1
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Alavi Z, Casanova-Morales N, Quiroga-Roger D, Wilson CAM. Towards the understanding of molecular motors and its relationship with local unfolding. Q Rev Biophys 2024; 57:e7. [PMID: 38715547 DOI: 10.1017/s0033583524000052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Molecular motors are machines essential for life since they convert chemical energy into mechanical work. However, the precise mechanism by which nucleotide binding, catalysis, or release of products is coupled to the work performed by the molecular motor is still not entirely clear. This is due, in part, to a lack of understanding of the role of force in the mechanical-structural processes involved in enzyme catalysis. From a mechanical perspective, one promising hypothesis is the Haldane-Pauling hypothesis which considers the idea that part of the enzymatic catalysis is strain-induced. It suggests that enzymes cannot be efficient catalysts if they are fully complementary to the substrates. Instead, they must exert strain on the substrate upon binding, using enzyme-substrate energy interaction (binding energy) to accelerate the reaction rate. A novel idea suggests that during catalysis, significant strain energy is built up, which is then released by a local unfolding/refolding event known as 'cracking'. Recent evidence has also shown that in catalytic reactions involving conformational changes, part of the heat released results in a center-of-mass acceleration of the enzyme, raising the possibility that the heat released by the reaction itself could affect the enzyme's integrity. Thus, it has been suggested that this released heat could promote or be linked to the cracking seen in proteins such as adenylate kinase (AK). We propose that the energy released as a consequence of ligand binding/catalysis is associated with the local unfolding/refolding events (cracking), and that this energy is capable of driving the mechanical work.
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Affiliation(s)
- Zahra Alavi
- Department of Physics, Loyola Marymount University, Los Angeles, CA, USA
| | | | - Diego Quiroga-Roger
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
| | - Christian A M Wilson
- Biochemistry and Molecular Biology Department, Faculty of Chemistry and Pharmaceutical Sciences, Universidad de Chile, Santiago, Chile
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2
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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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3
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Knight AL, Widjaja V, Lisi GP. Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes. Front Mol Biosci 2023; 10:1281062. [PMID: 37877120 PMCID: PMC10591084 DOI: 10.3389/fmolb.2023.1281062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Mesophilic and thermophilic enzyme counterparts are often studied to understand how proteins function under harsh conditions. To function well outside of standard temperature ranges, thermophiles often tightly regulate their structural ensemble through intra-protein communication (via allostery) and altered interactions with ligands. It has also become apparent in recent years that the enhancement or diminution of allosteric crosstalk can be temperature-dependent and distinguish thermophilic enzymes from their mesophilic paralogs. Since most studies of allostery utilize chemical modifications from pH, mutations, or ligands, the impact of temperature on allosteric function is comparatively understudied. Here, we discuss the biophysical methods, as well as critical case studies, that dissect temperature-dependent function of mesophilic-thermophilic enzyme pairs and their allosteric regulation across a range of temperatures.
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Affiliation(s)
| | | | - George P. Lisi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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4
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Ozber N, Carr SC, Morris JS, Liang S, Watkins JL, Caldo KM, Hagel JM, Ng KKS, Facchini PJ. Alkaloid binding to opium poppy major latex proteins triggers structural modification and functional aggregation. Nat Commun 2022; 13:6768. [PMID: 36351903 PMCID: PMC9646721 DOI: 10.1038/s41467-022-34313-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Opium poppy accumulates copious amounts of several benzylisoquinoline alkaloids including morphine, noscapine, and papaverine, in the specialized cytoplasm of laticifers, which compose an internal secretory system associated with phloem throughout the plant. The contiguous latex includes an abundance of related proteins belonging to the pathogenesis-related (PR)10 family known collectively as major latex proteins (MLPs) and representing at least 35% of the total cellular protein content. Two latex MLP/PR10 proteins, thebaine synthase and neopione isomerase, have recently been shown to catalyze late steps in morphine biosynthesis previously assigned as spontaneous reactions. Using a combination of sucrose density-gradient fractionation-coupled proteomics, differential scanning fluorimetry, isothermal titration calorimetry, and X-ray crystallography, we show that the major latex proteins are a family of alkaloid-binding proteins that display altered conformation in the presence of certain ligands. Addition of MLP/PR10 proteins to yeast strains engineered with morphine biosynthetic genes from the plant significantly enhanced the conversion of salutaridine to morphinan alkaloids.
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Affiliation(s)
- Natali Ozber
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Samuel C. Carr
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Jeremy S. Morris
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada ,grid.4367.60000 0001 2355 7002Present Address: Department of Biology, Washington University, St. Louis, MO 63130-4899 USA
| | - Siyu Liang
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Jacinta L. Watkins
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Kristian M. Caldo
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Jillian M. Hagel
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
| | - Kenneth K. S. Ng
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada ,grid.267455.70000 0004 1936 9596Present Address: Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4 Canada
| | - Peter J. Facchini
- grid.22072.350000 0004 1936 7697Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4 Canada
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5
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Tian H, Jiang X, Trozzi F, Xiao S, Larson EC, Tao P. Explore Protein Conformational Space With Variational Autoencoder. Front Mol Biosci 2021; 8:781635. [PMID: 34869602 PMCID: PMC8633506 DOI: 10.3389/fmolb.2021.781635] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/28/2021] [Indexed: 12/02/2022] Open
Abstract
Molecular dynamics (MD) simulations have been actively used in the study of protein structure and function. However, extensive sampling in the protein conformational space requires large computational resources and takes a prohibitive amount of time. In this study, we demonstrated that variational autoencoders (VAEs), a type of deep learning model, can be employed to explore the conformational space of a protein through MD simulations. VAEs are shown to be superior to autoencoders (AEs) through a benchmark study, with low deviation between the training and decoded conformations. Moreover, we show that the learned latent space in the VAE can be used to generate unsampled protein conformations. Additional simulations starting from these generated conformations accelerated the sampling process and explored hidden spaces in the conformational landscape.
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Affiliation(s)
- Hao Tian
- Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Department of Chemistry, Southern Methodist University, Dallas, TX, United States
| | - Xi Jiang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, United States
| | - Francesco Trozzi
- Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Department of Chemistry, Southern Methodist University, Dallas, TX, United States
| | - Sian Xiao
- Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Department of Chemistry, Southern Methodist University, Dallas, TX, United States
| | - Eric C. Larson
- Department of Computer Science, Southern Methodist University, Dallas, TX, United States
| | - Peng Tao
- Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Department of Chemistry, Southern Methodist University, Dallas, TX, United States
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6
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Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals. Proc Natl Acad Sci U S A 2020; 117:5977-5986. [PMID: 32123117 DOI: 10.1073/pnas.1916786117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding the molecular basis of adaptation to the environment is a central question in evolutionary biology, yet linking detected signatures of positive selection to molecular mechanisms remains challenging. Here we demonstrate that combining sequence-based phylogenetic methods with structural information assists in making such mechanistic interpretations on a genomic scale. Our integrative analysis shows that positively selected sites tend to colocalize on protein structures and that positively selected clusters are found in functionally important regions of proteins, indicating that positive selection can contravene the well-known principle of evolutionary conservation of functionally important regions. This unexpected finding, along with our discovery that positive selection acts on structural clusters, opens previously unexplored strategies for the development of better models of protein evolution. Remarkably, proteins where we detect the strongest evidence of clustering belong to just two functional groups: Components of immune response and metabolic enzymes. This gives a coherent picture of pathogens and xenobiotics as important drivers of adaptive evolution of mammals.
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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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8
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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: 122] [Impact Index Per Article: 20.3] [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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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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Moon S, Kim J, Bae E. Structural analyses of adenylate kinases from Antarctic and tropical fishes for understanding cold adaptation of enzymes. Sci Rep 2017; 7:16027. [PMID: 29167503 PMCID: PMC5700098 DOI: 10.1038/s41598-017-16266-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/09/2017] [Indexed: 12/19/2022] Open
Abstract
Psychrophiles are extremophilic organisms capable of thriving in cold environments. Proteins from these cold-adapted organisms can remain physiologically functional at low temperatures, but are structurally unstable even at moderate temperatures. Here, we report the crystal structure of adenylate kinase (AK) from the Antarctic fish Notothenia coriiceps, and identify the structural basis of cold adaptation by comparison with homologues from tropical fishes including Danio rerio. The structure of N. coriiceps AK (AKNc) revealed suboptimal hydrophobic packing around three Val residues in its central CORE domain, which are replaced with Ile residues in D. rerio AK (AKDr). The Val-to-Ile mutations that improve hydrophobic CORE packing in AKNc increased stability at high temperatures but decreased activity at low temperatures, suggesting that the suboptimal hydrophobic CORE packing is important for cold adaptation. Such linkage between stability and activity was also observed in AKDr. Ile-to-Val mutations that destabilized the tropical AK resulted in increased activity at low temperatures. Our results provide the structural basis of cold adaptation of a psychrophilic enzyme from a multicellular, eukaryotic organism, and highlight the similarities and differences in the structural adjustment of vertebrate and bacterial psychrophilic AKs during cold adaptation.
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Affiliation(s)
- Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
- iNtRON Biotechnology, Inc., Seongnam, 13202, Korea
| | - Junhyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
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11
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Rodionova IA, Zhang Z, Mehla J, Goodacre N, Babu M, Emili A, Uetz P, Saier MH. The phosphocarrier protein HPr of the bacterial phosphotransferase system globally regulates energy metabolism by directly interacting with multiple enzymes in Escherichia coli. J Biol Chem 2017. [PMID: 28634232 DOI: 10.1074/jbc.m117.795294] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The histidine-phosphorylatable phosphocarrier protein (HPr) is an essential component of the sugar-transporting phosphotransferase system (PTS) in many bacteria. Recent interactome findings suggested that HPr interacts with several carbohydrate-metabolizing enzymes, but whether HPr plays a regulatory role was unclear. Here, we provide evidence that HPr interacts with a large number of proteins in Escherichia coli We demonstrate HPr-dependent allosteric regulation of the activities of pyruvate kinase (PykF, but not PykA), phosphofructokinase (PfkB, but not PfkA), glucosamine-6-phosphate deaminase (NagB), and adenylate kinase (Adk). HPr is either phosphorylated on a histidyl residue (HPr-P) or non-phosphorylated (HPr). PykF is activated only by non-phosphorylated HPr, which decreases the PykF Khalf for phosphoenolpyruvate by 10-fold (from 3.5 to 0.36 mm), thus influencing glycolysis. PfkB activation by HPr, but not by HPr-P, resulted from a decrease in the Khalf for fructose-6-P, which likely influences both gluconeogenesis and glycolysis. Moreover, NagB activation by HPr was important for the utilization of amino sugars, and allosteric inhibition of Adk activity by HPr-P, but not by HPr, allows HPr to regulate the cellular energy charge coordinately with glycolysis. These observations suggest that HPr serves as a directly interacting global regulator of carbon and energy metabolism and probably of other physiological processes in enteric bacteria.
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Affiliation(s)
- Irina A Rodionova
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Zhongge Zhang
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Jitender Mehla
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Andrew Emili
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284
| | - Milton H Saier
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,.
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12
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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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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Tiwari SP, Fuglebakk E, Hollup SM, Skjærven L, Cragnolini T, Grindhaug SH, Tekle KM, Reuter N. WEBnm@ v2.0: Web server and services for comparing protein flexibility. BMC Bioinformatics 2014; 15:427. [PMID: 25547242 PMCID: PMC4339738 DOI: 10.1186/s12859-014-0427-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics-function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins. RESULTS We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma . CONCLUSION WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.
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Affiliation(s)
- Sandhya P Tiwari
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Edvin Fuglebakk
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Siv M Hollup
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Lars Skjærven
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Tristan Cragnolini
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
- Present address: University Chemical Laboratories, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Svenn H Grindhaug
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Kidane M Tekle
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen, Bergen, Norway.
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
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