51
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James JK, Nanda V. Comparative dynamics of tropomyosin in vertebrates and invertebrates. Proteins 2019; 88:265-273. [PMID: 31390486 DOI: 10.1002/prot.25797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/21/2022]
Abstract
Tropomyosin (Tpm) is an extended α-helical coiled-coil homodimer that regulates actinomyosin interactions in muscle. Molecular simulations of four Tpms, two from the vertebrate class Mammalia (rat and pig), and two from the invertebrate class Malacostraca (shrimp and lobster), showed that despite extensive sequence and structural homology across metazoans, dynamic behavior-particularly long-range structural fluctuations-were clearly distinct. Vertebrate Tpms were more flexible and sampled complex, multi-state conformational landscapes. Invertebrate Tpms were more rigid, sampling a highly constrained harmonic landscape. Filtering of trajectories by principle component analysis into essential subspaces showed significant overlap within but not between phyla. In vertebrate Tpms, hinge-regions decoupled long-range interhelical motions and suggested distinct domains. In contrast, crustacean Tpms did not exhibit long-range dynamic correlations-behaving more like a single rigid rod on the nanosecond time scale. These observations suggest there may be divergent mechanisms for Tpm binding to actin filaments, where conformational flexibility in mammalian Tpm allows a preorganized shape complementary to the filament surface, and where rigidity in the crustacean Tpm requires concerted bending and binding.
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Affiliation(s)
- Jose K James
- Center for Advanced Biotechnology and Medicine, and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
| | - Vikas Nanda
- Center for Advanced Biotechnology and Medicine, and the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey
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52
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de Alba E. Structure, interactions and self-assembly of ASC-dependent inflammasomes. Arch Biochem Biophys 2019; 670:15-31. [PMID: 31152698 PMCID: PMC8455077 DOI: 10.1016/j.abb.2019.05.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
The inflammasome is a multi-protein platform that assembles upon the presence of cues derived from infection or tissue damage, and triggers the inflammatory response. Inflammasome components include sensor proteins that detect danger signals, procaspase 1 and the adapter ASC (apoptosis-associated speck-like protein containing a CARD) tethering these molecules together. Upon inflammasome assembly, procaspase 1 self-activates and renders functional cytokines to arbitrate in the defense mechanism. This assembly is mediated by self-association and protein interactions via Death Domains. The inflammasome plays a critical role in innate immunity and its dysregulation is the culprit of many autoimmune disorders. An in-depth understanding of the factors involved in inflammasome assembly could help fight these conditions. This review describes our current knowledge on the biophysical aspects of inflammasome formation from the perspective of ASC. The specific characteristics of the three-dimensional solution structure and interdomain dynamics of ASC are explained in relation to its function in inflammasome assembly. Additionally, the review elaborates on the identification of ASC interacting surfaces at the amino acid level using NMR techniques. Finally, the macrostructures formed by full-length ASC and its two Death Domains studied with Transmission Electron Microscopy are compared in the context of a directional model for inflammasome assembly.
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Affiliation(s)
- Eva de Alba
- Department of Bioengineering. School of Engineering. University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
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53
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Crowder induced structural modulation of a multi-domain protein during its early stages of aggregation: A FRET-based and protein solvation study. Int J Biol Macromol 2019; 127:563-574. [DOI: 10.1016/j.ijbiomac.2019.01.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/02/2019] [Accepted: 01/11/2019] [Indexed: 12/31/2022]
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54
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Yamanaka M, Nakayama R, Fujii S, Wakai S, Sambongi Y, Hirota S. Conferment of CO-Controlled Dimer–Monomer Transition Property to Thermostable Cytochromec′ by Mutation in the Subunit–Subunit Interface. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masaru Yamanaka
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Ryoko Nakayama
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Sotaro Fujii
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Satoshi Wakai
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Sambongi
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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55
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Global response of diacylglycerol kinase towards substrate binding observed by 2D and 3D MAS NMR. Sci Rep 2019; 9:3995. [PMID: 30850624 PMCID: PMC6408475 DOI: 10.1038/s41598-019-40264-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/11/2019] [Indexed: 01/01/2023] Open
Abstract
Escherichia coli diacylglycerol kinase (DGK) is an integral membrane protein, which catalyses the ATP-dependent phosphorylation of diacylglycerol (DAG) to phosphatic acid (PA). It is a unique trimeric enzyme, which does not share sequence homology with typical kinases. It exhibits a notable complexity in structure and function despite of its small size. Here, chemical shift assignment of wild-type DGK within lipid bilayers was carried out based on 3D MAS NMR, utilizing manual and automatic analysis protocols. Upon nucleotide binding, extensive chemical shift perturbations could be observed. These data provide evidence for a symmetric DGK trimer with all of its three active sites concurrently occupied. Additionally, we could detect that the nucleotide substrate induces a substantial conformational change, most likely directing DGK into its catalytic active form. Furthermore, functionally relevant interprotomer interactions are identified by DNP-enhanced MAS NMR in combination with site-directed mutagenesis and functional assays.
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56
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Sayılgan JF, Haliloğlu T, Gönen M. Protein dynamics analysis reveals that missense mutations in cancer‐related genes appear frequently on hinge‐neighboring residues. Proteins 2019; 87:512-519. [DOI: 10.1002/prot.25673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/09/2019] [Accepted: 02/17/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Jan Fehmi Sayılgan
- Graduate School of Sciences and EngineeringKoç University İstanbul Turkey
| | - Türkan Haliloğlu
- Department of Chemical Engineering, School of EngineeringBoğaziçi University İstanbul Turkey
- Polymer Research CenterBoğaziçi University İstanbul Turkey
| | - Mehmet Gönen
- Department of Industrial Engineering, College of EngineeringKoç University İstanbul Turkey
- School of MedicineKoç University İstanbul Turkey
- Department of Biomedical Engineering, School of MedicineOregon Health and Science University Portland Oregon
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57
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Lee SH, Kim KJ. Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula. Biochem Biophys Res Commun 2019; 509:722-727. [PMID: 30611567 DOI: 10.1016/j.bbrc.2018.12.172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 11/25/2022]
Abstract
Metallosphaera sedula is a thermoacidophilic archaeon that has carbon fixation ability using the 3-hydroxypropionate/4-hydroxybutyrate(3-HP/4-HB) cycle, and has an incomplete TCA cycle to produce necessary biosynthetic precursors. The citrate synthase from M. sedula (MsCS) is an enzyme involved in the first step of the incomplete TCA cycle, catalyzing the conversion of oxaloacetate and acetyl-CoA into citrate and coenzyme A. To investigate the molecular mechanism of MsCS, we determined its crystal structure at 1.8 Å resolution. As other known CSs, MsCS functions as a dimer, and each monomer consists of two domains, a large domain and a small domain. We also determined the structure of the complex with acetyl-CoA and revealed the acetyl-CoA binding mode of MsCS. Structural comparison of MsCS with another CS in complex with oxaloacetate enabled us to predict the oxaloacetate binding site. Moreover, we performed inhibitory kinetic analyses of MsCS, and showed that the protein is inhibited by citrate and ATP by competitive and non-competitive inhibition modes, respectively, but not by NADH. Based on these results, we suggest that MsCS belongs to the type-I CS with structural and biochemical properties similar to those of CSs involved in the conventional TCA cycle.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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58
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Abstract
The native state of proteins is composed of conformers in dynamical equilibrium. In this chapter, different issues related to conformational diversity are explored using a curated and experimentally based database called CoDNaS (Conformational Diversity in the Native State). This database is a collection of redundant structures for the same sequence. CoDNaS estimates the degree of conformational diversity using different global and local structural similarity measures. It allows the user to explore how structural differences among conformers change as a function of several structural features providing further biological information. This chapter explores the measurement of conformational diversity and its relationship with sequence divergence. Also, it discusses how proteins with high conformational diversity could affect homology modeling techniques.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina
| | - Diego Javier Zea
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina.
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59
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Chu WT, Wang J. Quantifying the Intrinsic Conformation Energy Landscape Topography of Proteins with Large-Scale Open-Closed Transition. ACS CENTRAL SCIENCE 2018; 4:1015-1022. [PMID: 30159398 PMCID: PMC6107866 DOI: 10.1021/acscentsci.8b00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 06/08/2023]
Abstract
Large-scale conformational changes of proteins, including the open-closed transitions, are crucial for a variety of protein functions. These open-closed transitions are often associated with ligand binding. However, the understandings of the underlying mechanisms of the conformational changes within proteins during the open-closed transitions are still challenging at present. In this study, we quantified the intrinsic underlying conformational energy landscapes of five different proteins with large-scale open-closed transitions. This is realized by exploring the underlying density of states and the intrinsic conformational energy landscape topography measure Λ. Λ is a dimensionless ratio of conformational energy gap δE versus conformational energy roughness δE and configurational entropy S or size of the intrinsic conformational energy landscape. By quantifying the Λ of intrinsic open-closed conformational (Λoc) and intrinsic global folding (Λglobal) energy landscapes, we show that both intrinsic open-closed conformation energy and entropy landscapes are funneled toward the closed state. Furthermore, our results indicate the strong correlations between Λ and thermodynamics (conformational state transition temperature against trapping temperature) as well as between Λ and kinetics (open-closed kinetic time) of these proteins. This shows that the intrinsic conformational landscape topography determines both the conformational thermodynamic stability and kinetic speed of the conformational dynamics. Our investigations provide important insights for understanding the fundamental mechanisms of the protein conformational dynamics in a physical and global way.
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Affiliation(s)
- Wen-Ting Chu
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jin Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Department
of Chemistry & Physics, State University
of New York at Stony Brook, Stony
Brook, New York 11794, United States
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60
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Ciepluch K, Radulescu A, Hoffmann I, Raba A, Allgaier J, Richter D, Biehl R. Influence of PEGylation on Domain Dynamics of Phosphoglycerate Kinase: PEG Acts Like Entropic Spring for the Protein. Bioconjug Chem 2018; 29:1950-1960. [DOI: 10.1021/acs.bioconjchem.8b00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Karol Ciepluch
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich, 85748 Garching, Germany
| | - Ingo Hoffmann
- Institute Laue-Langevin (ILL), 71 rue des Martyrs, 38042 Grenoble, Cedex 9, France
| | - Andreas Raba
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jürgen Allgaier
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Richter
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science & Institute of Complex Systems (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425 Jülich, Germany
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61
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Dutta S, Eckmann JP, Libchaber A, Tlusty T. Green function of correlated genes in a minimal mechanical model of protein evolution. Proc Natl Acad Sci U S A 2018; 115:E4559-E4568. [PMID: 29712824 PMCID: PMC5960285 DOI: 10.1073/pnas.1716215115] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated the search for physical links between the observed genetic and dynamic cooperativity. We outline here a simplified theory of protein, which relates sequence correlations to physical interactions and to the emergence of mechanical function. Our protein is modeled as a strongly coupled amino acid network with interactions and motions that are captured by the mechanical propagator, the Green function. The propagator describes how the gene determines the connectivity of the amino acids and thereby, the transmission of forces. Mutations introduce localized perturbations to the propagator that scatter the force field. The emergence of function is manifested by a topological transition when a band of such perturbations divides the protein into subdomains. We find that epistasis-the interaction among mutations in the gene-is related to the nonlinearity of the Green function, which can be interpreted as a sum over multiple scattering paths. We apply this mechanical framework to simulations of protein evolution and observe long-range epistasis, which facilitates collective functional modes.
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Affiliation(s)
- Sandipan Dutta
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Korea
| | - Jean-Pierre Eckmann
- Département de Physique Théorique and Section de Mathématiques, Université de Genève, CH-1211 Geneva 4, Switzerland
| | - Albert Libchaber
- Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10021;
| | - Tsvi Tlusty
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 44919, Korea;
- Department of Physics, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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62
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Veevers R, Hayward S. Morphing and docking visualisation of biomolecular structures using Multi-Dimensional Scaling. J Mol Graph Model 2018; 82:108-116. [PMID: 29729647 DOI: 10.1016/j.jmgm.2018.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/28/2022]
Abstract
Protein structures are often solved at atomic resolution in two states defining a functional movement but intervening conformations are usually unknown. Morphing methods generate intervening conformations between two known structures. When viewed as an animation using molecular graphics, a smooth, direct morph enables the eye to track changes in structure that might be otherwise missed. We present a morphing method that aims to linearly interpolate interatomic distances and which uses SMACOF (Scaling by MAjorisation of COmplicated Function) and multigrid techniques with a cut-off distance based weighting that optimizes the MolProbity score of intervening structures. The all-atom morphs are smooth, move directly between the two structures, and are shown, in general, to pass closer to a set of known intermediates than those generated using other methods. The techniques are also used for docking by putting the unbound structures in a "near-approach pose" and then morphing to the bound complex. The resulting GPU-accelerated tools are available on a webserver, Morphit_Pro, at http://morphit-pro.cmp.uea.ac.uk/ and more than 5000 domains movements available at the DynDom website can now be viewed as morphs http://morphit-pro.cmp.uea.ac.uk/dyndom/.
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Affiliation(s)
- Ruth Veevers
- Computational Biology Laboratory, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Steven Hayward
- Computational Biology Laboratory, School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.
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63
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Abstract
Biological macromolecules often undergo large conformational rearrangements during a functional cycle. To simulate these structural transitions with full atomic detail typically demands extensive computational resources. Moreover, it is unclear how to incorporate, in a principled way, additional experimental information that could guide the structural transition. This article develops a probabilistic model for conformational transitions in biomolecules. The model can be viewed as a network of anharmonic springs that break, if the experimental data support the rupture of bonds. Hamiltonian Monte Carlo in internal coordinates is used to infer structural transitions from experimental data, thereby sampling large conformational transitions without distorting the structure. The model is benchmarked on a large set of conformational transitions. Moreover, we demonstrate the use of the probabilistic network model for integrative modeling of macromolecular complexes based on data from crosslinking followed by mass spectrometry.
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Affiliation(s)
- Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Felix Bernstein Institute for Mathematical Statistics in the Biosciences, Georg August University Göttingen, Goldschmidtstrasse 7, 37077, Göttingen, Germany
| | - Thach Nguyen
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, Georg August University Göttingen, Goldschmidtstrasse 7, 37077, Göttingen, Germany
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64
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Xia C, Rwere F, Im S, Shen AL, Waskell L, Kim JJP. Structural and Kinetic Studies of Asp632 Mutants and Fully Reduced NADPH-Cytochrome P450 Oxidoreductase Define the Role of Asp632 Loop Dynamics in the Control of NADPH Binding and Hydride Transfer. Biochemistry 2018; 57:945-962. [PMID: 29308883 PMCID: PMC5967631 DOI: 10.1021/acs.biochem.7b01102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Conformational changes in NADPH-cytochrome P450 oxidoreductase (CYPOR) associated with electron transfer from NADPH to electron acceptors via FAD and FMN have been investigated via structural studies of the four-electron-reduced NADP+-bound enzyme and kinetic and structural studies of mutants that affect the conformation of the mobile Gly631-Asn635 loop (Asp632 loop). The structure of four-electron-reduced, NADP+-bound wild type CYPOR shows the plane of the nicotinamide ring positioned perpendicular to the FAD isoalloxazine with its carboxamide group forming H-bonds with N1 of the flavin ring and the Thr535 hydroxyl group. In the reduced enzyme, the C8-C8 atoms of the two flavin rings are ∼1 Å closer than in the fully oxidized and one-electron-reduced structures, which suggests that flavin reduction facilitates interflavin electron transfer. Structural and kinetic studies of mutants Asp632Ala, Asp632Phe, Asp632Asn, and Asp632Glu demonstrate that the carboxyl group of Asp632 is important for stabilizing the Asp632 loop in a retracted position that is required for the binding of the NADPH ribityl-nicotinamide in a hydride-transfer-competent conformation. Structures of the mutants and reduced wild type CYPOR permit us to identify a possible pathway for NADP(H) binding to and release from CYPOR. Asp632 mutants unable to form stable H-bonds with the backbone amides of Arg634, Asn635, and Met636 exhibit decreased catalytic activity and severely impaired hydride transfer from NADPH to FAD, but leave interflavin electron transfer intact. Intriguingly, the Arg634Ala mutation slightly increases the cytochrome P450 2B4 activity. We propose that Asp632 loop movement, in addition to facilitating NADP(H) binding and release, participates in domain movements modulating interflavin electron transfer.
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Affiliation(s)
- Chuanwu Xia
- Medical College of Wisconsin, Milwaukee, Wisconsin 53226
| | - Freeborn Rwere
- University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Sangchoul Im
- University of Michigan Medical School, Ann Arbor, Michigan 48105
| | - Anna L. Shen
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lucy Waskell
- University of Michigan Medical School, Ann Arbor, Michigan 48105,Corresponding Author: Correspondence should be addressed to Lucy Waskell, M.D., Ph.D., Department of Anesthesiology, University of Michigan, Mail Stop 151, 2215 Fuller Rd., Ann Arbor, MI 48109-0112. . OR Jung Ja Kim, Ph.D., Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226.
| | - Jung-Ja P. Kim
- Medical College of Wisconsin, Milwaukee, Wisconsin 53226,Corresponding Author: Correspondence should be addressed to Lucy Waskell, M.D., Ph.D., Department of Anesthesiology, University of Michigan, Mail Stop 151, 2215 Fuller Rd., Ann Arbor, MI 48109-0112. . OR Jung Ja Kim, Ph.D., Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Rd., Milwaukee, WI 53226.
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65
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Rueda AJV, Monzon AM, Ardanaz SM, Iglesias LE, Parisi G. Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. BMC Bioinformatics 2018; 19:27. [PMID: 29382320 PMCID: PMC5791380 DOI: 10.1186/s12859-018-2044-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results Using proteins’ experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers. Electronic supplementary material The online version of this article (10.1186/s12859-018-2044-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Julia Velez Rueda
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Sebastián M Ardanaz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.
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66
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Carpinteri A, Piana G, Bassani A, Lacidogna G. Terahertz vibration modes in Na/K-ATPase. J Biomol Struct Dyn 2018; 37:256-264. [DOI: 10.1080/07391102.2018.1425638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alberto Carpinteri
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Gianfranco Piana
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Andrea Bassani
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
| | - Giuseppe Lacidogna
- Department of Structural, Geotechnical and Building Engineering, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129, Torino, Italy
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67
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Alternative substrate-bound conformation of bacterial solute-binding protein involved in the import of mammalian host glycosaminoglycans. Sci Rep 2017; 7:17005. [PMID: 29208901 PMCID: PMC5717064 DOI: 10.1038/s41598-017-16801-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Glycosaminoglycans (GAGs), constituted by repeating uronate and amino sugar units, are major components of mammalian extracellular matrices. Some indigenous and pathogenic bacteria target GAGs for colonization to and/or infection of host mammalian cells. In Gram-negative pathogenic Streptobacillus moniliformis, the solute-binding protein (Smon0123)-dependent ATP-binding cassette (ABC) transporter incorporates unsaturated GAG disaccharides into the cytoplasm after depolymerization by polysaccharide lyase. Smon0123, composed of N and C domains, adopts either a substrate-free open or a substrate-bound closed form by approaching two domains at 47° in comparison with the open form. Here we show an alternative 39°-closed conformation of Smon0123 bound to unsaturated chondroitin disaccharide sulfated at the C-4 and C-6 positions of N-acetyl-d-galactosamine residue (CΔ4S6S). In CΔ4S6S-bound Smon0123, Arg204 and Lys210 around the two sulfate groups were located at different positions from those at other substrate-bound 47°-closed conformations. Therefore, the two sulfate groups in CΔ4S6S shifted substrate-binding residue arrangements, causing dynamic conformational change. Smon0123 showed less affinity with CΔ4S6S than with non-sulfated and monosulfated substrates. ATPase activity of the Smon0123-dependent ABC transporter in the presence of CΔ4S6S was lower than that in the presence of other unsaturated chondroitin disaccharides, suggesting that CΔ4S6S-bound Smon0123 was unpreferable for docking with the ABC transporter.
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68
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Ma H, Li A, Gao K. Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Carbonic Anhydrase II Apo-Enzyme. ACS OMEGA 2017; 2:8414-8420. [PMID: 30023582 PMCID: PMC6045336 DOI: 10.1021/acsomega.7b01414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 11/15/2017] [Indexed: 05/30/2023]
Abstract
Human carbonic anhydrase II (HCA II) is an enzyme that catalyzes the reversible hydration of CO2 into bicarbonate (HCO3-) and a proton (H+) as well as other reactions at an extremely high rate. This enzyme plays fundamental roles in human physiology/pathology, such as controlling the pH level in cells and so on. However, the binding mechanism between apo-HCA II and CO2 or other ligands as well as related conformational changes remains poorly understood, and atomic investigation into it could promote our understanding of related internal physiological/pathological mechanisms. In this study, long-time atomic molecular dynamics simulations as well as the clustering and free-energy analysis were performed to reveal the dynamics of apo-HCA II as well as the mechanism upon ligand binding. Our simulations indicate that the crystallographic B-factors considerably underestimate the loop dynamics: multiple conformations can be adopted by loops 1 and 2, especially for loop 1 because loop 1 is one side of the binding pocket, and its left-to-right movement can compress or extend the binding pocket, leading to one inactive (closed) state, three intermediate (semiopen) states, and one active (open) state; CO2 cannot get into the binding pocket of the inactive state but can get into those of intermediate and active states. The coexistence of multiple conformational states proposes a possible conformational selection model for the binding mechanism between apo-HCA II and CO2 or other ligands, revising our previous view of its functional mechanism of conformational change upon ligand binding and offering valuable structural insights into the workings of HCA II.
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Affiliation(s)
- Huishu Ma
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Anbang Li
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
| | - Kaifu Gao
- Institute of Biophysics and Department
of Physics, Central China Normal University, Wuhan 430079, P. R. China
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69
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Guo J, Erskine P, Coker AR, Wood SP, Cooper JB. Structural studies of domain movement in active-site mutants of porphobilinogen deaminase from Bacillus megaterium. Acta Crystallogr F Struct Biol Commun 2017; 73:612-620. [PMID: 29095155 PMCID: PMC5683031 DOI: 10.1107/s2053230x17015436] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/23/2017] [Indexed: 11/10/2022] Open
Abstract
The enzyme porphobilinogen deaminase (PBGD) is one of the key enzymes in tetrapyrrole biosynthesis. It catalyses the formation of a linear tetrapyrrole from four molecules of the substrate porphobilinogen (PBG). It has a dipyrromethane cofactor (DPM) in the active site which is covalently linked to a conserved cysteine residue through a thioether bridge. The substrate molecules are linked to the cofactor in a stepwise head-to-tail manner during the reaction, which is catalysed by a conserved aspartate residue: Asp82 in the B. megaterium enzyme. Three mutations have been made affecting Asp82 (D82A, D82E and D82N) and their crystal structures have been determined at resolutions of 2.7, 1.8 and 1.9 Å, respectively. These structures reveal that whilst the D82E mutant possesses the DPM cofactor, in the D82N and D82A mutants the cofactor is likely to be missing, incompletely assembled or disordered. Comparison of the mutant PBGD structures with that of the wild-type enzyme shows that there are significant domain movements and suggests that the enzyme adopts `open' and `closed' conformations, potentially in response to substrate binding.
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Affiliation(s)
- Jingxu Guo
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Peter Erskine
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
| | - Alun R. Coker
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Steve P. Wood
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
| | - Jonathan B. Cooper
- Division of Medicine, University College London, Gower Street, London WC1E 6BT, England
- Department of Biological Sciences, Birkbeck, University of London, Malet Street, Bloomsbury, London WC1E 7HX, England
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70
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Monzon AM, Zea DJ, Marino-Buslje C, Parisi G. Homology modeling in a dynamical world. Protein Sci 2017; 26:2195-2206. [PMID: 28815769 DOI: 10.1002/pro.3274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022]
Abstract
A key concept in template-based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
| | - Diego Javier Zea
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Cristina Marino-Buslje
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
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71
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Yang Z, Cao Y, Hao D, Yuan X, Zhang L, Zhang S. Binding profiles of cholesterol ester transfer protein with current inhibitors: a look at mechanism and drawback. J Biomol Struct Dyn 2017; 36:2567-2580. [PMID: 28777919 DOI: 10.1080/07391102.2017.1363661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
- Department of Applied Chemistry, School of Science, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yang Cao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Dongxiao Hao
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Jinan University, Guangzhou 510632, China
| | - Lei Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi’an Jiaotong University, No. 28 Xianning West Road, Xi’an 710049, China
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72
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Nguyen T, Habeck M. A probabilistic model for detecting rigid domains in protein structures. Bioinformatics 2017; 32:i710-i717. [PMID: 27587693 DOI: 10.1093/bioinformatics/btw442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. RESULTS We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. AVAILABILITY AND IMPLEMENTATION The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection CONTACT : mhabeck@gwdg.de.
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Affiliation(s)
- Thach Nguyen
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen
| | - Michael Habeck
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
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73
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Gao K, Zhao Y. A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State Model. J Phys Chem B 2017; 121:2952-2960. [PMID: 28319394 DOI: 10.1021/acs.jpcb.7b00062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is a novel β-lactamase enzyme that confers enteric bacteria with nearly complete resistance to all β-lactam antibiotics, so it raises a formidable and global threat to human health. However, the binding mechanism between apo-NDM-1 and antibiotics as well as related conformational changes remains poorly understood, which largely hinders the overcoming of its antibiotic resistance. In our study, long-time conventional molecular dynamics simulation and Markov state models were applied to reveal both the dynamical and conformational landscape of apo-NDM-1: the MD simulation demonstrates that loop L3, which is responsible for antibiotic binding, is the most flexible and undergoes dramatic conformational changes; moreover, the Markov state model built from the simulation maps four metastable states including open, semiopen, and closed conformations of loop L3 as well as frequent transitions between the states. Our findings propose a possible conformational selection model for the binding mechanism between apo-NDM-1 and antibiotics, which facilitates the design of novel inhibitors and antibiotics.
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Affiliation(s)
- Kaifu Gao
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
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74
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Habeck M. Bayesian Modeling of Biomolecular Assemblies with Cryo-EM Maps. Front Mol Biosci 2017; 4:15. [PMID: 28382301 PMCID: PMC5360716 DOI: 10.3389/fmolb.2017.00015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/07/2017] [Indexed: 01/09/2023] Open
Abstract
A growing array of experimental techniques allows us to characterize the three-dimensional structure of large biological assemblies at increasingly higher resolution. In addition to X-ray crystallography and nuclear magnetic resonance in solution, new structure determination methods such cryo-electron microscopy (cryo-EM), crosslinking/mass spectrometry and solid-state NMR have emerged. Often it is not sufficient to use a single experimental method, but complementary data need to be collected by using multiple techniques. The integration of all datasets can only be achieved by computational means. This article describes Inferential structure determination, a Bayesian approach to integrative modeling of biomolecular complexes with hybrid structural data. I will introduce probabilistic models for cryo-EM maps and outline Markov chain Monte Carlo algorithms for sampling model structures from the posterior distribution. I will focus on rigid and flexible modeling with cryo-EM data and discuss some of the computational challenges of Bayesian inference in the context of biomolecular modeling.
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Affiliation(s)
- Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical ChemistryGöttingen, Germany; Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of GöttingenGöttingen, Germany
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75
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Abstract
We introduce a numerical scheme to evolve functional elastic materials that can accomplish a specified mechanical task. In this scheme, the number of solutions, their spatial architectures, and the correlations among them can be computed. As an example, we consider an "allosteric" task, which requires the material to respond specifically to a stimulus at a distant active site. We find that functioning materials evolve a less-constrained trumpet-shaped region connecting the stimulus and active sites, and that the amplitude of the elastic response varies nonmonotonically along the trumpet. As previously shown for some proteins, we find that correlations appearing during evolution alone are sufficient to identify key aspects of this design. Finally, we show that the success of this architecture stems from the emergence of soft edge modes recently found to appear near the surface of marginally connected materials. Overall, our in silico evolution experiment offers a window to study the relationship between structure, function, and correlations emerging during evolution.
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76
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Monzon AM, Zea DJ, Fornasari MS, Saldaño TE, Fernandez-Alberti S, Tosatto SCE, Parisi G. Conformational diversity analysis reveals three functional mechanisms in proteins. PLoS Comput Biol 2017; 13:e1005398. [PMID: 28192432 PMCID: PMC5330503 DOI: 10.1371/journal.pcbi.1005398] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 02/28/2017] [Accepted: 02/02/2017] [Indexed: 02/02/2023] Open
Abstract
Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call "rigid" (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Diego Javier Zea
- Bioinformatics Unit, Fundación Instituto Leloir (CONICET), Buenos Aires, Argentina
| | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Tadeo E. Saldaño
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | - Sebastian Fernandez-Alberti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes (CONICET), Bernal, Buenos Aires, Argentina
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77
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High anisotropy and frustration: the keys to regulating protein function efficiently in crowded environments. Curr Opin Struct Biol 2017; 42:50-58. [DOI: 10.1016/j.sbi.2016.10.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/16/2016] [Accepted: 10/19/2016] [Indexed: 11/17/2022]
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78
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Medvedev KE, Kolchanov NA, Afonnikov DA. High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations. J Biomol Struct Dyn 2017; 36:68-82. [DOI: 10.1080/07391102.2016.1268070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Kirill E. Medvedev
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nikolay A. Kolchanov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
| | - Dmitry A. Afonnikov
- Systems Biology Department, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Chair of Informational Biology, Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia
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79
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Nicolaï A, Barakat F, Delarue P, Senet P. Fingerprints of Conformational States of Human Hsp70 at Sub-THz Frequencies. ACS OMEGA 2016; 1:1067-1074. [PMID: 30023501 PMCID: PMC6044683 DOI: 10.1021/acsomega.6b00157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/25/2016] [Indexed: 06/08/2023]
Abstract
Large multidomain proteins occur in different conformational states to function. Detection and monitoring of these different structural states are of crucial interest for understanding the mechanics of proteins. Using computational methods, we show that different protein conformational states of the two-domain 70 kDa human Heat-shock protein (hHsp70), with similar vibrational density of states, lead to remarkably different far-IR spectra at acoustical frequencies (ν < 300 GHz). We found that the slow damped motions of the positively charged residues of hHsp70 contribute the most to collective IR active modes at low frequencies (ν < 300 GHz). We predicted that different structural states and functional modes of large proteins, such as hHsp70, might be detected in the sub-THz frequency range by single-molecule spectroscopy similar to the recent extraordinary acoustic Raman spectroscopy (Wheaton S.; Nat. Photonics2015, 9, 68-72).
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80
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Lv D, Wang C, Li C, Tan J, Zhang X. An efficient perturbation method to predict the functionally key sites of glutamine binding protein. Comput Biol Chem 2016; 67:62-68. [PMID: 28061385 DOI: 10.1016/j.compbiolchem.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/09/2016] [Accepted: 12/15/2016] [Indexed: 12/16/2022]
Abstract
Glutamine-Binding Protein (GlnBP) of Escherichia coli, an important member of the periplasmic binding protein family, is responsible for the first step in the active transport of glutamine across the cytoplasmic membrane. In this work, the functionally key regulation sites of GlnBP were identified by utilizing a perturbation method proposed by our group, in which the residues whose perturbations markedly change the binding free energy between GlnBP and glutamine are considered to be functionally key residues. The results show that besides the substrate binding sites, some other residues distant from the binding pocket, including the ones in the hinge regions between the two domains, the front- and back- door channels and the exposed region, are important for the function of glutamine binding and transport. The predicted results are well consistent with the theoretical and experimental data, which indicates that our method is an effective approach to identify the key residues important for both ligand binding and long-range allosteric signal transmission. This work can provide some insights into the function performance of GlnBP and the physical mechanism of its allosteric regulation.
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Affiliation(s)
- Dashuai Lv
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Jianjun Tan
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoyi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
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81
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Nicolaï A, Delarue P, Senet P. Theoretical Insights into Sub-Terahertz Acoustic Vibrations of Proteins Measured in Single-Molecule Experiments. J Phys Chem Lett 2016; 7:5128-5136. [PMID: 27973880 DOI: 10.1021/acs.jpclett.6b01812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Proteins are an important class of nanobioparticles with acoustical modes in the sub-THz frequency range. There is considerable interest to measure and establish the role of these acoustical vibrations for biological function. So far, the technique providing the most detailed information about the acoustical modes of proteins is the very recent Extraordinary Acoustic Raman (EAR) spectroscopy. In this technique, proteins are trapped in nanoholes and excited by two optical lasers of slightly different wavelengths producing an electric field at low frequency (<100 GHz). We demonstrate that the acoustical modes of proteins studied by EAR spectroscopy are both infrared- and Raman-active modes, and we provided interpretation of the spectroscopic fingerprints measured at the single-molecule level. A combination of the present calculations with techniques based on the excitation of a single nanobioparticle by an electric field, such as EAR spectroscopy, should provide a wealth of information on the role of molecular dynamics for biological function.
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Affiliation(s)
- Adrien Nicolaï
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Patrice Delarue
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
| | - Patrick Senet
- Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Dijon Cedex, France
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82
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Gao K, Jia Y, Yang M. A Network of Conformational Transitions Revealed by Molecular Dynamics Simulations of the Binary Complex of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase with MgATP. Biochemistry 2016; 55:6931-6939. [PMID: 27951655 DOI: 10.1021/acs.biochem.6b00720] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that, in its binary form, even bound by analogues of MgATP, loops 2 and 3 remain rather flexible; this raises questions about the putative large-scale induced-fit conformational change of the HPPK-MgATP binary complex. In this work, long-time all-atomic molecular dynamics simulations were conducted to investigate the loop dynamics in this complex. Our simulations show that, with loop 3 closed, multiple conformations of loop 2, including the open, semiopen, and closed forms, are all accessible to the binary complex. These results provide valuable structural insights into the details of conformational changes upon 6-hydroxymethyl-7,8-dihydropterin (HP) binding and biological activities of HPPK. Conformational network analysis and principal component analysis related to the loops are also discussed.
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Affiliation(s)
- Kaifu Gao
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Ya Jia
- Institute of Biophysics and Department of Physics, Central China Normal University , Wuhan 430079, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
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83
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Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc 2016; 4:042004. [PMID: 28192292 PMCID: PMC5308470 DOI: 10.1088/2050-6120/4/4/042004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.
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84
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Incorporation of side chain flexibility into protein binding pockets using MTflex. Bioorg Med Chem 2016; 24:4978-4987. [DOI: 10.1016/j.bmc.2016.08.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/15/2023]
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85
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Biswas S, Chowdhury PK. Correlated and Anticorrelated Domain Movement of Human Serum Albumin: A Peek into the Complexity of the Crowded Milieu. J Phys Chem B 2016; 120:4897-911. [DOI: 10.1021/acs.jpcb.6b01671] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Saikat Biswas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pramit Kumar Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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86
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Monzon AM, Rohr CO, Fornasari MS, Parisi G. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw038. [PMID: 27022160 PMCID: PMC4809262 DOI: 10.1093/database/baw038] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/02/2016] [Indexed: 01/01/2023]
Abstract
CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL:http://ufq.unq.edu.ar/codnas
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Affiliation(s)
| | - Cristian Oscar Rohr
- Instituto de Ecología Genética y Evolución de Buenos Aires (IEGEBA)-Laboratorio de Genómica Médica y Evolución, Universidad Nacional de Buenos Aires, Argentina
| | | | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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87
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Saldaño TE, Monzon AM, Parisi G, Fernandez-Alberti S. Evolutionary Conserved Positions Define Protein Conformational Diversity. PLoS Comput Biol 2016; 12:e1004775. [PMID: 27008419 PMCID: PMC4805271 DOI: 10.1371/journal.pcbi.1004775] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/27/2016] [Indexed: 12/18/2022] Open
Abstract
Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix.
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88
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Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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89
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Shasmal M, Dey S, Shaikh TR, Bhakta S, Sengupta J. E. coli metabolic protein aldehyde-alcohol dehydrogenase-E binds to the ribosome: a unique moonlighting action revealed. Sci Rep 2016; 6:19936. [PMID: 26822933 PMCID: PMC4731797 DOI: 10.1038/srep19936] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/21/2015] [Indexed: 11/24/2022] Open
Abstract
It is becoming increasingly evident that a high degree of regulation is involved in the protein synthesis machinery entailing more interacting regulatory factors. A multitude of proteins have been identified recently which show regulatory function upon binding to the ribosome. Here, we identify tight association of a metabolic protein aldehyde-alcohol dehydrogenase E (AdhE) with the E. coli 70S ribosome isolated from cell extract under low salt wash conditions. Cryo-EM reconstruction of the ribosome sample allows us to localize its position on the head of the small subunit, near the mRNA entrance. Our study demonstrates substantial RNA unwinding activity of AdhE which can account for the ability of ribosome to translate through downstream of at least certain mRNA helices. Thus far, in E. coli, no ribosome-associated factor has been identified that shows downstream mRNA helicase activity. Additionally, the cryo-EM map reveals interaction of another extracellular protein, outer membrane protein C (OmpC), with the ribosome at the peripheral solvent side of the 50S subunit. Our result also provides important insight into plausible functional role of OmpC upon ribosome binding. Visualization of the ribosome purified directly from the cell lysate unveils for the first time interactions of additional regulatory proteins with the ribosome.
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Affiliation(s)
- Manidip Shasmal
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Sandip Dey
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Tanvir R Shaikh
- Structural Biology Programme, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sayan Bhakta
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
| | - Jayati Sengupta
- Structural Biology &Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata-700 032, India
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90
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Rashin AA, Jernigan RL. Clusters of Structurally Similar MHC I HLA-A2 Molecules, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity. Biochemistry 2016; 55:167-85. [PMID: 26600404 DOI: 10.1021/acs.biochem.5b01077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Only α1 and α2 domains of the α-chain of the major histocompatibility complex (MHC) directly bind peptide antigens (Ag-s) and the T-cell receptor (TCR). Significant plasticity was found in the TCR but only minor in (α1 + α2). The α3-domain position variation was noted only in connection to its binding the coreceptor CD8. We apply our methods for identifying functional conformational changes in proteins to a systematic study of similarities between 43 X-ray structures of the entire α chains of MHC-I HLA-A2. Out of 903 different αHLA-A2 pairs 203 show similarities within the earlier determined uncertainty threshold and unexpectedly form three similarity clusters (SCs) with all/most structures in a cluster similar within the uncertainty threshold. Pairs from different SCs always differ above the threshold, mainly due to variations in the α3 position/structure. All structures in SC3 cannot bind the CD8 coreceptor. Strong hydrogen bonds between (α1 + α2) and α3 differ between SC1 and SC2 but are nearly invariant within each SC. Small conformational changes in the (α1 + α2), caused by Ag-s differences, act as an α3 "allosteric switch" between SC2 and SC1. Binding of CD8 to SC2-HLA-A2 (Tax-type Ag-s) changes it to SC1-HLA-A2 (HuD-type Ag-s). HuD binding to HLA-A2 is much less stable than Tax binding. CD8-liganded HLA-A2 preference for binding HuD suggests that CD8-HLA-A2 may present a weakly binding peptide for TCR recognition, supporting the hypothesis that CD8 increases TCR avidity to weak Ag-s. Other HLA-A2 functions may involve α3. TCR-A6-liganded-Tax-type-HLA-A2s form two small clusters, similar to either A6-liganded-HuD or A6-liganded-native-Tax HLA-A2s.
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Affiliation(s)
- Alexander A Rashin
- BioChemComp Inc , 543 Sagamore Avenue, Teaneck, New Jersey 07666, United States
- LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, 112 Office and Lab Building, Iowa State University , Ames, Iowa 50011-3020, United States
| | - Robert L Jernigan
- LH Baker Center for Bioinformatics and Department of Biochemistry, Biophysics and Molecular Biology, 112 Office and Lab Building, Iowa State University , Ames, Iowa 50011-3020, United States
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91
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Dutta D, Mishra S. Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme. Phys Chem Chem Phys 2016; 18:1671-80. [DOI: 10.1039/c5cp06024a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Conformational dynamics induced by substrate binding in DapE enzyme.
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Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
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92
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Abstract
Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states).
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93
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Kobayashi C, Matsunaga Y, Koike R, Ota M, Sugita Y. Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins. J Phys Chem B 2015; 119:14584-93. [PMID: 26536148 DOI: 10.1021/acs.jpcb.5b07668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due to the slow time scale. We show that a simple modification of the structure-based coarse-grained (CG) model enables a stable and efficient MD simulation of those proteins. "Motion Tree", a tree diagram that describes conformational changes between two structures in a protein, provides information on rigid structural units (domains) and the magnitudes of domain motions. In our new CG model, which we call the DoME (domain motion enhanced) model, interdomain interactions are defined as being inversely proportional to the magnitude of the domain motions in the diagram, whereas intradomain interactions are kept constant. We applied the DoME model in combination with the Go model to simulations of adenylate kinase (AdK). The results of the DoME-Go simulation are consistent with an all-atom MD simulation for 10 μs as well as known experimental data. Unlike the conventional Go model, the DoME-Go model yields stable simulation trajectories against temperature changes and conformational transitions are easily sampled despite domain rigidity. Evidently, identification of domains and their interfaces is useful approach for CG modeling of multidomain proteins.
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Affiliation(s)
- Chigusa Kobayashi
- RIKEN Advanced Institute for Computational Science, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
| | - Yasuhiro Matsunaga
- RIKEN Advanced Institute for Computational Science, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
| | - Ryotaro Koike
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Motonori Ota
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Yuji Sugita
- RIKEN Advanced Institute for Computational Science, 6-7-1 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan.,RIKEN Quantitative Biology Center, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 640-0047, Japan
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94
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Gao K, He H, Yang M, Yan H. Molecular dynamics simulations of the Escherichia coli HPPK apo-enzyme reveal a network of conformational transitions. Biochemistry 2015; 54:6734-42. [PMID: 26492157 DOI: 10.1021/acs.biochem.5b01012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) catalyzes the first reaction in the folate biosynthetic pathway. Comparison of its X-ray and nuclear magnetic resonance structures suggests that the enzyme undergoes significant conformational change upon binding to its substrates, especially in three catalytic loops. Experimental research has shown that even when confined by crystal contacts, loops 2 and 3 remain rather flexible when the enzyme is in its apo form, raising questions about the putative large-scale induced-fit conformational change of HPPK. To investigate the loop dynamics in a crystal-free environment, we performed conventional molecular dynamics simulations of the apo-enzyme at two different temperatures (300 and 350 K). Our simulations show that the crystallographic B-factors considerably underestimate the loop dynamics; multiple conformations of loops 2 and 3, including the open, semi-open, and closed conformations that an enzyme must adopt throughout its catalytic cycle, are all accessible to the apo-enzyme. These results revise our previous view of the functional mechanism of conformational change upon MgATP binding and offer valuable structural insights into the workings of HPPK. In this paper, conformational network analysis and principal component analysis related to the loops are discussed to support the presented conclusions.
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Affiliation(s)
- Kaifu Gao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Hongqing He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences , Wuhan 430071, P. R. China
| | - Honggao Yan
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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95
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Kanamori E, Kawaguchi SI, Kuramitsu S, Kouyama T, Murakami M. Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8. Biophys Physicobiol 2015; 12:47-56. [PMID: 27493854 PMCID: PMC4736845 DOI: 10.2142/biophysico.12.0_47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 09/16/2015] [Indexed: 12/01/2022] Open
Abstract
The crystal structures of citrate synthase from the thermophilic eubacteria Thermus thermophilus HB8 (TtCS) were determined for an open form at 1.5 Å resolution and for closed form at 2.3 Å resolution, respectively. In the absence of ligands TtCS in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. TtCS was also co-crystallized with citrate and coenzyme-A to form an orthorhombic crystal with two homodimers in the asymmetric unit. Citrate and CoA are found in the active site situated between the large domain and the small domain in all subunit whereas the complex shows two distinct closed conformations, the fully closed form and partially closed form. Structural comparisons are performed to describe conformational changes associated with binding of products of TtCS. Upon binding of citrate, basic residues in the active site move toward citrate and make a hydrogen bond network in the active site, inducing a large-scale rotation of the small domain relative to the large domain. CoA is sandwiched between the small and large domains and then the cysteamine tail is inserted into the active site with a cooperative rotation around mainchain dihedrals in the hinge region connecting helices M and N. According to this rotation these helices are extended to close the active site completely. The considerable flexibility and structural rearrangements in the hinge region are crucial for an ordered bibi reaction in catalysis for microbial CSs.
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Affiliation(s)
- Eiji Kanamori
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Shin-Ichi Kawaguchi
- Graduate School Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Seiki Kuramitsu
- Graduate School of Science, Osaka University, Osaka 560-0043, Japan
| | - Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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96
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Tan ML, Perrin BS, Niu S, Huang Q, Ichiye T. Protein dynamics and the all-ferrous [Fe4 S4 ] cluster in the nitrogenase iron protein. Protein Sci 2015; 25:12-8. [PMID: 26271353 PMCID: PMC4815322 DOI: 10.1002/pro.2772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 01/09/2023]
Abstract
In nitrogen fixation by Azotobacter vinelandii nitrogenase, the iron protein (FeP) binds to and subsequently transfers electrons to the molybdenum–FeP, which contains the nitrogen fixation site, along with hydrolysis of two ATPs. However, the nature of the reduced state cluster is not completely clear. While reduced FeP is generally thought to contain an [Fe4S4]1+ cluster, evidence also exists for an all‐ferrous [Fe4S4]0 cluster. Since the former indicates a single electron is transferred per two ATPs hydrolyzed while the latter indicates two electrons could be transferred per two ATPs hydrolyzed, an all‐ferrous [Fe4S4]0 cluster in FeP is potenially two times more efficient. However, the 1+/0 reduction potential has been measured in the protein at both 460 and 790 mV, causing the biological significance to be questioned. Here, “density functional theory plus Poisson Boltzmann” calculations show that cluster movement relative to the protein surface observed in the crystal structures could account for both measured values. In addition, elastic network mode analysis indicates that such movement occurs in low frequency vibrations of the protein, implying protein dynamics might lead to variations in reduction potential. Furthermore, the different reductants used in the conflicting measurements of the reduction potential could be differentially affecting the protein dynamics. Moreover, even if the all‐ferrous cluster is not the biologically relevant cluster, mutagenesis to stabilize the conformation with the more exposed cluster may be useful for bioengineering more efficient enzymes.
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Affiliation(s)
- Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - Qi Huang
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057.,Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
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97
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Wells SA, van der Kamp MW, McGeagh JD, Mulholland AJ. Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions. PLoS One 2015; 10:e0133372. [PMID: 26241964 PMCID: PMC4524684 DOI: 10.1371/journal.pone.0133372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/25/2015] [Indexed: 12/19/2022] Open
Abstract
Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.
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Affiliation(s)
- Stephen A. Wells
- Department of Chemistry, University of Bath, Bath, United Kingdom
- * E-mail:
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - John D. McGeagh
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United Kingdom
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98
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Peng Y, Zeng W, Ye H, Han K, Dharmarajan V, Novick S, Wilson I, Griffin P, Friedman J, Lerner R. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. ACTA ACUST UNITED AC 2015; 22:1134-43. [DOI: 10.1016/j.chembiol.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
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99
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Chapman BK, Davulcu O, Skalicky JJ, Brüschweiler RP, Chapman MS. Parsimony in Protein Conformational Change. Structure 2015; 23:1190-8. [PMID: 26095029 DOI: 10.1016/j.str.2015.05.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/13/2015] [Accepted: 05/03/2015] [Indexed: 01/25/2023]
Abstract
Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ℓ(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (φ, ψ) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within α helices and β sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium.
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Affiliation(s)
- Brynmor K Chapman
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Omar Davulcu
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah, Emma Eccles Jones Medical Research Building, 15 North Medical Drive East, Salt Lake City, UT 84112-5650, USA
| | - Rafael P Brüschweiler
- Department of Chemistry & Biochemistry, The Ohio State University, Newman and Wolfrom Laboratory, 100 West 18th Avenue, Columbus, OH 43210-1173, USA
| | - Michael S Chapman
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, School of Medicine L-224, 3181 SW Sam Jackson Park Road, Portland, OR 97239-3098, USA.
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Wieninger SA, Ullmann GM. CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion. J Chem Theory Comput 2015; 11:2841-54. [DOI: 10.1021/acs.jctc.5b00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Silke A. Wieninger
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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