1
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Riva D, Orlando M, Rabattoni V, Pollegioni L. On the quaternary structure of human D-3-phosphoglycerate dehydrogenase. Protein Sci 2024; 33:e5089. [PMID: 39012001 PMCID: PMC11250409 DOI: 10.1002/pro.5089] [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: 04/10/2024] [Revised: 05/27/2024] [Accepted: 06/10/2024] [Indexed: 07/17/2024]
Abstract
D-3-phosphoglycerate dehydrogenase (PHGDH) catalyzes the NAD+-dependent conversion of D-3-phospho-glycerate to 3-phosphohydroxypyruvate, the first step in the phosphorylated pathway for L-serine (L-Ser) biosynthesis. L-Ser plays different relevant metabolic roles in eukaryotic cells: alterations in L-Ser metabolism have been linked to serious neurological disorders. The human PHGDH (hPHGDH), showing a homotetrameric state in solution, is made of four domains, among which there are two regulatory domains at the C-terminus: the aspartate kinase-chorismate mutase-tyrA prephenate dehydrogenase (ACT) and allosteric substrate-binding (ASB) domains. The structure of hPHGDH was solved only for a truncated, dimeric form harboring the N-terminal end containing the substrate and the cofactor binding domains. A model ensemble of the tetrameric hPHGDH was generated using AlphaFold coupled with molecular dynamics refinement. By analyzing the inter-subunit interactions at the tetrameric interface, the residues F418, L478, P479, R454, and Y495 were selected and their role was studied by the alanine-scanning mutagenesis approach. The F418A variant modifies the putative ASB, slightly alters the activity, the fraction of protein in the tetrameric state, and the protein stability; it seems relevant in dimers' recognition to yield the tetrameric oligomer. On the contrary, the R454A, L478A, P479A, and Y495A variants (ACT domain) determine a loss of the tetrameric assembly, resulting in low stability and misfolding, triggering the aggregation and hampering the activity. The predicted tetrameric interface seems mediated by residues at the ACT domain, and the tetramer formation seems crucial for proper folding of hPHGDH, which, in turn, is essential for both stability and functionality.
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Affiliation(s)
- Daniele Riva
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Marco Orlando
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
- Present address:
Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Valentina Rabattoni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
| | - Loredano Pollegioni
- Department of Biotechnology and Life SciencesUniversity of InsubriaVareseItaly
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2
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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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3
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Murtas G, Zerbini E, Rabattoni V, Motta Z, Caldinelli L, Orlando M, Marchesani F, Campanini B, Sacchi S, Pollegioni L. Biochemical and cellular studies of three human 3-phosphoglycerate dehydrogenase variants responsible for pathological reduced L-serine levels. Biofactors 2024; 50:181-200. [PMID: 37650587 DOI: 10.1002/biof.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/12/2023] [Indexed: 09/01/2023]
Abstract
In the brain, the non-essential amino acid L-serine is produced through the phosphorylated pathway (PP) starting from the glycolytic intermediate 3-phosphoglycerate: among the different roles played by this amino acid, it can be converted into D-serine and glycine, the two main co-agonists of NMDA receptors. In humans, the enzymes of the PP, namely phosphoglycerate dehydrogenase (hPHGDH, which catalyzes the first and rate-limiting step of this pathway), 3-phosphoserine aminotransferase, and 3-phosphoserine phosphatase are likely organized in the cytosol as a metabolic assembly (a "serinosome"). The hPHGDH deficiency is a pathological condition biochemically characterized by reduced levels of L-serine in plasma and cerebrospinal fluid and clinically identified by severe neurological impairment. Here, three single-point variants responsible for hPHGDH deficiency and Neu-Laxova syndrome have been studied. Their biochemical characterization shows that V261M, V425M, and V490M substitutions alter either the kinetic (both maximal activity and Km for 3-phosphoglycerate in the physiological direction) and the structural properties (secondary, tertiary, and quaternary structure, favoring aggregation) of hPHGDH. All the three variants have been successfully ectopically expressed in U251 cells, thus the pathological effect is not due to hindered expression level. At the cellular level, mistargeting and aggregation phenomena have been observed in cells transiently expressing the pathological protein variants, as well as a reduced L-serine cellular level. Previous studies demonstrated that the pharmacological supplementation of L-serine in hPHGDH deficiencies could ameliorate some of the related symptoms: our results now suggest the use of additional and alternative therapeutic approaches.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Elena Zerbini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Valentina Rabattoni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Zoraide Motta
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Marco Orlando
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | | | | | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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4
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Krieger JM, Sorzano COS, Carazo JM. Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing. Int J Mol Sci 2023; 24:14245. [PMID: 37762547 PMCID: PMC10532346 DOI: 10.3390/ijms241814245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.
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Affiliation(s)
- James M. Krieger
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | | | - Jose Maria Carazo
- Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain
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5
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Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I. Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure 2023; 31:607-618.e3. [PMID: 36948205 PMCID: PMC10164121 DOI: 10.1016/j.str.2023.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
PR65, a horseshoe-shaped scaffold composed of 15 HEAT (observed in Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats, forms, together with catalytic and regulatory subunits, the heterotrimeric protein phosphatase PP2A. We examined the role of PR65 in enabling PP2A enzymatic activity with computations at various levels of complexity, including hybrid approaches that combine full-atomic and elastic network models. Our study points to the high flexibility of this scaffold allowing for end-to-end distance fluctuations of 40-50 Å between compact and extended conformations. Notably, the intrinsic dynamics of PR65 facilitates complexation with the catalytic subunit and is retained in the PP2A complex enabling PR65 to engage the two domains of the catalytic subunit and provide the mechanical framework for enzymatic activity, with support from the regulatory subunit. In particular, the intra-repeat coils at the C-terminal arm play an important role in allosterically mediating the collective dynamics of PP2A, pointing to target sites for modulating PR65 function.
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Affiliation(s)
- Burak T Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zakaria L Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
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6
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Jiang H, Zu S, Lu Y, Sun Z, Adeerjiang A, Guo Q, Zhang H, Dong C, Wu Q, Ding H, Du D, Wang M, Liu C, Tang Y, Liang Z, Luo C. A RhoA structure with switch II flipped outward revealed the conformational dynamics of switch II region. J Struct Biol 2023; 215:107942. [PMID: 36781028 DOI: 10.1016/j.jsb.2023.107942] [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: 12/07/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Small GTPase RhoA switches from GTP-bound state to GDP-bound state by hydrolyzing GTP, which is accelerated by GTPases activating proteins (GAPs). However, less study of RhoA structural dynamic changes was conducted during this process, which is essential for understanding the molecular mechanism of GAP dissociation. Here, we solved a RhoA structure in GDP-bound state with switch II flipped outward. Because lacking the intermolecular interactions with guanine nucleotide, we proposed this conformation of RhoA could be an intermediate after GAP dissociation. Further molecular dynamics simulations found the conformational changes of switch regions are indeed existing in RhoA and involved in the regulation of GAP dissociation and GEF recognition. Besides, the guanine nucleotide binding pocket extended to switch II region, indicating a potential "druggable" cavity for RhoA. Taken together, our study provides a deeper understanding of the dynamic properties of RhoA switch regions and highlights the direction for future drug development.
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Affiliation(s)
- Hao Jiang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Shijia Zu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Yu Lu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Zhongya Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Akejiang Adeerjiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Qiao Guo
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Huimin Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China
| | - Chen Dong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Qiqi Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Daohai Du
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Yong Tang
- Ensem Therapeutics, Inc, 200 Boston Ave, Medford, MA 02155, USA
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.
| | - Cheng Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China; School of Life Science and Technology, Shanghai Tech University, 100 Haike Road, Shanghai 201210, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China.
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7
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Vymětal J, Vondrášek J. Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. J Chem Inf Model 2022; 62:4783-4798. [PMID: 36122323 DOI: 10.1021/acs.jcim.2c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computer simulations of biomolecules such as molecular dynamics often suffer from insufficient sampling. Due to limited computational resources, insufficient sampling prevents obtaining proper equilibrium distributions of observed properties. To deal with this problem, we proposed a simulation protocol for efficient resampling of collected off-equilibrium trajectories. These trajectories are utilized for the initial mapping of the conformational space, which is later properly resampled by the introduced Iterative Landmark-Based Umbrella Sampling (ILBUS) method. Reconstruction of static equilibrium properties is achieved by the multistate Bennett acceptance ratio (MBAR) method, which enables efficient use of simulated data. The ILBUS protocol is geometry-based and does not demand any additional collective variable or a dimensional-reduction technique. The only requirement is a set of suitably spaced reference conformations, which serve as landmarks in the mapped conformational space. Additionally, the ILBUS protocol encompasses an iterative process that optimizes the force constant used in the umbrella sampling simulation. Such tuning is an inherent feature of the protocol and does not need to be performed by the user in advance. Furthermore, even the simulations with suboptimal force constants can be used in estimates by MBAR. We demonstrate the feasibility and the performance of this approach in the study of the conformational landscape of the alanine dipeptide, met-enkephalin, and adenylate kinase.
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Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Praha 6, Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Praha 6, Czech Republic
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8
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Iyer M, Jaroszewski L, Sedova M, Godzik A. What the protein data bank tells us about the evolutionary conservation of protein conformational diversity. Protein Sci 2022; 31:e4325. [PMID: 35762711 PMCID: PMC9207624 DOI: 10.1002/pro.4325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 11/09/2022]
Abstract
Proteins sample a multitude of different conformations by undergoing small- and large-scale conformational changes that are often intrinsic to their functions. Information about these changes is often captured in the Protein Data Bank by the apparently redundant deposition of independent structural solutions of identical proteins. Here, we mine these data to examine the conservation of large-scale conformational changes between homologous proteins. This is important for both practical reasons, such as predicting alternative conformations of a protein by comparative modeling, and conceptual reasons, such as understanding the extent of conservation of different features in evolution. To study this question, we introduce a novel approach to compare conformational changes between proteins by the comparison of their difference distance maps (DDMs). We found that proteins undergoing similar conformational changes have similar DDMs and that this similarity could be quantified by the correlation between the DDMs. By comparing the DDMs of homologous protein pairs, we found that large-scale conformational changes show a high level of conservation across a broad range of sequence identities. This shows that conformational space is usually conserved between homologs, even relatively distant ones.
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Affiliation(s)
- Mallika Iyer
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Lukasz Jaroszewski
- Biosciences Division, University of California Riverside School of Medicine, Riverside, California, USA
| | - Mayya Sedova
- Biosciences Division, University of California Riverside School of Medicine, Riverside, California, USA
| | - Adam Godzik
- Biosciences Division, University of California Riverside School of Medicine, Riverside, California, USA
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9
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Malik A, Banerjee A, Pal A, Mitra P. A sequence space search engine for computational protein design to modulate molecular functionality. J Biomol Struct Dyn 2022; 41:2937-2946. [PMID: 35220920 DOI: 10.1080/07391102.2022.2042386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
De-novo protein design explores the untapped sequence space that is otherwise less discovered during the evolutionary process. This necessitates an efficient sequence space search engine for effective convergence in computational protein design. We propose a greedy simulated annealing-based Monte-Carlo parallel search algorithm for better sequence-structure compatibility probing in protein design. The guidance provided by the evolutionary profile, the greedy approach, and the cooling schedule adopted in the Monte Carlo simulation ensures sufficient exploration and exploitation of the search space leading to faster convergence. On evaluating the proposed algorithm, we find that a dataset of 76 target scaffolds report an average root-mean-square-deviation (RMSD) of 1.07 Å and an average TM-Score of 0.93 with the modeled designed protein sequences. High sequence recapitulation of 48.7% (59.4%) observed in the design sequences for all (hydrophobic) solvent-inaccessible residues again establish the goodness of the proposed algorithm. A high (93.4%) intra-group recapitulation of hydrophobic residues in the solvent-inaccessible region indicates that the proposed protein design algorithm preserves the core residues in the protein and provides alternative residue combinations in the solvent-accessible regions of the target protein. Furthermore, a COFACTOR-based protein functional analysis shows that the design sequences exhibit altered molecular functionality and introduce new molecular functions compared to the target scaffolds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayush Malik
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Anupam Banerjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Abantika Pal
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India
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10
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Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Front Mol Biosci 2022; 9:832847. [PMID: 35187088 PMCID: PMC8855042 DOI: 10.3389/fmolb.2022.832847] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022] Open
Abstract
Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomic molecular dynamics (MD) simulations with the goal of rapidly sampling large and cooperative conformational changes at full atomic resolution. We present here a systematic comparison of the utility and limits of four such hybrid methods that have been introduced in recent years: MD with excited normal modes (MDeNM), collective modes-driven MD (CoMD), and elastic network model (ENM)-based generation, clustering, and relaxation of conformations (ClustENM) as well as its updated version integrated with MD simulations (ClustENMD). We analyzed the predicted conformational spaces using each of these four hybrid methods, applied to four well-studied proteins, triosephosphate isomerase (TIM), 3-phosphoglycerate kinase (PGK), HIV-1 protease (PR) and HIV-1 reverse transcriptase (RT), which provide extensive ensembles of experimental structures for benchmarking and comparing the methods. We show that a rigorous multi-faceted comparison and multiple metrics are necessary to properly assess the differences between conformational ensembles and provide an optimal protocol for achieving good agreement with experimental data. While all four hybrid methods perform well in general, being especially useful as computationally efficient methods that retain atomic resolution, the systematic analysis of the same systems by these four hybrid methods highlights the strengths and limitations of the methods and provides guidance for parameters and protocols to be adopted in future studies.
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Affiliation(s)
- Burak T. Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - James M. Krieger
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Balint Dudas
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zakaria L. Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mauricio G. S. Costa
- Programa de Computação Científica, Vice-Presiden̂cia de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ana Ligia Scott
- Laboratory of Bioinformatics and Computational Biology, Center of Mathematics, Computation and Cognition, Federal University of ABC-UFABC, Santo André, Brazil
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Ivet Bahar, ; David Perahia, ; Pemra Doruker,
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