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Vander Meersche Y, Cretin G, Gheeraert A, Gelly JC, Galochkina T. ATLAS: protein flexibility description from atomistic molecular dynamics simulations. Nucleic Acids Res 2024; 52:D384-D392. [PMID: 37986215 PMCID: PMC10767941 DOI: 10.1093/nar/gkad1084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/15/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
Dynamical behaviour is one of the most crucial protein characteristics. Despite the advances in the field of protein structure resolution and prediction, analysis and prediction of protein dynamic properties remains a major challenge, mostly due to the low accessibility of data and its diversity and heterogeneity. To address this issue, we present ATLAS, a database of standardised all-atom molecular dynamics simulations, accompanied by their analysis in the form of interactive diagrams and trajectory visualisation. ATLAS offers a large-scale view and valuable insights on protein dynamics for a large and representative set of proteins, by combining data obtained through molecular dynamics simulations with information extracted from experimental structures. Users can easily analyse dynamic properties of functional protein regions, such as domain limits (hinge positions) and residues involved in interaction with other biological molecules. Additionally, the database enables exploration of proteins with uncommon dynamic properties conditioned by their environment such as chameleon subsequences and Dual Personality Fragments. The ATLAS database is freely available at https://www.dsimb.inserm.fr/ATLAS.
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Affiliation(s)
- Yann Vander Meersche
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Gabriel Cretin
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Aria Gheeraert
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, BIGR, F-75014 Paris, France
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Pražnikar J. Using graphlet degree vectors to predict atomic displacement parameters in protein structures. Acta Crystallogr D Struct Biol 2023; 79:1109-1119. [PMID: 37987168 PMCID: PMC10833351 DOI: 10.1107/s2059798323009142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
In structural biology, atomic displacement parameters, commonly used in the form of B values, describe uncertainties in atomic positions. Their distribution over the structure can provide hints on local structural reliability and mobility. A spatial macromolecular model can be represented by a graph whose nodes are atoms and whose edges correspond to all interatomic contacts within a certain distance. Small connected subgraphs, called graphlets, provide information about the wiring of a particular atom. The multiple linear regression approach based on this information aims to predict a distribution of values of isotropic atomic displacement parameters (B values) within a protein structure, given the atomic coordinates and molecular packing. By modeling the dynamic component of atomic uncertainties, this method allows the B values obtained from experimental crystallographic or cryo-electron microscopy studies to be reproduced relatively well.
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Affiliation(s)
- Jure Pražnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, Koper, Slovenia
- Department of Biochemistry, Molecular and Structural Biology, Institute Jožef Stefan, Jamova 39, Ljubljana, Slovenia
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Štambuk N, Konjevoda P, Štambuk A. How ambiguity codes specify molecular descriptors and information flow in Code Biology. Biosystems 2023; 233:105034. [PMID: 37739308 DOI: 10.1016/j.biosystems.2023.105034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
The article presents IUPAC ambiguity codes for incomplete nucleic acid specification, and their use in Code Biology. It is shown how to use this nomenclature in order to extract accurate information on different properties of the biological systems. We investigated the use of ambiguity codes, as mathematical and logical operators and truth table elements, for the encoding of amino acids by means of the Standard Genetic Code. It is explained how to use ambiguity codes and truth functions in order to obtain accurate information on different properties of the biological systems. Nucleotide ambiguity codes could be applied to: 1. encoding descriptive information of nucleotides, amino acids and proteins (e.g., of polarity, relative solvent accessibility, atom depth, etc.), and 2. system modelling ranging from standard bioinformatics tools to classic evolutionary models (i.e. from Miyazawa-Jernigan statistical potential to Kimura three-substitution-type model, respectively). It is shown that the algorithms based on IUPAC ambiguity codes, Boolean functions and truth table, Probabilistic Square of Opposition/Semiotic Square and Klein 4-groups-could be used for the bioinformatics analyses and Relational data modelling in natural science. Underlying mathematical, logical and semiotic concepts of interest are presented and addressed.
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Affiliation(s)
- Nikola Štambuk
- Centre for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Albert Štambuk
- Faculty of Kinesiology, University of Zagreb, Horvaćanski zavoj 15, HR-10000 Zagreb, Croatia
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de Sá Ribeiro F, Lima LMTR. Linking B-factor and temperature-induced conformational transition. Biophys Chem 2023; 298:107027. [PMID: 37172417 DOI: 10.1016/j.bpc.2023.107027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K-1, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.
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Affiliation(s)
- Fernando de Sá Ribeiro
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Química Biológica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Luís Maurício T R Lima
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Metrologia, Tecnologia e Qualidade (INMETRO), Duque de Caxias, RJ 25250-020, Brazil.
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Li H, Liang Z, Li Y, Wen J, Zhang R. Molecular docking and molecular dynamics simulation study on the toxicity mechanism of bongkrekic acid. Toxicon 2023; 223:107021. [PMID: 36621683 DOI: 10.1016/j.toxicon.2023.107021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023]
Abstract
BKA belongs to gram-negative brevibacterium. It can cause poisoning in humans or animals and can be fatal in severe cases. There are few investigations on toxic mechanisms of BKA because of foodborne factors. MD simulations were used to study the stability and intermolecular interactions of BKA and ANT complexes to reveal the mechanism of BKA in this paper. BKA blocked ANT protein translocation mainly through Van der Waals force, hydrophobic and hydrogen bonding interactions by the MD simulations. The conformational flexibility of the complex system during different simulation times indicated that BKA affected the conformational changes of ANT through strong interactions of hydrogen bonds with active domain residues Gln-93, Tyr-196, Arg-287 and Arg-245. The results of binding free energy, principal component analysis, hydrophobic interactions and root-mean-square fluctuation showed that the prominent binding force of Tyr-196 with C26 of BKA was significant to the toxicity. The active site interactions analysis indicated that the essential positively charged polar amino acids which play a crucial role within the active site of the ANT protein undergo conformational changes with BKA as the branch point.
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Affiliation(s)
- Hongmei Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhen Liang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Ying Li
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Jiazhen Wen
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Rong Zhang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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Hammerschmidt SJ, Huber S, Braun NJ, Lander M, Steinmetzer T, Kersten C. Thermodynamic characterization of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its acyclic analogs. Arch Pharm (Weinheim) 2022; 356:e2200518. [PMID: 36480352 DOI: 10.1002/ardp.202200518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
Cyclization of small molecules is a widely applied strategy in drug design for ligand optimization to improve affinity, as it eliminates the putative need for structural preorganization of the ligand before binding, or to improve pharmacokinetic properties. In this work, we provide a deeper insight into the binding thermodynamics of a macrocyclic Zika virus NS2B/NS3 protease inhibitor and its linear analogs. Characterization of the thermodynamic binding profiles by isothermal titration calorimetry experiments revealed an unfavorable entropy of the macrocycle compared to the open linear reference ligands. Molecular dynamic simulations and X-ray crystal structure analysis indicated only minor benefits from macrocyclization to fixate a favorable conformation, while linear ligands retained some flexibility even in the protein-bound complex structure, possibly explaining the initially surprising effect of a higher entropic penalty for the macrocyclic ligand.
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Affiliation(s)
- Stefan J Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Simon Huber
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Niklas J Braun
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Marc Lander
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Mainz, Germany
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Soft disorder modulates the assembly path of protein complexes. PLoS Comput Biol 2022; 18:e1010713. [DOI: 10.1371/journal.pcbi.1010713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 12/01/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Abstract
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles over the years: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide statistical evidence for the involvement of highly mobile and disordered regions in complex assembly. We ordered the entire set of X-ray crystallographic structures in the Protein Data Bank into hierarchies of progressive interactions involving identical or very similar protein chains, yielding 40205 hierarchies of protein complexes with increasing numbers of partners. We then examine them as proxies for the assembly pathways. Using this database, we show that upon oligomerisation, the new interfaces tend to be observed at residues that were characterised as softly disordered (flexible, amorphous or missing residues) in the complexes preceding them in the hierarchy. We also rule out the possibility that this correlation is just a surface effect by restricting the analysis to residues on the surface of the complexes. Interestingly, we find that the location of soft disordered residues in the sequence changes as the number of partners increases. Our results show that there is a general mechanism for protein assembly that involves soft disorder and modulates the way protein complexes are assembled. This work highlights the difficulty of predicting the structure of large protein complexes from sequence and emphasises the importance of linking predictors of soft disorder to the next generation of predictors of complex structure. Finally, we investigate the relationship between the Alphafold2’s confidence metric pLDDT for structure prediction in unbound versus bound structures, and soft disorder. We show a strong correlation between Alphafold2 low confidence residues and the union of all regions of soft disorder observed in the hierarchy. This paves the way for using the pLDDT metric as a proxy for predicting interfaces and assembly paths.
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Toward Real Real-Space Refinement of Atomic Models. Int J Mol Sci 2022; 23:ijms232012101. [PMID: 36292954 PMCID: PMC9603565 DOI: 10.3390/ijms232012101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
High-quality atomic models providing structural information are the results of their refinement versus diffraction data (reciprocal-space refinement), or versus experimental or experimentally based maps (real-space refinement). A proper real-space refinement can be achieved by comparing such a map with a map calculated from the atomic model. Similar to density distributions, the maps of a limited and even inhomogeneous resolution can also be calculated as sums of terms, known as atomic images, which are three-dimensional peaky functions surrounded by Fourier ripples. These atomic images and, consequently, the maps for the respective models, can be expressed analytically as functions of coordinates, atomic displacement parameters, and the local resolution. This work discusses the practical feasibility of such calculation for the real-space refinement of macromolecular atomic models.
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