1
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Basciu A, Athar M, Kurt H, Neville C, Malloci G, Muredda FC, Bosin A, Ruggerone P, Bonvin AMJJ, Vargiu AV. Predicting binding events in very flexible, allosteric, multi-domain proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597018. [PMID: 38895346 PMCID: PMC11185556 DOI: 10.1101/2024.06.02.597018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Knowledge of the structures formed by proteins and small ligands is of fundamental importance for understanding molecular principles of chemotherapy and for designing new and more effective drugs. Due to the still high costs and to the several limitations of experimental techniques, it is most often desirable to predict these ligand-protein complexes in silico, particularly when screening for new putative drugs from databases of millions of compounds. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology aimed at generating bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites. Validation was performed on the enzyme adenylate kinase (ADK), a paradigmatic example of proteins that undergo very large conformational changes upon ligand binding. By only exploiting the unbound structure and the putative binding sites of the protein, we generated a significant fraction of bound-like structures, which employed in ensemble-docking calculations allowed to find native-like poses of substrates, inhibitors, and catalytically incompetent binders. Our protocol provides a general framework for the generation of bound-like conformations of flexible proteins that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening for difficult targets, prediction of the impact of amino acid mutations on structure and dynamics, and protein engineering.
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Affiliation(s)
- Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Han Kurt
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Christine Neville
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Fabrizio C. Muredda
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Andrea Bosin
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Alexandre M. J. J. Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Attilio V. Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
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2
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Kidder KM, Shell MS, Noid WG. Surveying the energy landscape of coarse-grained mappings. J Chem Phys 2024; 160:054105. [PMID: 38310476 DOI: 10.1063/5.0182524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/28/2023] [Indexed: 02/05/2024] Open
Abstract
Simulations of soft materials often adopt low-resolution coarse-grained (CG) models. However, the CG representation is not unique and its impact upon simulated properties is poorly understood. In this work, we investigate the space of CG representations for ubiquitin, which is a typical globular protein with 72 amino acids. We employ Monte Carlo methods to ergodically sample this space and to characterize its landscape. By adopting the Gaussian network model as an analytically tractable atomistic model for equilibrium fluctuations, we exactly assess the intrinsic quality of each CG representation without introducing any approximations in sampling configurations or in modeling interactions. We focus on two metrics, the spectral quality and the information content, that quantify the extent to which the CG representation preserves low-frequency, large-amplitude motions and configurational information, respectively. The spectral quality and information content are weakly correlated among high-resolution representations but become strongly anticorrelated among low-resolution representations. Representations with maximal spectral quality appear consistent with physical intuition, while low-resolution representations with maximal information content do not. Interestingly, quenching studies indicate that the energy landscape of mapping space is very smooth and highly connected. Moreover, our study suggests a critical resolution below which a "phase transition" qualitatively distinguishes good and bad representations.
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Affiliation(s)
- Katherine M Kidder
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - M Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
| | - W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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3
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Brown C, Agarwal A, Luque A. pyCapsid: identifying dominant dynamics and quasi-rigid mechanical units in protein shells. Bioinformatics 2024; 40:btad761. [PMID: 38113434 PMCID: PMC10786678 DOI: 10.1093/bioinformatics/btad761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 11/01/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023] Open
Abstract
SUMMARY pyCapsid is a Python package developed to facilitate the characterization of the dynamics and quasi-rigid mechanical units of protein shells and other protein complexes. The package was developed in response to the rapid increase of high-resolution structures, particularly capsids of viruses, requiring multiscale biophysical analyses. Given a protein shell, pyCapsid generates the collective vibrations of its amino-acid residues, identifies quasi-rigid mechanical regions associated with the disassembly of the structure, and maps the results back to the input proteins for interpretation. pyCapsid summarizes the main results in a report that includes publication-quality figures. AVAILABILITY AND IMPLEMENTATION pyCapsid's source code is available under MIT License on GitHub. It is compatible with Python 3.8-3.10 and has been deployed in two leading Python package-management systems, PIP and Conda. Installation instructions and tutorials are available in the online documentation and in the pyCapsid's YouTube playlist. In addition, a cloud-based implementation of pyCapsid is available as a Google Colab notebook. pyCapsid Colab does not require installation and generates the same report and outputs as the installable version. Users can post issues regarding pyCapsid in the repository's issues section.
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Affiliation(s)
- Colin Brown
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Department of Physics, San Diego State University, San Diego, CA 92116, United States
| | - Anuradha Agarwal
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
| | - Antoni Luque
- Viral Information Institute, San Diego State University, San Diego, CA 92116, United States
- Computational Science Research Center, San Diego State University, San Diego, CA 92116, United States
- Department of Mathematics and Statistics, San Diego State University, San Diego, CA 92116, United States
- Department of Biology, University of Miami, Coral Gables, FL 33146, United States
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4
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Delgado A, Vera-Villalobos J, Paz JL, Lossada C, Hurtado-León ML, Marrero-Ponce Y, Toro-Mendoza J, Alvarado YJ, González-Paz L. Macromolecular crowding impact on anti-CRISPR AcrIIC3/NmeCas9 complex: Insights from scaled particle theory, molecular dynamics, and elastic networks models. Int J Biol Macromol 2023:125113. [PMID: 37257544 DOI: 10.1016/j.ijbiomac.2023.125113] [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: 02/16/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
The coupling of Cas9 and its inhibitor AcrIIC3, both from the bacterium Neisseria meningitidis (Nme), form a homodimer of the (NmeCas9/AcrIIC3)2 type. This coupling was studied to assess the impact of their interaction with the crowders in the following environments: (1) homogeneous crowded, (2) heterogeneous, and (3) microheterogeneous cytoplasmic. For this, statistical thermodynamic models based on the scaled particle theory (SPT) were used, considering the attractive and repulsive protein-crowders contributions and the stability of the formation of spherocylindrical homodimers and the effects of changes in the size of spherical dimers were estimated. Studies based on models of dynamics, elastic networks, and statistical potentials to the formation of complexes NmeCas9/AcrIIC3 using PEG as the crowding agent support the predictions from SPT. Macromolecular crowding stabilizes the formation of the dimers, being more significant when the attractive protein-crowder interactions are weaker and the crowders are smaller. The coupling is favored towards the formation of spherical and compact dimers due to crowding addition (excluded-volume effects) and the thermodynamic stability of the dimers is markedly dependent on the size of the crowders. These results support the experimental mechanistic proposal of inhibition of NmeCas9 mediated by AcrIIC3.
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Affiliation(s)
- Ariana Delgado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela; Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Química, Laboratorio de Química Teórica y Computacional (LQTC), 4001 Maracaibo, Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - José Luis Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), 4001 Maracaibo, Zulia, Venezuela
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Venezuela
| | - Yovani Marrero-Ponce
- Universidad San Francisco de Quito (USFQ), Grupo de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades Médicas, Quito 170157, Pichincha, Ecuador; Departamento de Ciencias de la Computación, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Baja California 22860, Mexico; Instituto de Simulación Computacional (ISC-USFQ), Diego de Robles y vía Interoceánica, Quito 170157, Pichincha, Ecuador
| | - Jhoan Toro-Mendoza
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela
| | - Ysaías J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica Teórica y Experimental (LQBTE), 4001 Maracaibo, Zulia, Venezuela.
| | - Lenin González-Paz
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Biomedicina Molecular (CBM), Laboratorio de Biocomputación (LB), 4001 Maracaibo, Zulia, Venezuela.
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5
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González-Paz L, Lossada C, Hurtado-León ML, Fernández-Materán FV, Paz JL, Parvizi S, Cardenas Castillo RE, Romero F, Alvarado YJ. Intrinsic Dynamics of the ClpXP Proteolytic Machine Using Elastic Network Models. ACS OMEGA 2023; 8:7302-7318. [PMID: 36873006 PMCID: PMC9979342 DOI: 10.1021/acsomega.2c04347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/25/2022] [Indexed: 06/18/2023]
Abstract
ClpXP complex is an ATP-dependent mitochondrial matrix protease that binds, unfolds, translocates, and subsequently degrades specific protein substrates. Its mechanisms of operation are still being debated, and several have been proposed, including the sequential translocation of two residues (SC/2R), six residues (SC/6R), and even long-pass probabilistic models. Therefore, it has been suggested to employ biophysical-computational approaches that can determine the kinetics and thermodynamics of the translocation. In this sense, and based on the apparent inconsistency between structural and functional studies, we propose to apply biophysical approaches based on elastic network models (ENM) to study the intrinsic dynamics of the theoretically most probable hydrolysis mechanism. The proposed models ENM suggest that the ClpP region is decisive for the stabilization of the ClpXP complex, contributing to the flexibility of the residues adjacent to the pore, favoring the increase in pore size and, therefore, with the energy of interaction of its residues with a larger portion of the substrate. It is predicted that the complex may undergo a stable configurational change once assembled and that the deformability of the system once assembled is oriented, to increase the rigidity of the domains of each region (ClpP and ClpX) and to gain flexibility of the pore. Our predictions could suggest under the conditions of this study the mechanism of the interaction of the system, of which the substrate passes through the unfolding of the pore in parallel with a folding of the bottleneck. The variations in the distance calculated by molecular dynamics could allow the passage of a substrate with a size equivalent to ∼3 residues. The theoretical behavior of the pore and the stability and energy of binding to the substrate based on ENM models suggest that in this system, there are thermodynamic, structural, and configurational conditions that allow a possible translocation mechanism that is not strictly sequential.
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Affiliation(s)
- Lenin González-Paz
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - Maria Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC), Departamento de Biología, Laboratorio
de Genética y Biología Molecular (LGBM), Universidad del Zulia (LUZ), 4001 Maracaibo, Zulia, República Bolivariana
de Venezuela
| | - Francelys V. Fernández-Materán
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB), Instituto Venezolano de Investigaciones
Científicas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
| | - José Luis Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, 15081 Lima, Perú
| | - Shayan Parvizi
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | | | - Freddy Romero
- Pulmonary,
Critical Care and Sleep Medicine, Baylor
College of Medicine, Houston, Texas 77030, United States
| | - Ysaias J. Alvarado
- Centro
de Biomedicina Molecular (CBM), Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE), Instituto
Venezolano de Investigaciones Cientificas (IVIC), 4001 Maracaibo, Zulia, República Bolivariana de Venezuela
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6
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González-Paz L, Hurtado-León ML, Lossada C, Fernández-Materán FV, Vera-Villalobos J, Loroño M, Paz JL, Jeffreys L, Alvarado YJ. Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models. J Mol Liq 2021; 340:117284. [PMID: 34421159 PMCID: PMC8367659 DOI: 10.1016/j.molliq.2021.117284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 12/24/2022]
Abstract
The COVID-19 pandemic has accelerated the study of the potential of multi-target drugs (MTDs). The mixture of homologues called ivermectin (avermectin-B1a + avermectin-B1b) has been shown to be a MTD with potential antiviral activity against SARS-CoV-2 in vitro. However, there are few reports on the effect of each homologue on the flexibility and stiffness of proteins associated with COVID-19, described as ivermectin targets. We observed that each homologue was stably bound to the proteins studied and was able to induce detectable changes with Elastic Network Models (ENM). The perturbations induced by each homologue were characteristic of each compound and, in turn, were represented by a disruption of native intramolecular networks (interactions between residues). The homologues were able to slightly modify the conformation and stability of the connection points between the Cα atoms of the residues that make up the structural network of proteins (nodes), compared to free proteins. Each homologue was able to modified differently the distribution of quasi-rigid regions of the proteins, which could theoretically alter their biological activities. These results could provide a biophysical-computational view of the potential MTD mechanism that has been reported for ivermectin.
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Affiliation(s)
- Lenin González-Paz
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela.,Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Estudios Botánicos y Agroforestales (CEBA), Laboratorio de Protección Vegetal (LPV), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Universidad del Zulia (LUZ), Facultad Experimental de Ciencias (FEC), Departamento de Biología. Laboratorio de Genética y Biología Molecular (LGBM), 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Carla Lossada
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Francelys V Fernández-Materán
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad de Ciencias Naturales y Matemáticas, Departamento de Química y Ciencias Ambientales, Laboratorio de Análisis Químico Instrumental (LAQUINS), Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Marcos Loroño
- Departamento Académico de Química Analítica e Instrumental, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - J L Paz
- Departamento Académico de Química Inorgánica, Facultad de Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Laura Jeffreys
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Ysaias J Alvarado
- Instituto Venezolano de Investigaciones Científicas (IVIC), Centro de Investigación y Tecnología de Materiales (CITeMA), Laboratorio de Caracterización Molecular y Biomolecular, 4001 Maracaibo, Republica Bolivariana de Venezuela
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7
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Dang TKL, Nguyen T, Habeck M, Gültas M, Waack S. A graph-based algorithm for detecting rigid domains in protein structures. BMC Bioinformatics 2021; 22:66. [PMID: 33579190 PMCID: PMC7881620 DOI: 10.1186/s12859-021-03966-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
Background Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains. Results We develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively. Conclusions The results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.
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Affiliation(s)
- Truong Khanh Linh Dang
- Institute of Computer Science, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany.
| | - Thach Nguyen
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany
| | - Michael Habeck
- Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany.,Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Microscopic Image Analysis Group, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Margarethe von Wrangell-Weg 7, 37075, Göttingen, Germany.,Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Stephan Waack
- Institute of Computer Science, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany
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8
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Giulini M, Menichetti R, Shell MS, Potestio R. An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules. J Chem Theory Comput 2020; 16:6795-6813. [PMID: 33108737 PMCID: PMC7659038 DOI: 10.1021/acs.jctc.0c00676] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Indexed: 02/06/2023]
Abstract
In theoretical modeling of a physical system, a crucial step consists of the identification of those degrees of freedom that enable a synthetic yet informative representation of it. While in some cases this selection can be carried out on the basis of intuition and experience, straightforward discrimination of the important features from the negligible ones is difficult for many complex systems, most notably heteropolymers and large biomolecules. We here present a thermodynamics-based theoretical framework to gauge the effectiveness of a given simplified representation by measuring its information content. We employ this method to identify those reduced descriptions of proteins, in terms of a subset of their atoms, that retain the largest amount of information from the original model; we show that these highly informative representations share common features that are intrinsically related to the biological properties of the proteins under examination, thereby establishing a bridge between protein structure, energetics, and function.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - M Scott Shell
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Raffaello Potestio
- Physics Department, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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9
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Galdadas I, Gervasio FL, Cournia Z. Unravelling the effect of the E545K mutation on PI3Kα kinase. Chem Sci 2020; 11:3511-3515. [PMID: 34703536 PMCID: PMC8493679 DOI: 10.1039/c9sc05903b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
PI3Kα controls several cellular processes and its aberrant signalling is implicated in tumorigenesis. One of its hotspot mutations, E545K, increases PI3Kα lipid kinase activity, but its mode of action is only partially understood. Here, we perform biased and unbiased molecular dynamics simulations of PI3Kα and uncover, for the first time, the free energy landscape of the E545K PI3Kα mutant. We reveal the mechanism by which E545K leads to PI3Kα activation in atomic-level detail, which is considerably more complex than previously thought.
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Affiliation(s)
- Ioannis Galdadas
- Department of Chemistry, University College London London WC1E 6BT UK
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London London WC1E 6BT UK
- Institute of Structural and Molecular Biology, University College London London WC1E 6BT UK
- Pharmaceutical Sciences, University of Geneva Geneva CH-1211 Switzerland
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens Athens 11527 Greece
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10
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Lakhani B, Thayer KM, Black E, Beveridge DL. Spectral analysis of molecular dynamics simulations on PDZ: MD sectors. J Biomol Struct Dyn 2020; 38:781-790. [PMID: 31262238 PMCID: PMC7307555 DOI: 10.1080/07391102.2019.1588169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 02/23/2019] [Indexed: 02/06/2023]
Abstract
The idea of protein "sectors" posits that sparse subsets of amino acid residues form cooperative networks that are key elements of protein stability, ligand binding, and allosterism. To date, protein sectors have been calculated by the statistical coupling analysis (SCA) method of Ranganathan and co-workers via the spectral analysis of conservation-weighted evolutionary covariance matrices obtained from a multiple sequence alignments of homologous families of proteins. SCA sectors, a knowledge-based protocol, have been indentified with functional properties and allosterism for a number of systems. In this study, we investigate the utility of the sector idea for the analysis of physics-based molecular dynamics (MD) trajectories of proteins. Our test case for this procedure is PSD95- PDZ3, one of the smallest proteins for which allosterism has been observed. It has served previously as a model system for a number of prediction algorithms, and is well characterized by X-ray crystallography, NMR spectroscopy and site specific mutagenisis. All-atom MD simulations were performed for a total of 500 nanoseconds using AMBER, and MD-calculated covariance matrices for the fluctuations of residue displacements and non-bonded interaction energies were subjected to spectral analysis in a manner analogous to that of SCA. The composition of MD sectors was compared with results from SCA, site specific mutagenesis, and allosterism. The concordance indicates that MD sectors are a viable protocol for analyzing MD trajectories and provide insight into the physical origin of the phenomenon.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharat Lakhani
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Department of Molecular Biology & Biochemistry, Wesleyan University, Middletown CT 06459, USA
| | - Kelly M. Thayer
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Chemistry Department, Wesleyan University, Middletown CT 06459, USA
- Department of Mathematics and Computer Science, Wesleyan University, Middletown CT 06459, USA
| | - Emily Black
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
| | - David L. Beveridge
- Program in Molecular Biophysics, Wesleyan University, Middletown CT 06459, USA
- Chemistry Department, Wesleyan University, Middletown CT 06459, USA
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11
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Koike R, Ota M. All Atom Motion Tree detects side chain-related motions and their coupling with domain motion in proteins. Biophys Physicobiol 2019; 16:280-286. [PMID: 31984182 PMCID: PMC6976028 DOI: 10.2142/biophysico.16.0_280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Structural changes of proteins are closely related with their molecular function. We previously developed a computational tool, Motion Tree (MT), to compare protein structures and describe structural changes using solely the Cα atoms. Here, we have extended MT to incorporate all heavy atoms to analyze side chain-related (SCR) motions. All Atom Motion Tree (AAMT) was applied to 76 proteins that exhibited a simple domain motion identified by MT. AAMT also detected 921 SCR motions. We examined the coupling of domain and SCR motions and classified the structural changes in terms of coupling. The statistical results indicated that it is common for coupled SCR motions to also couple with the domain motion. The classification correlates properties of domain motions and SCR motions. The AAMT results suggest that a large domain motion with a sizable domain boundary is accompanied by SCR motions composed of more than a single residue, which induces further couplings of SCR motions.
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Affiliation(s)
- Ryotaro Koike
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Motonori Ota
- Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
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12
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Westerlund AM, Delemotte L. InfleCS: Clustering Free Energy Landscapes with Gaussian Mixtures. J Chem Theory Comput 2019; 15:6752-6759. [PMID: 31647864 DOI: 10.1021/acs.jctc.9b00454] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This has remained a formidable task, despite a plethora of existing clustering methods. We present InfleCS, a novel method for extracting well-defined core states from free energy landscapes. The method is based on a Gaussian mixture free energy estimator and exploits the shape of the estimated density landscape. The core states that naturally arise from the clustering allow for detailed characterization of the conformational ensemble. The clustering quality is evaluated on three toy models with different properties, where the method is shown to consistently outperform other conventional and state-of-the-art clustering methods. Finally, the method is applied to a temperature enhanced molecular dynamics simulation of Ca2+-bound Calmodulin. Through the free energy landscape, we discover a pathway between a canonical and a compact state, revealing conformational changes driven by electrostatic interactions.
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Affiliation(s)
- Annie M Westerlund
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics , KTH Royal Institute of Technology , Box 1031, SE-171 21 Solna , Sweden
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13
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Nüske F, Boninsegna L, Clementi C. Coarse-graining molecular systems by spectral matching. J Chem Phys 2019; 151:044116. [DOI: 10.1063/1.5100131] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Feliks Nüske
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, Texas 77005-1892, USA
| | - Lorenzo Boninsegna
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, Texas 77005-1892, USA
| | - Cecilia Clementi
- Center for Theoretical Biological Physics and Department of Chemistry, Rice University, Houston, Texas 77005-1892, USA
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14
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Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun 2019; 75:19-32. [PMID: 30605122 PMCID: PMC6317454 DOI: 10.1107/s2053230x18015108] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.
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Affiliation(s)
| | - A. Jiménez
- National Center of Biotechnology (CSIC), Spain
| | - J. Mota
- National Center of Biotechnology (CSIC), Spain
| | - J. L. Vilas
- National Center of Biotechnology (CSIC), Spain
| | - D. Maluenda
- National Center of Biotechnology (CSIC), Spain
| | - M. Martínez
- National Center of Biotechnology (CSIC), Spain
| | | | - T. Majtner
- National Center of Biotechnology (CSIC), Spain
| | - J. Segura
- National Center of Biotechnology (CSIC), Spain
| | | | - Y. Rancel
- National Center of Biotechnology (CSIC), Spain
| | - L. del Caño
- National Center of Biotechnology (CSIC), Spain
| | - P. Conesa
- National Center of Biotechnology (CSIC), Spain
| | - R. Melero
- National Center of Biotechnology (CSIC), Spain
| | - S. Jonic
- Sorbonne Université, UMR CNRS 7590, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | | | - F. Cazals
- Inria Sophia Antipolis – Méditerranée, France
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15
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Spronk CAEM, Żerko S, Górka M, Koźmiński W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. J Biol Inorg Chem 2018; 23:1309-1330. [PMID: 30264175 DOI: 10.1007/s00775-018-1616-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/05/2018] [Indexed: 01/03/2023]
Abstract
Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.
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Affiliation(s)
- Chris A E M Spronk
- JSC Spronk, Vilnius, Lithuania.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Mario Piccioli
- Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy
| | - Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Faith C Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ryan C Johnson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Heidi Hu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Michael Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. .,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.
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16
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Westerlund AM, Delemotte L. Effect of Ca2+ on the promiscuous target-protein binding of calmodulin. PLoS Comput Biol 2018; 14:e1006072. [PMID: 29614072 PMCID: PMC5898786 DOI: 10.1371/journal.pcbi.1006072] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/13/2018] [Accepted: 03/07/2018] [Indexed: 01/05/2023] Open
Abstract
Calmodulin (CaM) is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.
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Affiliation(s)
- Annie M. Westerlund
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail:
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17
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Structural dynamics is a determinant of the functional significance of missense variants. Proc Natl Acad Sci U S A 2018; 115:4164-4169. [PMID: 29610305 PMCID: PMC5910821 DOI: 10.1073/pnas.1715896115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Discrimination of clinically relevant mutations from neutral mutations is of paramount importance in precision medicine and pharmacogenomics. Our study shows that current computational predictions of pathogenicity, mostly based on analysis of sequence conservation, may be improved by considering the changes in the structural dynamics of the protein due to point mutations. We introduce and demonstrate the utility of a classifier that takes advantage of efficient evaluation of structural dynamics by elastic network models. Accurate evaluation of the effect of point mutations on protein function is essential to assessing the genesis and prognosis of many inherited diseases and cancer types. Currently, a wealth of computational tools has been developed for pathogenicity prediction. Two major types of data are used to this aim: sequence conservation/evolution and structural properties. Here, we demonstrate in a systematic way that another determinant of the functional impact of missense variants is the protein’s structural dynamics. Measurable improvement is shown in pathogenicity prediction by taking into consideration the dynamical context and implications of the mutation. Our study suggests that the class of dynamics descriptors introduced here may be used in conjunction with existing features to not only increase the prediction accuracy of the impact of variants on biological function, but also gain insight into the physical basis of the effect of missense variants.
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18
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Paladino A, Marchetti F, Ponzoni L, Colombo G. The Interplay between Structural Stability and Plasticity Determines Mutation Profiles and Chaperone Dependence in Protein Kinases. J Chem Theory Comput 2018; 14:1059-1070. [DOI: 10.1021/acs.jctc.7b00997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antonella Paladino
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Filippo Marchetti
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Luca Ponzoni
- Molecular
and Statistical Biophysics, International School for Advanced Studies (SISSA), I-34136 Trieste, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
- Dipartimento
di Chimica, Università di Pavia, V.le Taramelli 12, 27100 Pavia, Italy
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19
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Boninsegna L, Banisch R, Clementi C. A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures. J Chem Theory Comput 2017; 14:453-460. [PMID: 29207235 DOI: 10.1021/acs.jctc.7b00990] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Macromolecular systems are composed of a very large number of atomic degrees of freedom. There is strong evidence suggesting that structural changes occurring in large biomolecular systems at long time scale dynamics may be captured by models coarser than atomistic, although a suitable or optimal coarse-graining is a priori unknown. Here we propose a systematic approach to learning a coarse representation of a macromolecule from microscopic simulation data. In particular, the definition of effective coarse variables is achieved by partitioning the degrees of freedom both in the structural (physical) space and in the conformational space. The identification of groups of microscopic particles forming dynamical coherent states in different metastable states leads to a multiscale description of the system, in space and time. The application of this approach to the folding dynamics of two proteins provides a revised view of the classical idea of prestructured regions (foldons) that combine during a protein-folding process and suggests a hierarchical characterization of the assembly process of folded structures.
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Affiliation(s)
- Lorenzo Boninsegna
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Ralf Banisch
- Department of Mathematics and Computer Science, Freie Universität Berlin , Arnimallee 6, 14195 Berlin, Germany
| | - Cecilia Clementi
- Department of Chemistry, and Center for Theoretical Biological Physics, Rice University , 6100 Main Street, Houston, Texas 77005, United States.,Department of Mathematics and Computer Science, Freie Universität Berlin , Arnimallee 6, 14195 Berlin, Germany
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20
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Patterns of coevolving amino acids unveil structural and dynamical domains. Proc Natl Acad Sci U S A 2017; 114:E10612-E10621. [PMID: 29183970 DOI: 10.1073/pnas.1712021114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Patterns of interacting amino acids are so preserved within protein families that the sole analysis of evolutionary comutations can identify pairs of contacting residues. It is also known that evolution conserves functional dynamics, i.e., the concerted motion or displacement of large protein regions or domains. Is it, therefore, possible to use a pure sequence-based analysis to identify these dynamical domains? To address this question, we introduce here a general coevolutionary coupling analysis strategy and apply it to a curated sequence database of hundreds of protein families. For most families, the sequence-based method partitions amino acids into a few clusters. When viewed in the context of the native structure, these clusters have the signature characteristics of viable protein domains: They are spatially separated but individually compact. They have a direct functional bearing too, as shown for various reference cases. We conclude that even large-scale structural and functionally related properties can be recovered from inference methods applied to evolutionary-related sequences. The method introduced here is available as a software package and web server (spectrus.sissa.it/spectrus-evo_webserver).
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21
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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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22
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Ponzoni L, Rossetti G, Maggi L, Giorgetti A, Carloni P, Micheletti C. Unifying view of mechanical and functional hotspots across class A GPCRs. PLoS Comput Biol 2017; 13:e1005381. [PMID: 28158180 PMCID: PMC5315405 DOI: 10.1371/journal.pcbi.1005381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 02/17/2017] [Accepted: 01/25/2017] [Indexed: 01/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors’ functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. The biological functionality of several receptors and enzymes depends on their capability to sustain large-scale structural fluctuations and adopt different conformational states in response to ligand binding. This is the case for G protein-coupled receptors (GPCRs), the largest superfamily of signaling proteins in mammals and a primary pharmaceutical target. To better understand the functional dynamics of GPCRs, we have analysed the inter-residue distance variations across the available structures for several receptors of the rhodopsin-like family (class A). We first reconstructed the network of mechanical, rigid-like couplings between nearby amino acids and then identified those acting as dynamical/mechanical hubs. These were the sites whose virtual removal led to a significant softening of the overall mechanical network. After validating the biological relevance of these sites by comparison against known key functional sites, we singled out those regions which emerge as prominent mechanical hubs and yet have an otherwise still unknown functional role. The most relevant of such novel putative functional sites, which could be probed by mutagenesis experiments, is at interface of two transmembrane helices and we expect it to be crucial for assisting GPCRs conformational response to agonist binding.
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Affiliation(s)
| | - Giulia Rossetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- JSC: Division Computational Science – Simulation Laboratory Biology – Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich, Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- * E-mail: (LP); (GR)
| | - Luca Maggi
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
| | - Alejandro Giorgetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
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23
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Rossetti G, Musiani F, Abad E, Dibenedetto D, Mouhib H, Fernandez CO, Carloni P. Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations. Phys Chem Chem Phys 2017; 18:5702-6. [PMID: 26553504 DOI: 10.1039/c5cp04549e] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We perform here enhanced sampling simulations of N-terminally acetylated human α-synuclein, an intrinsically disordered protein involved in Parkinson's disease. The calculations, consistent with experiments, suggest that the post-translational modification leads to the formation of a transient amphipathic α-helix. The latter, absent in the non-physiological form, alters protein dynamics at the N-terminal and intramolecular interactions.
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Affiliation(s)
- G Rossetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany. and Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany and Department of Oncology, Hematology and Stem Cell Transplantation, RWTH Aachen University, Aachen, Germany
| | - F Musiani
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany. and Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy and Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - E Abad
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany. and German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - D Dibenedetto
- German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - H Mouhib
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - C O Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR), Universidad Nacional de Rosario, 27 de Febrero 210 bis, S2002LRK-Rosario, Argentina and Institute for Drug Discovery of Rosario (IIDEFAR), Universidad Nacional de Rosario, Rosario, 27 de Febrero 210 bis, S2002LRK-Rosario, Argentina
| | - P Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, 52425 Jülich, Germany. and German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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24
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Calligari P, Gerolin M, Abergel D, Polimeno A. Decomposition of Proteins into Dynamic Units from Atomic Cross-Correlation Functions. J Chem Theory Comput 2016; 13:309-319. [DOI: 10.1021/acs.jctc.6b00702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Paolo Calligari
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
| | - Marco Gerolin
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Daniel Abergel
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Université Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
| | - Antonino Polimeno
- Dipartimento
di Scienze Chimiche, Università di Padova, via Marzolo, 1, I-35131 Padova, Italy
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