD) simulations. Therefore, conformations generated by ACM are significantly better at reproducing the SAXS data than are those from MD simulations.
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Affiliation(s)
- Bin Wen
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Xiaobing Zuo
- Advanced Photon Source, Argonne National Laboratory, Chicago, Illinois
| | - Qingguo Gong
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
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15
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Yang S. Methods for SAXS-based structure determination of biomolecular complexes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7902-10. [PMID: 24888261 PMCID: PMC4285438 DOI: 10.1002/adma.201304475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, current and recent SAXS-driven developments are described, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.
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Affiliation(s)
- Sichun Yang
- Center for Proteomics and Department of Pharmacology, Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106-4988, USA
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16
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Niebling S, Björling A, Westenhoff S. MARTINI bead form factors for the analysis of time-resolved X-ray scattering of proteins. J Appl Crystallogr 2014; 47:1190-1198. [PMID: 25242909 PMCID: PMC4119947 DOI: 10.1107/s1600576714009959] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/02/2014] [Indexed: 11/11/2023] Open
Abstract
Time-resolved small- and wide-angle X-ray scattering (SAXS and WAXS) methods probe the structural dynamics of proteins in solution. Although technologically advanced, these methods are in many cases limited by data interpretation. The calculation of X-ray scattering profiles is computationally demanding and poses a bottleneck for all SAXS/WAXS-assisted structural refinement and, in particular, for the analysis of time-resolved data. A way of speeding up these calculations is to represent biomolecules as collections of coarse-grained scatterers. Here, such coarse-graining schemes are presented and discussed and their accuracies examined. It is demonstrated that scattering factors coincident with the popular MARTINI coarse-graining scheme produce reliable difference scattering in the range 0 < q < 0.75 Å-1. The findings are promising for future attempts at X-ray scattering data analysis, and may help to bridge the gap between time-resolved experiments and their interpretation.
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Affiliation(s)
- Stephan Niebling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Alexander Björling
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
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17
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Olek AT, Rayon C, Makowski L, Kim HR, Ciesielski P, Badger J, Paul LN, Ghosh S, Kihara D, Crowley M, Himmel ME, Bolin JT, Carpita NC. The structure of the catalytic domain of a plant cellulose synthase and its assembly into dimers. THE PLANT CELL 2014; 26:2996-3009. [PMID: 25012190 PMCID: PMC4145127 DOI: 10.1105/tpc.114.126862] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 05/03/2023]
Abstract
Cellulose microfibrils are para-crystalline arrays of several dozen linear (1→4)-β-d-glucan chains synthesized at the surface of the cell membrane by large, multimeric complexes of synthase proteins. Recombinant catalytic domains of rice (Oryza sativa) CesA8 cellulose synthase form dimers reversibly as the fundamental scaffold units of architecture in the synthase complex. Specificity of binding to UDP and UDP-Glc indicates a properly folded protein, and binding kinetics indicate that each monomer independently synthesizes single glucan chains of cellulose, i.e., two chains per dimer pair. In contrast to structure modeling predictions, solution x-ray scattering studies demonstrate that the monomer is a two-domain, elongated structure, with the smaller domain coupling two monomers into a dimer. The catalytic core of the monomer is accommodated only near its center, with the plant-specific sequences occupying the small domain and an extension distal to the catalytic domain. This configuration is in stark contrast to the domain organization obtained in predicted structures of plant CesA. The arrangement of the catalytic domain within the CesA monomer and dimer provides a foundation for constructing structural models of the synthase complex and defining the relationship between the rosette structure and the cellulose microfibrils they synthesize.
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Affiliation(s)
- Anna T Olek
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054
| | - Catherine Rayon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115 Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Hyung Rae Kim
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971
| | - Peter Ciesielski
- National Renewable Energy Laboratory, Biomolecular Science Group, Golden, Colorado 80401-3305
| | - John Badger
- DeltaG Technologies, San Diego, California 92122
| | - Lake N Paul
- Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907-2057
| | - Subhangi Ghosh
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971 Department of Computer Science, Purdue University, West Lafayette, Indiana 47907-2107
| | - Michael Crowley
- National Renewable Energy Laboratory, Biomolecular Science Group, Golden, Colorado 80401-3305
| | - Michael E Himmel
- National Renewable Energy Laboratory, Biomolecular Science Group, Golden, Colorado 80401-3305
| | - Jeffrey T Bolin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971
| | - Nicholas C Carpita
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054 Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1971 Bindley Bioscience Center, Purdue University, West Lafayette, Indiana 47907-2057
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18
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Seyler SL, Beckstein O. Sampling large conformational transitions: adenylate kinase as a testing ground. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.919497] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Adenylate Kinase Isoform Network: A Major Hub in Cell Energetics and Metabolic Signaling. SYSTEMS BIOLOGY OF METABOLIC AND SIGNALING NETWORKS 2014. [DOI: 10.1007/978-3-642-38505-6_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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20
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WEN BIN, SHI YUNYU, ZHANG ZHIYONG. CLUSTERING MULTI-DOMAIN PROTEIN STRUCTURES IN THE ESSENTIAL DYNAMICS SUBSPACE. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A multi-domain protein is able to exist as equilibrium of different conformations in solution, which may be critical to its biological function. Besides experimental techniques, computational methods like molecular dynamics (MD) simulations are suitable to study inter-domain motions of the protein and sample different conformational states. A MD simulation usually generates a trajectory containing large amount of protein structures, and a post-processing cluster analysis would be necessary to group similar structures into clusters and identify these typical conformations of the multi-domain protein. In this paper, the widely used k-means clustering algorithm is implemented in the protein essential dynamics (ED) subspace defined by principal component analysis on the MD trajectory. Cluster analysis of the formin binding protein 21 (FBP21) tandem WW domains demonstrate that the k-means clustering results by measuring distances between structures in the ED subspace are superior to those by using other metrics like pairwise inter-domain residue distances.
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Affiliation(s)
- BIN WEN
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - YUNYU SHI
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - ZHIYONG ZHANG
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
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21
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Ravikumar KM, Huang W, Yang S. Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. J Chem Phys 2013; 138:024112. [PMID: 23320673 DOI: 10.1063/1.4774148] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A generalized method, termed Fast-SAXS-pro, for computing small angle x-ray scattering (SAXS) profiles of proteins, nucleic acids, and their complexes is presented. First, effective coarse-grained structure factors of DNA nucleotides are derived using a simplified two-particle-per-nucleotide representation. Second, SAXS data of a 18-bp double-stranded DNA are measured and used for the calibration of the scattering contribution from excess electron density in the DNA solvation layer. Additional test on a 25-bp DNA duplex validates this SAXS computational method and suggests that DNA has a different contribution from its hydration surface to the total scattering compared to RNA and protein. To account for such a difference, a sigmoidal function is implemented for the treatment of non-uniform electron density across the surface of a protein/nucleic-acid complex. This treatment allows differential scattering from the solvation layer surrounding protein/nucleic-acid complexes. Finally, the applications of this Fast-SAXS-pro method are demonstrated for protein/DNA and protein/RNA complexes.
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Affiliation(s)
- Krishnakumar M Ravikumar
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4988, USA
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Daily MD, Yu H, Phillips GN, Cui Q. Allosteric activation transitions in enzymes and biomolecular motors: insights from atomistic and coarse-grained simulations. Top Curr Chem (Cham) 2013; 337:139-64. [PMID: 23468286 PMCID: PMC3976962 DOI: 10.1007/128_2012_409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The chemical step in enzymes is usually preceded by a kinetically distinct activation step that involves large-scale conformational transitions. In "simple" enzymes this step corresponds to the closure of the active site; in more complex enzymes, such as biomolecular motors, the activation step is more complex and may involve interactions with other biomolecules. These activation transitions are essential to the function of enzymes and perturbations in the scale and/or rate of these transitions are implicated in various serious human diseases; incorporating key flexibilities into engineered enzymes is also considered a major remaining challenge in rational enzyme design. Therefore it is important to understand the underlying mechanism of these transitions. This is a significant challenge to both experimental and computational studies because of the allosteric and multi-scale nature of such transitions. Using our recent studies of two enzyme systems, myosin and adenylate kinase (AK), we discuss how atomistic and coarse-grained simulations can be used to provide insights into the mechanism of activation transitions in realistic systems. Collectively, the results suggest that although many allosteric transitions can be viewed as domain displacements mediated by flexible hinges, there are additional complexities and various deviations. For example, although our studies do not find any evidence for "cracking" in AK, our results do underline the contribution of intra-domain properties (e.g., dihedral flexibility) to the rate of the transition. The study of mechanochemical coupling in myosin highlights that local changes important to chemistry require stabilization from more extensive structural changes; in this sense, more global structural transitions are needed to activate the chemistry in the active site. These discussions further emphasize the importance of better understanding factors that control the degree of co-operativity for allosteric transitions, again hinting at the intimate connection between protein stability and functional flexibility. Finally, a number of topics of considerable future interest are briefly discussed.
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Affiliation(s)
- Michael D Daily
- Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
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23
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Wang Y, Gan L, Wang E, Wang J. Exploring the Dynamic Functional Landscape of Adenylate Kinase Modulated by Substrates. J Chem Theory Comput 2012; 9:84-95. [PMID: 26589012 DOI: 10.1021/ct300720s] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adenylate kinase (ADK) has been explored widely, through both experimental and theoretical studies. However, still less is known about how the functional dynamics of ADK is modulated explicitly by its natural substrates. Here, we report a quantitative study of the dynamic energy landscape for ADK responding to the substrate binding by integrating both experimental investigations and theoretical modeling. We make theoretical predictions which are in remarkable agreement with the single molecule experiments on the substrate-bound complex. With our combined models of ADK in its apo form, in the presence of AMP or ATP, and in complex with both substrates, we specifically address the following key questions: (1) Are there intermediate state(s) during their catalytic cycle and if so how many? (2) How many pathways are there along the open-to-closed transitions and what are their corresponding weights? (3) How do substrates influence the pathway weights and the stability of the intermediates? (4) Which lid's motion is rate-limiting along the turnover cycle, the NMP or the LID domain? Our models predict two major parallel stepwise pathways and two on-pathway intermediates which are denoted as IN (NMP domain open while LID domain closed) and IL (LID domain open and NMP domain closed), respectively. Further investigation of temperature effects suggests that the IN pathway is dominant at room temperature, but the IL pathway is dominant at the optimal temperature. This leads us to propose that the IL pathway is more dominant by entropy and IN pathway by enthalpy. Remarkably, our results show that even with maximum concentrations of natural substrates, ADK still fluctuates between multiple functional states, reflecting an intrinsic capability of large-scale conformational fluctuations which may be essential to its biological function. The results based on the dual-ligands model provide the theoretical validation of random bisubstrate biproducts (Bi-Bi) mechanism for the enzymatic reaction of ADK. Additionally, the pathway flux analysis strongly suggests that the motion of the NMP domain is the rate-determining step for the conformational cycle (opening and closing).
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Affiliation(s)
- Yong Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Linfeng Gan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P.R. China.,College of Physics, Jilin University, Changchun, Jilin, P.R. China.,Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, New York 11794-3400, United States
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