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Margelevičius M. GTalign: spatial index-driven protein structure alignment, superposition, and search. Nat Commun 2024; 15:7305. [PMID: 39181863 PMCID: PMC11344802 DOI: 10.1038/s41467-024-51669-z] [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: 01/04/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024] Open
Abstract
With protein databases growing rapidly due to advances in structural and computational biology, the ability to accurately align and rapidly search protein structures has become essential for biological research. In response to the challenge posed by vast protein structure repositories, GTalign offers an innovative solution to protein structure alignment and search-an algorithm that achieves optimal superposition at high speeds. Through the design and implementation of spatial structure indexing, GTalign parallelizes all stages of superposition search across residues and protein structure pairs, yielding rapid identification of optimal superpositions. Rigorous evaluation across diverse datasets reveals GTalign as the most accurate among structure aligners while presenting orders of magnitude in speedup at state-of-the-art accuracy. GTalign's high speed and accuracy make it useful for numerous applications, including functional inference, evolutionary analyses, protein design, and drug discovery, contributing to advancing understanding of protein structure and function.
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2
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Hamamsy T, Morton JT, Blackwell R, Berenberg D, Carriero N, Gligorijevic V, Strauss CEM, Leman JK, Cho K, Bonneau R. Protein remote homology detection and structural alignment using deep learning. Nat Biotechnol 2024; 42:975-985. [PMID: 37679542 PMCID: PMC11180608 DOI: 10.1038/s41587-023-01917-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 07/26/2023] [Indexed: 09/09/2023]
Abstract
Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure-structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.
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Grants
- R35GM122515 National Science Foundation (NSF)
- IOS-1546218 National Science Foundation (NSF)
- R35 GM122515 NIGMS NIH HHS
- R01 DK103358 NIDDK NIH HHS
- CBET- 1728858 National Science Foundation (NSF)
- R01 AI130945 NIAID NIH HHS
- This research was supported by NIH R01DK103358, the Simons Foundation, NSF- IOS-1546218, R35GM122515, NSF CBET- 1728858, NIH R01AI130945, to T.H. This research was supported by the intramural research program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) to J.T.M. This research was supported by the Flatiron Institute as part of the Simons Foundation to Robert Blackwell, J.K.L., and N.C. This research was supported by Los Alamos National Lab to C.S. This research was supported by the Samsung Advanced Institute of Technology (Next Generation Deep Learning: from pattern recognition to AI), Samsung Research (Improving Deep Learning using Latent Structure), and NSF Award 1922658 to K.C.
- Simons Foundation
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
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Affiliation(s)
- Tymor Hamamsy
- Center for Data Science, New York University, New York, NY, USA
| | - James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert Blackwell
- Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Daniel Berenberg
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
- Prescient Design, New York, NY, USA
| | - Nicholas Carriero
- Scientific Computing Core, Flatiron Institute, Simons Foundation, New York, NY, USA
| | | | | | - Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Kyunghyun Cho
- Center for Data Science, New York University, New York, NY, USA.
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
- Prescient Design, New York, NY, USA.
- CIFAR, Toronto, Ontario, Canada.
| | - Richard Bonneau
- Center for Data Science, New York University, New York, NY, USA.
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
- Prescient Design, New York, NY, USA.
- Department of Biology, New York University, New York, NY, USA.
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3
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Fazekas Z, K Menyhárd D, Perczel A. LoCoHD: a metric for comparing local environments of proteins. Nat Commun 2024; 15:4029. [PMID: 38740745 DOI: 10.1038/s41467-024-48225-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
Protein folds and the local environments they create can be compared using a variety of differently designed measures, such as the root mean squared deviation, the global distance test, the template modeling score or the local distance difference test. Although these measures have proven to be useful for a variety of tasks, each fails to fully incorporate the valuable chemical information inherent to atoms and residues, and considers these only partially and indirectly. Here, we develop the highly flexible local composition Hellinger distance (LoCoHD) metric, which is based on the chemical composition of local residue environments. Using LoCoHD, we analyze the chemical heterogeneity of amino acid environments and identify valines having the most conserved-, and arginines having the most variable chemical environments. We use LoCoHD to investigate structural ensembles, to evaluate critical assessment of structure prediction (CASP) competitors, to compare the results with the local distance difference test (lDDT) scoring system, and to evaluate a molecular dynamics simulation. We show that LoCoHD measurements provide unique information about protein structures that is distinct from, for example, those derived using the alignment-based RMSD metric, or the similarly distance matrix-based but alignment-free lDDT metric.
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Affiliation(s)
- Zsolt Fazekas
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- ELTE Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary.
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Budapest, Hungary.
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4
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Çınaroğlu S, Biggin PC. Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems. J Chem Inf Model 2023; 63:6095-6108. [PMID: 37759363 PMCID: PMC10565830 DOI: 10.1021/acs.jcim.3c01041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Indexed: 09/29/2023]
Abstract
Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. The complexity generated by both components possessing many degrees of freedom poses a significant issue for methods that attempt to directly compute the enthalpic contribution to binding. Indeed, the prevailing assumption has been that the errors associated with such approaches would be too large for them to be meaningful. Nevertheless, we currently have no indication of how well the present methods would perform in terms of predicting the enthalpy of binding for protein-peptide complexes. To that end, we carefully assembled and curated a set of 11 protein-peptide complexes where there is structural and isothermal titration calorimetry data available and then computed the absolute enthalpy of binding. The initial "out of the box" calculations were, as expected, very modest in terms of agreement with the experiment. However, careful inspection of the outliers allows for the identification of key sampling problems such as distinct conformations of peptide termini not being sampled or suboptimal cofactor parameters. Additional simulations guided by these aspects can lead to a respectable correlation with isothermal titration calorimetry (ITC) experiments (R2 of 0.88 and an RMSE of 1.48 kcal/mol overall). Although one cannot know prospectively whether computed ITC values will be correct or not, this work shows that if experimental ITC data are available, then this in conjunction with computed ITC, can be used as a tool to know if the ensemble being simulated is representative of the true ensemble or not. That is important for allowing the correct interpretation of the detailed dynamics of the system with respect to the measured enthalpy. The results also suggest that computational calorimetry is becoming increasingly feasible. We provide the data set as a resource for the community, which could be used as a benchmark to help further progress in this area.
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Affiliation(s)
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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5
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Malik AJ, Langer D, Verma CS, Poole AM, Allison JR. Structome: a tool for the rapid assembly of datasets for structural phylogenetics. BIOINFORMATICS ADVANCES 2023; 3:vbad134. [PMID: 38046099 PMCID: PMC10692761 DOI: 10.1093/bioadv/vbad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/17/2023] [Accepted: 09/29/2023] [Indexed: 12/05/2023]
Abstract
Summary Protein structures carry signal of common ancestry and can therefore aid in reconstructing their evolutionary histories. To expedite the structure-informed inference process, a web server, Structome, has been developed that allows users to rapidly identify protein structures similar to a query protein and to assemble datasets useful for structure-based phylogenetics. Structome was created by clustering ∼ 94 % of the structures in RCSB PDB using 90% sequence identity and representing each cluster by a centroid structure. Structure similarity between centroid proteins was calculated, and annotations from PDB, SCOP, and CATH were integrated. To illustrate utility, an H3 histone was used as a query, and results show that the protein structures returned by Structome span both sequence and structural diversity of the histone fold. Additionally, the pre-computed nexus-formatted distance matrix, provided by Structome, enables analysis of evolutionary relationships between proteins not identifiable using searches based on sequence similarity alone. Our results demonstrate that, beginning with a single structure, Structome can be used to rapidly generate a dataset of structural neighbours and allows deep evolutionary history of proteins to be studied. Availability and Implementation Structome is available at: https://structome.bii.a-star.edu.sg.
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Affiliation(s)
- Ashar J Malik
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671 Singapore
| | - Desiree Langer
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
| | - Chandra S Verma
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 138671 Singapore
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
- Digital Life Institute, University of Auckland, Auckland 1142, New Zealand
| | - Jane R Allison
- School of Biological Sciences, University of Auckland, 1142 Auckland, New Zealand
- Digital Life Institute, University of Auckland, Auckland 1142, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 1142 Auckland, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, 8041 Christchurch, New Zealand
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6
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Caswell B, Summers TJ, Licup GL, Cantu DC. Mutation Space of Spatially Conserved Amino Acid Sites in Proteins. ACS OMEGA 2023; 8:24302-24310. [PMID: 37457482 PMCID: PMC10339398 DOI: 10.1021/acsomega.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
The mutation space of spatially conserved (MSSC) amino acid residues is a protein structural quantity developed and described in this work. The MSSC quantifies how many mutations and which different mutations, i.e., the mutation space, occur in each amino acid site in a protein. The MSSC calculates the mutation space of amino acids in a target protein from the spatially conserved residues in a group of multiple protein structures. Spatially conserved amino acid residues are identified based on their relative positions in the protein structure. The MSSC examines each residue in a target protein, compares it to the residues present in the same relative position in other protein structures, and uses physicochemical criteria of mutations found in each conserved spatial site to quantify the mutation space of each amino acid in the target protein. The MSSC is analogous to scoring each site in a multiple sequence alignment but in three-dimensional space considering the spatial location of residues instead of solely the order in which they appear in a protein sequence. MSSC analysis was performed on example cases, and it reproduces the well-known observation that, regardless of secondary structure, solvent-exposed residues are more likely to be mutated than internal ones. The MSSC code is available on GitHub: "https://github.com/Cantu-Research-Group/Mutation_Space".
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7
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Sykes J, Holland BR, Charleston MA. A review of visualisations of protein fold networks and their relationship with sequence and function. Biol Rev Camb Philos Soc 2023; 98:243-262. [PMID: 36210328 PMCID: PMC10092621 DOI: 10.1111/brv.12905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/12/2023]
Abstract
Proteins form arguably the most significant link between genotype and phenotype. Understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is difficult. One way to investigate these relationships is by considering the space of protein folds and how one might move from fold to fold through similarity, or potential evolutionary relationships. The many individual characterisations of fold space presented in the literature can tell us a lot about how well the current Protein Data Bank represents protein fold space, how convergence and divergence may affect protein evolution, how proteins affect the whole of which they are part, and how proteins themselves function. A synthesis of these different approaches and viewpoints seems the most likely way to further our knowledge of protein structure evolution and thus, facilitate improved protein structure design and prediction.
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Affiliation(s)
- Janan Sykes
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
| | - Michael A Charleston
- School of Natural Sciences, University of Tasmania, Private Bag 37, Hobart, Tasmania, 7001, Australia
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8
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McGreig JE, Uri H, Antczak M, Sternberg MJE, Michaelis M, Wass MN. 3DLigandSite: structure-based prediction of protein-ligand binding sites. Nucleic Acids Res 2022; 50:W13-W20. [PMID: 35412635 PMCID: PMC9252821 DOI: 10.1093/nar/gkac250] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/13/2022] [Accepted: 04/03/2022] [Indexed: 01/13/2023] Open
Abstract
3DLigandSite is a web tool for the prediction of ligand-binding sites in proteins. Here, we report a significant update since the first release of 3DLigandSite in 2010. The overall methodology remains the same, with candidate binding sites in proteins inferred using known binding sites in related protein structures as templates. However, the initial structural modelling step now uses the newly available structures from the AlphaFold database or alternatively Phyre2 when AlphaFold structures are not available. Further, a sequence-based search using HHSearch has been introduced to identify template structures with bound ligands that are used to infer the ligand-binding residues in the query protein. Finally, we introduced a machine learning element as the final prediction step, which improves the accuracy of predictions and provides a confidence score for each residue predicted to be part of a binding site. Validation of 3DLigandSite on a set of 6416 binding sites obtained 92% recall at 75% precision for non-metal binding sites and 52% recall at 75% precision for metal binding sites. 3DLigandSite is available at https://www.wass-michaelislab.org/3dligandsite. Users submit either a protein sequence or structure. Results are displayed in multiple formats including an interactive Mol* molecular visualization of the protein and the predicted binding sites.
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Affiliation(s)
- Jake E McGreig
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Hannah Uri
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Magdalena Antczak
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Martin Michaelis
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Mark N Wass
- School of Biosciences, Division of Natural Sciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
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9
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Robinson SL, Piel J, Sunagawa S. A roadmap for metagenomic enzyme discovery. Nat Prod Rep 2021; 38:1994-2023. [PMID: 34821235 PMCID: PMC8597712 DOI: 10.1039/d1np00006c] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
Covering: up to 2021Metagenomics has yielded massive amounts of sequencing data offering a glimpse into the biosynthetic potential of the uncultivated microbial majority. While genome-resolved information about microbial communities from nearly every environment on earth is now available, the ability to accurately predict biocatalytic functions directly from sequencing data remains challenging. Compared to primary metabolic pathways, enzymes involved in secondary metabolism often catalyze specialized reactions with diverse substrates, making these pathways rich resources for the discovery of new enzymology. To date, functional insights gained from studies on environmental DNA (eDNA) have largely relied on PCR- or activity-based screening of eDNA fragments cloned in fosmid or cosmid libraries. As an alternative, shotgun metagenomics holds underexplored potential for the discovery of new enzymes directly from eDNA by avoiding common biases introduced through PCR- or activity-guided functional metagenomics workflows. However, inferring new enzyme functions directly from eDNA is similar to searching for a 'needle in a haystack' without direct links between genotype and phenotype. The goal of this review is to provide a roadmap to navigate shotgun metagenomic sequencing data and identify new candidate biosynthetic enzymes. We cover both computational and experimental strategies to mine metagenomes and explore protein sequence space with a spotlight on natural product biosynthesis. Specifically, we compare in silico methods for enzyme discovery including phylogenetics, sequence similarity networks, genomic context, 3D structure-based approaches, and machine learning techniques. We also discuss various experimental strategies to test computational predictions including heterologous expression and screening. Finally, we provide an outlook for future directions in the field with an emphasis on meta-omics, single-cell genomics, cell-free expression systems, and sequence-independent methods.
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Affiliation(s)
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.
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10
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Ahlberg Gagner V, Jensen M, Katona G. Estimating the probability of coincidental similarity between atomic displacement parameters with machine learning. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/ac022d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
High-resolution diffraction studies of macromolecules incorporate the tensor form of the anisotropic displacement parameter (ADP) of atoms from their mean position. The comparison of these parameters requires a statistical framework that can handle the experimental and modeling errors linked to structure determination. Here, a Bayesian machine learning model is introduced that approximates ADPs with the random Wishart distribution. This model allows for the comparison of random samples from a distribution that is trained on experimental structures. The comparison revealed that the experimental similarity between atoms is larger than predicted by the random model for a substantial fraction of the comparisons. Different metrics between ADPs were evaluated and categorized based on how useful they are at detecting non-accidental similarity and whether they can be replaced by other metrics. The most complementary comparisons were provided by Euclidean, Riemann and Wasserstein metrics. The analysis of ADP similarity and the positional distance of atoms in bovine trypsin revealed a set of atoms with striking ADP similarity over a long physical distance, and generally the physical distance between atoms and their ADP similarity do not correlate strongly. A substantial fraction of long- and short-range ADP similarities does not form by coincidence and are reproducibly observed in different crystal structures of the same protein.
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11
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Bordin N, Sillitoe I, Lees JG, Orengo C. Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds. Front Mol Biosci 2021; 8:668184. [PMID: 34041266 PMCID: PMC8141709 DOI: 10.3389/fmolb.2021.668184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
This article is dedicated to the memory of Cyrus Chothia, who was a leading light in the world of protein structure evolution. His elegant analyses of protein families and their mechanisms of structural and functional evolution provided important evolutionary and biological insights and firmly established the value of structural perspectives. He was a mentor and supervisor to many other leading scientists who continued his quest to characterise structure and function space. He was also a generous and supportive colleague to those applying different approaches. In this article we review some of his accomplishments and the history of protein structure classifications, particularly SCOP and CATH. We also highlight some of the evolutionary insights these two classifications have brought. Finally, we discuss how the expansion and integration of protein sequence data into these structural families helps reveal the dark matter of function space and can inform the emergence of novel functions in Metazoa. Since we cover 25 years of structural classification, it has not been feasible to review all structure based evolutionary studies and hence we focus mainly on those undertaken by the SCOP and CATH groups and their collaborators.
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Affiliation(s)
- Nicola Bordin
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Ian Sillitoe
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Jonathan G Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Christine Orengo
- Institute of Structural and Molecular Biology, University College London, London, United Kingdom
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12
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Fukutani T, Miyazawa K, Iwata S, Satoh H. G-RMSD: Root Mean Square Deviation Based Method for Three-Dimensional Molecular Similarity Determination. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Tomonori Fukutani
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kohei Miyazawa
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Satoru Iwata
- Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroko Satoh
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Research Organization of Information and Systems (ROIS), 4-3-13 Toranomon, Minato-ku, Tokyo 105-0001, Japan
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13
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Benchmarking Methods of Protein Structure Alignment. J Mol Evol 2020; 88:575-597. [PMID: 32725409 DOI: 10.1007/s00239-020-09960-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/10/2020] [Indexed: 10/23/2022]
Abstract
The function of a protein is primarily determined by its structure and amino acid sequence. Many biological questions of interest rely on being able to accurately determine the group of structures to which domains of a protein belong; this can be done through alignment and comparison of protein structures. Dozens of different methods for Protein Structure Alignment (PSA) have been proposed that use a wide range of techniques. The aim of this study is to determine the ability of PSA methods to identify pairs of protein domains known to share differing levels of structural similarity, and to assess their utility for clustering domains from several different folds into known groups. We present the results of a comprehensive investigation into eighteen PSA methods, to our knowledge the largest piece of independent research on this topic. Overall, SP-AlignNS (non-sequential) was found to be the best method for classification, and among the best performing methods for clustering. Methods (where possible) were split into the algorithm used to find the optimal alignment and the score used to assess similarity. This allowed us to largely separate the algorithm from the score it maximizes and thus, to assess their effectiveness independently of each other. Surprisingly, we found that some hybrids of mismatched scores and algorithms performed better than either of the native methods at classification and, in some cases, clustering as well. It is hoped that this investigation and the accompanying discussion will be useful for researchers selecting or designing methods to align protein structures.
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14
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Carpentier M, Chomilier J. Protein multiple alignments: sequence-based versus structure-based programs. Bioinformatics 2020; 35:3970-3980. [PMID: 30942864 DOI: 10.1093/bioinformatics/btz236] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures. RESULTS We compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs. AVAILABILITY AND IMPLEMENTATION All data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Jacques Chomilier
- Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), BiBiP, Paris, France
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15
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Fallaize CJ, Green PJ, Mardia KV, Barber S. Bayesian protein sequence and structure alignment. J R Stat Soc Ser C Appl Stat 2020. [DOI: 10.1111/rssc.12394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Peter J. Green
- University of Bristol UK
- University of Technology Sydney Australia
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16
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Zhao J, Cao Y, Zhang L. Exploring the computational methods for protein-ligand binding site prediction. Comput Struct Biotechnol J 2020; 18:417-426. [PMID: 32140203 PMCID: PMC7049599 DOI: 10.1016/j.csbj.2020.02.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/23/2020] [Accepted: 02/11/2020] [Indexed: 12/21/2022] Open
Abstract
Proteins participate in various essential processes in vivo via interactions with other molecules. Identifying the residues participating in these interactions not only provides biological insights for protein function studies but also has great significance for drug discoveries. Therefore, predicting protein-ligand binding sites has long been under intense research in the fields of bioinformatics and computer aided drug discovery. In this review, we first introduce the research background of predicting protein-ligand binding sites and then classify the methods into four categories, namely, 3D structure-based, template similarity-based, traditional machine learning-based and deep learning-based methods. We describe representative algorithms in each category and elaborate on machine learning and deep learning-based prediction methods in more detail. Finally, we discuss the trends and challenges of the current research such as molecular dynamics simulation based cryptic binding sites prediction, and highlight prospective directions for the near future.
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Affiliation(s)
- Jingtian Zhao
- College of Computer Science, Sichuan University, Chengdu 610065, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Le Zhang
- College of Computer Science, Sichuan University, Chengdu 610065, China
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17
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Ng WM, Stelfox AJ, Bowden TA. Unraveling virus relationships by structure-based phylogenetic classification. Virus Evol 2020; 6:veaa003. [PMID: 32064119 PMCID: PMC7015158 DOI: 10.1093/ve/veaa003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Delineation of the intricacies of protein function from macromolecular structure constitutes a continual obstacle in the study of cell and pathogen biology. Structure-based phylogenetic analysis has emerged as a powerful tool for addressing this challenge, allowing the detection and quantification of conserved architectural properties between proteins, including those with low or no detectable sequence homology. With a focus on viral protein structure, we highlight how a number of investigations have utilized this powerful method to infer common functionality and ancestry.
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Affiliation(s)
- Weng M Ng
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice J Stelfox
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
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18
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Allosteric Binding Sites On Nuclear Receptors: Focus On Drug Efficacy and Selectivity. Int J Mol Sci 2020; 21:ijms21020534. [PMID: 31947677 PMCID: PMC7014104 DOI: 10.3390/ijms21020534] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 12/29/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023] Open
Abstract
Nuclear receptors (NRs) are highly relevant drug targets in major indications such as oncologic, metabolic, reproductive, and immunologic diseases. However, currently, marketed drugs designed towards the orthosteric binding site of NRs often suffer from resistance mechanisms and poor selectivity. The identification of two superficial allosteric sites, activation function-2 (AF-2) and binding function-3 (BF-3), as novel drug targets sparked the development of inhibitors, while selectivity concerns due to a high conservation degree remained. To determine important pharmacophores and hydration sites among AF-2 and BF-3 of eight hormonal NRs, we systematically analyzed over 10 μ s of molecular dynamics simulations including simulations in explicit water and solvent mixtures. In addition, a library of over 300 allosteric inhibitors was evaluated by molecular docking. Based on our results, we suggest the BF-3 site to offer a higher potential for drug selectivity as opposed to the AF-2 site that is more conserved among the selected receptors. Detected similarities among the AF-2 sites of various NRs urge for a broader selectivity assessment in future studies. In combination with the Supplementary Material, this work provides a foundation to improve both selectivity and potency of allosteric inhibitors in a rational manner and increase the therapeutic applicability of this promising compound class.
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19
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Deng L, Zhong G, Liu C, Luo J, Liu H. MADOKA: an ultra-fast approach for large-scale protein structure similarity searching. BMC Bioinformatics 2019; 20:662. [PMID: 31870277 PMCID: PMC6929402 DOI: 10.1186/s12859-019-3235-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 01/22/2023] Open
Abstract
Background Protein comparative analysis and similarity searches play essential roles in structural bioinformatics. A couple of algorithms for protein structure alignments have been developed in recent years. However, facing the rapid growth of protein structure data, improving overall comparison performance and running efficiency with massive sequences is still challenging. Results Here, we propose MADOKA, an ultra-fast approach for massive structural neighbor searching using a novel two-phase algorithm. Initially, we apply a fast alignment between pairwise structures. Then, we employ a score to select pairs with more similarity to carry out a more accurate fragment-based residue-level alignment. MADOKA performs about 6–100 times faster than existing methods, including TM-align and SAL, in massive alignments. Moreover, the quality of structural alignment of MADOKA is better than the existing algorithms in terms of TM-score and number of aligned residues. We also develop a web server to search structural neighbors in PDB database (About 360,000 protein chains in total), as well as additional features such as 3D structure alignment visualization. The MADOKA web server is freely available at: http://madoka.denglab.org/ Conclusions MADOKA is an efficient approach to search for protein structure similarity. In addition, we provide a parallel implementation of MADOKA which exploits massive power of multi-core CPUs.
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Affiliation(s)
- Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Guolun Zhong
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chenzhe Liu
- School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Judong Luo
- Department of Radiation Oncology, the Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China.
| | - Hui Liu
- Lab of Information Management, Changzhou University, Changzhou, 213164, China.
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20
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Noby N, Hussein A, Saeed H, Embaby AM. "Recombinant cold -adapted halotolerant, organic solvent-stable esterase (estHIJ) from Bacillus halodurans. Anal Biochem 2019; 591:113554. [PMID: 31863727 DOI: 10.1016/j.ab.2019.113554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/08/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Esterases and lipases enduring harsh conditions, including low temperature and extreme tolerance to organic solvents, have attracted great attention in recent times. In the current study, a full open reading frame of 747 bp that encodes a novel, cold-adapted esterase (estHIJ) of 248 amino acids from Bacillus halodurans strain NAH-Egypt was heterologously cloned and expressed in E. coli BL21 (DE3) Rosetta. Amino acid sequence analysis revealed that estHIJ belongs to family XIII of lipolytic enzymes, with a characteristic pentapeptide motif (G-L-S-L-G). The recombinant estHIJ was purified using Ni-affinity chromatography to homogeneity with purification fold, yield, specific activity, and molecular weight (MW) of 3.5, 47.5%, 19.8 U/mg and 29 kDa, respectively. The enzyme showed preferential substrate specificity towards pNP-acetate (C2), with catalytic efficiency of 46,825 min-1 mM-1 estHIJ displayed optimal activity at 30 °C and pH (7.0-8.0). estHIJ demonstrated robust stability in the presence of 50% (v/v) non-polar solvents and 4 M NaCl after 15 h and 6 h of incubation, respectively. The promising features of the recombinant estHIJ underpin its potential in several fields, e.g., the synthesis of pharmaceutical compounds and the food industry.
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Affiliation(s)
- Nehad Noby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Ahmed Hussein
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Hesham Saeed
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Amira M Embaby
- Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt.
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21
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Gagnér VA, Lundholm I, Garcia-Bonete MJ, Rodilla H, Friedman R, Zhaunerchyk V, Bourenkov G, Schneider T, Stake J, Katona G. Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Sci Rep 2019; 9:19281. [PMID: 31848402 PMCID: PMC6917748 DOI: 10.1038/s41598-019-55777-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.
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Affiliation(s)
- Viktor Ahlberg Gagnér
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ida Lundholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Helena Rodilla
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Gleb Bourenkov
- European Molecular Biology Laboratory Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
| | - Thomas Schneider
- European Molecular Biology Laboratory Hamburg Outstation, EMBL c/o DESY, Notkestrasse 85, 22603, Hamburg, Germany
| | - Jan Stake
- Department of Microtechnology and Nanoscience, Chalmers University of Technology, Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
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22
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Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop. Sci China Chem 2019. [DOI: 10.1007/s11426-019-9623-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Kuenze G, Duran AM, Woods H, Brewer KR, McDonald EF, Vanoye CG, George AL, Sanders CR, Meiler J. Upgraded molecular models of the human KCNQ1 potassium channel. PLoS One 2019; 14:e0220415. [PMID: 31518351 PMCID: PMC6743773 DOI: 10.1371/journal.pone.0220415] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 07/15/2019] [Indexed: 11/29/2022] Open
Abstract
The voltage-gated potassium channel KCNQ1 (KV7.1) assembles with the KCNE1 accessory protein to generate the slow delayed rectifier current, IKS, which is critical for membrane repolarization as part of the cardiac action potential. Loss-of-function (LOF) mutations in KCNQ1 are the most common cause of congenital long QT syndrome (LQTS), type 1 LQTS, an inherited genetic predisposition to cardiac arrhythmia and sudden cardiac death. A detailed structural understanding of KCNQ1 is needed to elucidate the molecular basis for KCNQ1 LOF in disease and to enable structure-guided design of new anti-arrhythmic drugs. In this work, advanced structural models of human KCNQ1 in the resting/closed and activated/open states were developed by Rosetta homology modeling guided by newly available experimentally-based templates: X. leavis KCNQ1 and various resting voltage sensor structures. Using molecular dynamics (MD) simulations, the capacity of the models to describe experimentally established channel properties including state-dependent voltage sensor gating charge interactions and pore conformations, PIP2 binding sites, and voltage sensor–pore domain interactions were validated. Rosetta energy calculations were applied to assess the utility of each model in interpreting mutation-evoked KCNQ1 dysfunction by predicting the change in protein thermodynamic stability for 50 experimentally characterized KCNQ1 variants with mutations located in the voltage-sensing domain. Energetic destabilization was successfully predicted for folding-defective KCNQ1 LOF mutants whereas wild type-like mutants exhibited no significant energetic frustrations, which supports growing evidence that mutation-induced protein destabilization is an especially common cause of KCNQ1 dysfunction. The new KCNQ1 Rosetta models provide helpful tools in the study of the structural basis for KCNQ1 function and can be used to generate hypotheses to explain KCNQ1 dysfunction.
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Affiliation(s)
- Georg Kuenze
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Amanda M. Duran
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Hope Woods
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kathryn R. Brewer
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Eli Fritz McDonald
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Carlos G. Vanoye
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Alfred L. George
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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24
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The Arabian camel, Camelus dromedarius interferon epsilon: Functional expression, in vitro refolding, purification and cytotoxicity on breast cancer cell lines. PLoS One 2019; 14:e0213880. [PMID: 31490936 PMCID: PMC6730848 DOI: 10.1371/journal.pone.0213880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023] Open
Abstract
The current study highlights, for the first time, cloning, overexpression and purification of the novel interferon epsilon (IFNƐ), from the Arabian camel Camelus dromedaries. The study then assesses the cytotoxicity of IFNε against two human breast cancer cell lines MDA-MB-231 and MCF-7. Full-length cDNA encoding interferon epsilon (IFNε) was isolated and cloned from the liver of the Arabian camel, C. dromedarius using reverse transcription-polymerase chain reaction. The sequence analysis of the camel IFNε cDNA showed a 582-bp open reading frame encoding a protein of 193 amino acids with an estimated molecular weight of 21.230 kDa. A BLAST search analysis revealed that the C. dromedarius IFNε shared high sequence identity with the IFN genes of other species, such as Camelus ferus, Vicugna pacos, and Homo sapiens. Expression of the camel IFNε cDNA in Escherichia coli gave a fusion protein band of 24.97 kDa after induction with either isopropyl β-D-1-thiogalactopyranoside or lactose for 5 h. Recombinant IFNε protein was overexpressed in the form of inclusion bodies that were easily solubilized and refolded using SDS and KCl. The solubilized inclusion bodies were purified to apparent homogeneity using nickel affinity chromatography. We examined the effect of IFNε on two breast cancer cell lines MDA-MB-231 and MCF-7. In both cell lines, IFNε inhibited cell survival in a dose dependent manner as observed by MTT assay, morphological changes and apoptosis assay. Caspase-3 expression level was found to be increased in MDA-MB-231 treated cells as compared to untreated cells.
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25
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Fleury C, Gracy J, Gautier MF, Pons JL, Dufayard JF, Labesse G, Ruiz M, de Lamotte F. Comprehensive classification of the plant non-specific lipid transfer protein superfamily towards its sequence-structure-function analysis. PeerJ 2019; 7:e7504. [PMID: 31428542 PMCID: PMC6698131 DOI: 10.7717/peerj.7504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/17/2019] [Indexed: 11/20/2022] Open
Abstract
Background Non-specific Lipid Transfer Proteins (nsLTPs) are widely distributed in the plant kingdom and constitute a superfamily of related proteins. Several hundreds of different nsLTP sequences—and counting—have been characterized so far, but their biological functions remain unclear. It has been clear for years that they present a certain interest for agronomic and nutritional issues. Deciphering their functions means collecting and analyzing a variety of data from gene sequence to protein structure, from cellular localization to the physiological role. As a huge and growing number of new protein sequences are available nowadays, extracting meaningful knowledge from sequence–structure–function relationships calls for the development of new tools and approaches. As nsLTPs show high evolutionary divergence, but a conserved common right handed superhelix structural fold, and as they are involved in a large number of key roles in plant development and defense, they are a stimulating case study for validating such an approach. Methods In this study, we comprehensively investigated 797 nsLTP protein sequences, including a phylogenetic analysis on canonical protein sequences, three-dimensional structure modeling and functional annotation using several well-established bioinformatics programs. Additionally, two integrative methodologies using original tools were developed. The first was a new method for the detection of (i) conserved amino acid residues involved in structure stabilization and (ii) residues potentially involved in ligand interaction. The second was a structure–function classification based on the evolutionary trace display method using a new tree visualization interface. We also present a new tool for visualizing phylogenetic trees. Results Following this new protocol, an updated classification of the nsLTP superfamily was established and a new functional hypothesis for key residues is suggested. Lastly, this work allows a better representation of the diversity of plant nsLTPs in terms of sequence, structure and function.
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Affiliation(s)
| | - Jérôme Gracy
- CBS, CNRS Univ Montpellier INSERM, Montpellier, France
| | | | - Jean-Luc Pons
- CBS, CNRS Univ Montpellier INSERM, Montpellier, France
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26
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Kumar R, Henrissat B, Coutinho PM. Intrinsic dynamic behavior of enzyme:substrate complexes govern the catalytic action of β-galactosidases across clan GH-A. Sci Rep 2019; 9:10346. [PMID: 31316086 PMCID: PMC6637243 DOI: 10.1038/s41598-019-46589-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 06/28/2019] [Indexed: 01/18/2023] Open
Abstract
The conformational itineraries taken by carbohydrate residues in the catalytic subsite of retaining glycoside hydrolases (GHs), harness the link between substrate conformation and reactivity. GHs' active sites may be described as a combination of subsites dedicated to the binding of individual sugar residues and to catalysis. The three-dimensional structure of GH:carbohydrate complexes has demonstrated that carbohydrate ring conformation changes in an ordered manner during catalysis. Here we demonstrate in silico that a link exists between subsite binding dynamics and substrate specificity for β-galactosidases from clan GH-A families GH1, GH2, GH35, GH42 and GH59. Different oligosaccharides were docked in the active site of reference β-galactosidase structures using Vina-Carb. Subsequent molecular dynamics (MD) simulations revealed that these enzymes favor a high degree of flexibility and ring distortion of the substrate the lytic subsite -1. Although the β-galactosidase families examined are structurally and mechanistically related, distinct patterns of ring distortion were unveiled for the different families. For β-galactosidases, three different family-dependent reaction itineraries (1S3 → 4H3‡ → 4C1, 1,4B → 4H3/ 4E‡ → 4C1, and 1S5 → 4E/ 4H5‡ → 4C1) were identified, all compatible with the antiperiplanar lone pair hypothesis (ALPH) for the hydrolysis of β-glycosides. This comparative study reveals the fuzzy character of the changes in carbohydrate ring geometry prior to carbohydrate hydrolysis.
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Affiliation(s)
- Rajender Kumar
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Clinical Microbiology, Umeå University, SE-901 85, Umeå, Sweden
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288, Marseille, France
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, 23218, Jeddah, Saudi Arabia
| | - Pedro M Coutinho
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288, Marseille, France.
- USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288, Marseille, France.
- Polytech Marseille, Aix-Marseille Université, Marseille, France.
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27
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Wang D, Geng L, Zhao YJ, Yang Y, Huang Y, Zhang Y, Shen HB. Artificial intelligence-based multi-objective optimization protocol for protein structure refinement. Bioinformatics 2019; 36:437-448. [PMID: 31274151 PMCID: PMC7999140 DOI: 10.1093/bioinformatics/btz544] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/06/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION Protein structure refinement is an important step of protein structure prediction. Existing approaches have generally used a single scoring function combined with Monte Carlo method or Molecular Dynamics algorithm. The one-dimension optimization of a single energy function may take the structure too far away without a constraint. The basic motivation of our study is to reduce the bias problem caused by minimizing only a single energy function due to the very diversity of different protein structures. RESULTS We report a new Artificial Intelligence-based protein structure Refinement method called AIR. Its fundamental idea is to use multiple energy functions as multi-objectives in an effort to correct the potential inaccuracy from a single function. A multi-objective particle swarm optimization algorithm-based structure refinement is designed, where each structure is considered as a particle in the protocol. With the refinement iterations, the particles move around. The quality of particles in each iteration is evaluated by three energy functions, and the non-dominated particles are put into a set called Pareto set. After enough iteration times, particles from the Pareto set are screened and part of the top solutions are outputted as the final refined structures. The multi-objective energy function optimization strategy designed in the AIR protocol provides a different constraint view of the structure, by extending the one-dimension optimization to a new three-dimension space optimization driven by the multi-objective particle swarm optimization engine. Experimental results on CASP11, CASP12 refinement targets and blind tests in CASP 13 turn to be promising. AVAILABILITY AND IMPLEMENTATION The AIR is available online at: www.csbio.sjtu.edu.cn/bioinf/AIR/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Yu-Jun Zhao
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
| | - Yang Yang
- Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Huang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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28
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Spänig S, Heider D. Encodings and models for antimicrobial peptide classification for multi-resistant pathogens. BioData Min 2019; 12:7. [PMID: 30867681 PMCID: PMC6399931 DOI: 10.1186/s13040-019-0196-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/24/2019] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial peptides (AMPs) are part of the inherent immune system. In fact, they occur in almost all organisms including, e.g., plants, animals, and humans. Remarkably, they show effectivity also against multi-resistant pathogens with a high selectivity. This is especially crucial in times, where society is faced with the major threat of an ever-increasing amount of antibiotic resistant microbes. In addition, AMPs can also exhibit antitumor and antiviral effects, thus a variety of scientific studies dealt with the prediction of active peptides in recent years. Due to their potential, even the pharmaceutical industry is keen on discovering and developing novel AMPs. However, AMPs are difficult to verify in vitro, hence researchers conduct sequence similarity experiments against known, active peptides. Unfortunately, this approach is very time-consuming and limits potential candidates to sequences with a high similarity to known AMPs. Machine learning methods offer the opportunity to explore the huge space of sequence variations in a timely manner. These algorithms have, in principal, paved the way for an automated discovery of AMPs. However, machine learning models require a numerical input, thus an informative encoding is very important. Unfortunately, developing an appropriate encoding is a major challenge, which has not been entirely solved so far. For this reason, the development of novel amino acid encodings is established as a stand-alone research branch. The present review introduces state-of-the-art encodings of amino acids as well as their properties in sequence and structure based aggregation. Moreover, albeit a well-chosen encoding is essential, performant classifiers are required, which is reflected by a tendency towards specifically designed models in the literature. Furthermore, we introduce these models with a particular focus on encodings derived from support vector machines and deep learning approaches. Albeit a strong focus has been set on AMP predictions, not all of the mentioned encodings have been elaborated as part of antimicrobial research studies, but rather as general protein or peptide representations.
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Affiliation(s)
- Sebastian Spänig
- Department of Bioinformatics, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
| | - Dominik Heider
- Department of Bioinformatics, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Marburg, Germany
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29
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Abstract
The native state of proteins is composed of conformers in dynamical equilibrium. In this chapter, different issues related to conformational diversity are explored using a curated and experimentally based database called CoDNaS (Conformational Diversity in the Native State). This database is a collection of redundant structures for the same sequence. CoDNaS estimates the degree of conformational diversity using different global and local structural similarity measures. It allows the user to explore how structural differences among conformers change as a function of several structural features providing further biological information. This chapter explores the measurement of conformational diversity and its relationship with sequence divergence. Also, it discusses how proteins with high conformational diversity could affect homology modeling techniques.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina
| | - Diego Javier Zea
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Argentina.
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30
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Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol 2018; 4:112-123. [PMID: 30478291 DOI: 10.1038/s41564-018-0292-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
Abstract
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.
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Affiliation(s)
- Etienne Ruppé
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France. .,IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.
| | - Amine Ghozlane
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - Julien Tap
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Danone Nutricia Research, Palaiseau, France
| | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Nicolas Maziers
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Irene Clares
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Teresa M Coque
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Luis Máiz
- Unit for Cystic Fibrosis, Ramon y Cajal University Hospital, Madrid, Spain
| | - Tiphaine Goulenok
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Victoire de Lastours
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Nawal Amor
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Bruno Fantin
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Ingrid Wieder
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malbert Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xinglin Zhang
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandre G de Brevern
- INSERM UMR_S 1134, Paris Diderot University, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles, INTS, GR-Ex, Paris, France
| | - Jean-Michel Batto
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Hervé M Blottière
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Pierre Léonard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Véronique Léjard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Aline Letur
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Levenez
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Kevin Weiszer
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Haimet
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Sean P Kennedy
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Centre of Host Microbiome Interactions, King's College, London, UK
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Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia. BMC Bioinformatics 2018; 19:414. [PMID: 30453883 PMCID: PMC6245605 DOI: 10.1186/s12859-018-2381-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Although the etiology of chronic lymphocytic leukemia (CLL), the most common type of adult leukemia, is still unclear, strong evidence implicates antigen involvement in disease ontogeny and evolution. Primary and 3D structure analysis has been utilised in order to discover indications of antigenic pressure. The latter has been mostly based on the 3D models of the clonotypic B cell receptor immunoglobulin (BcR IG) amino acid sequences. Therefore, their accuracy is directly dependent on the quality of the model construction algorithms and the specific methods used to compare the ensuing models. Thus far, reliable and robust methods that can group the IG 3D models based on their structural characteristics are missing. Results Here we propose a novel method for clustering a set of proteins based on their 3D structure focusing on 3D structures of BcR IG from a large series of patients with CLL. The method combines techniques from the areas of bioinformatics, 3D object recognition and machine learning. The clustering procedure is based on the extraction of 3D descriptors, encoding various properties of the local and global geometrical structure of the proteins. The descriptors are extracted from aligned pairs of proteins. A combination of individual 3D descriptors is also used as an additional method. The comparison of the automatically generated clusters to manual annotation by experts shows an increased accuracy when using the 3D descriptors compared to plain bioinformatics-based comparison. The accuracy is increased even more when using the combination of 3D descriptors. Conclusions The experimental results verify that the use of 3D descriptors commonly used for 3D object recognition can be effectively applied to distinguishing structural differences of proteins. The proposed approach can be applied to provide hints for the existence of structural groups in a large set of unannotated BcR IG protein files in both CLL and, by logical extension, other contexts where it is relevant to characterize BcR IG structural similarity. The method does not present any limitations in application and can be extended to other types of proteins.
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32
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Navigating Among Known Structures in Protein Space. Methods Mol Biol 2018. [PMID: 30298400 DOI: 10.1007/978-1-4939-8736-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Present-day protein space is the result of 3.7 billion years of evolution, constrained by the underlying physicochemical qualities of the proteins. It is difficult to differentiate between evolutionary traces and effects of physicochemical constraints. Nonetheless, as a rule of thumb, instances of structural reuse, or focusing on structural similarity, are likely attributable to physicochemical constraints, whereas sequence reuse, or focusing on sequence similarity, may be more indicative of evolutionary relationships. Both types of relationships have been studied and can provide meaningful insights to protein biophysics and evolution, which in turn can lead to better algorithms for protein search, annotation, and maybe even design.In broad strokes, studies of protein space vary in the entities they represent, the similarity measure comparing these entities, and the representation used. The entities can be, for example, protein chains, domains, supra-domains, or smaller protein sub-parts denoted themes. The measures of similarity between the entities can be based on sequence, structure, function, or any combination of these. The representation can be global, encompassing the whole space, or local, focusing on a particular region surrounding protein(s) of interest. Global representations include lists of grouped proteins, protein networks, and maps. Networks are the abstraction that is derived most directly from the similarity data: each node is the protein entity (e.g., a domain), and edges connect similar domains. Selecting the entities, the similarity measure, and the abstraction are three intertwined decisions: the similarity measures allow us to identify the entities, and the selection of entities influences what is a meaningful similarity measure. Similarly, we seek entities that are related to each other in a way, for which a simple representation describes their relationships succinctly and accurately. This chapter will cover studies that rely on different entities, similarity measures, and a range of representations to better understand protein structure space. Scholars may use publicly available navigators offering a global representation, and in particular the hierarchical classifications SCOP, CATH, and ECOD, or a local representation, which encompass structural alignment algorithms. Alternatively, scholars can configure their own navigator using existing tools. To demonstrate this DIY (do it yourself) approach for navigating in protein space, we investigate substrate-binding proteins. By presenting sequence similarities among this large and diverse protein family as a network, we can infer that one member (pdb ID 4ntl; of yet unknown function) may bind methionine and suggest a putative binding mechanism.
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33
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Checa-Rojas A, Delgadillo-Silva LF, Velasco-Herrera MDC, Andrade-Domínguez A, Gil J, Santillán O, Lozano L, Toledo-Leyva A, Ramírez-Torres A, Talamas-Rohana P, Encarnación-Guevara S. GSTM3 and GSTP1: novel players driving tumor progression in cervical cancer. Oncotarget 2018; 9:21696-21714. [PMID: 29774096 PMCID: PMC5955133 DOI: 10.18632/oncotarget.24796] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 03/01/2018] [Indexed: 12/16/2022] Open
Abstract
The molecular processes and proteomic markers leading to tumor progression (TP) in cervical cancer (CC) are either unknown or only partially understood. TP affects metabolic and regulatory mechanisms that can be identified as proteomic changes. To identify which proteins are differentially expressed and to understand the mechanisms of cancer progression, we analyzed the dynamics of the tumor proteome in CC cell lines. This analysis revealed two proteins that are up-regulated during TP, GSTM3 and GSTP1. These proteins are involved in cell maintenance, cell survival and the cellular stress response via the NF-κB and MAP kinase pathways during TP. Furthermore, GSTM3 and GSTP1 knockdown showed that evasion of apoptosis was affected, and tumor proliferation was significantly reduced. Our data indicate the critical role of GST proteins in the regulation and progression of cervical cancer cells. Hence, we suggest GSTM3 and GSTP1 as novel biomarkers and potential therapeutic targets for treating cervical cancer. SIGNIFICANCE CC is particularly hazardous in the advanced stages, and there are few therapeutic strategies specifically targeting these stages. We performed analyses on CC tumor proteome dynamics and identified GSTM3 and GSTP1 as novel potential therapeutic targets. Knockdown of these proteins showed that they are involved in cell survival, cell proliferation and cellular evasion of apoptosis.
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Affiliation(s)
- Alberto Checa-Rojas
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis Fernando Delgadillo-Silva
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | | | - Andrés Andrade-Domínguez
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Jeovanis Gil
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Orlando Santillán
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alfredo Toledo-Leyva
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, México
| | - Alberto Ramírez-Torres
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Patricia Talamas-Rohana
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, Delegación Gustavo A. Madero, México
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas. Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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34
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Schaarschmidt J, Monastyrskyy B, Kryshtafovych A, Bonvin AM. Assessment of contact predictions in CASP12: Co-evolution and deep learning coming of age. Proteins 2018; 86 Suppl 1:51-66. [PMID: 29071738 PMCID: PMC5820169 DOI: 10.1002/prot.25407] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022]
Abstract
Following up on the encouraging results of residue-residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology-based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution-based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single-domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures.
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Affiliation(s)
- Joerg Schaarschmidt
- Faculty of Science ‐ ChemistryComputational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtThe Netherlands
| | | | | | - Alexandre M.J.J. Bonvin
- Faculty of Science ‐ ChemistryComputational Structural Biology Group, Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrechtThe Netherlands
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35
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Golden M, García-Portugués E, Sørensen M, Mardia KV, Hamelryck T, Hein J. A Generative Angular Model of Protein Structure Evolution. Mol Biol Evol 2018; 34:2085-2100. [PMID: 28453724 PMCID: PMC5850488 DOI: 10.1093/molbev/msx137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a generative, evolutionary model of protein structure and sequence that is valid on a local length scale. The model concerns the local dependencies between sequence and structure evolution in a pair of homologous proteins. The evolutionary trajectory between the two structures in the protein pair is treated as a random walk in dihedral angle space, which is modeled using a novel angular diffusion process on the two-dimensional torus. Coupling sequence and structure evolution in our model allows for modeling both “smooth” conformational changes and “catastrophic” conformational jumps, conditioned on the amino acid changes. The model has interpretable parameters and is comparatively more realistic than previous stochastic models, providing new insights into the relationship between sequence and structure evolution. For example, using the trained model we were able to identify an apparent sequence–structure evolutionary motif present in a large number of homologous protein pairs. The generative nature of our model enables us to evaluate its validity and its ability to simulate aspects of protein evolution conditioned on an amino acid sequence, a related amino acid sequence, a related structure or any combination thereof.
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Affiliation(s)
- Michael Golden
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Eduardo García-Portugués
- Department of Statistics, Carlos III University of Madrid, Madrid, Spain.,Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark.,Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael Sørensen
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kanti V Mardia
- Department of Statistics, University of Oxford, Oxford, United Kingdom.,Department of Mathematics, University of Leeds, Leeds, United Kingdom
| | - Thomas Hamelryck
- Bioinformatics Centre, Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Image Section, Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Jotun Hein
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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36
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Rueda AJV, Monzon AM, Ardanaz SM, Iglesias LE, Parisi G. Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. BMC Bioinformatics 2018; 19:27. [PMID: 29382320 PMCID: PMC5791380 DOI: 10.1186/s12859-018-2044-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results Using proteins’ experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers. Electronic supplementary material The online version of this article (10.1186/s12859-018-2044-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Julia Velez Rueda
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Sebastián M Ardanaz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.
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37
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A Critical Note on Symmetry Contact Artifacts and the Evaluation of the Quality of Homology Models. Symmetry (Basel) 2018. [DOI: 10.3390/sym10010025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Saeed H, Ali H, Soudan H, Embaby A, El-Sharkawy A, Farag A, Hussein A, Ataya F. Molecular cloning, structural modeling and production of recombinant Aspergillus terreus l. asparaginase in Escherichia coli. Int J Biol Macromol 2018; 106:1041-1051. [DOI: 10.1016/j.ijbiomac.2017.08.110] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/15/2022]
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39
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Hafsa NE, Berjanskii MV, Arndt D, Wishart DS. Rapid and reliable protein structure determination via chemical shift threading. JOURNAL OF BIOMOLECULAR NMR 2018; 70:33-51. [PMID: 29196969 DOI: 10.1007/s10858-017-0154-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .
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Affiliation(s)
- Noor E Hafsa
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada
| | - Mark V Berjanskii
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David Arndt
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB, T6G 2E8, Canada.
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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40
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Monzon AM, Zea DJ, Marino-Buslje C, Parisi G. Homology modeling in a dynamical world. Protein Sci 2017; 26:2195-2206. [PMID: 28815769 DOI: 10.1002/pro.3274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/31/2022]
Abstract
A key concept in template-based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity. In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved using a priori information coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair TBM results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.
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Affiliation(s)
- Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
| | - Diego Javier Zea
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Cristina Marino-Buslje
- Structural Bioinformatics Unit, Fundación Instituto Leloir, CONICET, C1405BWE Ciudad Autónoma de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, B1876BXD, Bernal, Argentina
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41
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Fotoohifiroozabadi S, Mohamad MS, Deris S. Samira-VP: A simple protein alignment method with rechecking the alphabet vector positions. J Bioinform Comput Biol 2017; 15:1750004. [PMID: 28274174 DOI: 10.1142/s0219720017500044] [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: 11/18/2022]
Abstract
Protein structure alignment and comparisons that are based on an alphabetical demonstration of protein structure are more simple to run with faster evaluation processes; thus, their accuracy is not as reliable as three-dimension (3D)-based tools. As a 1D method candidate, TS-AMIR used the alphabetic demonstration of secondary-structure elements (SSE) of proteins and compared the assigned letters to each SSE using the [Formula: see text]-gram method. Although the results were comparable to those obtained via geometrical methods, the SSE length and accuracy of adjacency between SSEs were not considered in the comparison process. Therefore, to obtain further information on accuracy of adjacency between SSE vectors, the new approach of assigning text to vectors was adopted according to the spherical coordinate system in the present study. Moreover, dynamic programming was applied in order to account for the length of SSE vectors. Five common datasets were selected for method evaluation. The first three datasets were small, but difficult to align, and the remaining two datasets were used to compare the capability of the proposed method with that of other methods on a large protein dataset. The results showed that the proposed method, as a text-based alignment approach, obtained results comparable to both 1D and 3D methods. It outperformed 1D methods in terms of accuracy and 3D methods in terms of runtime.
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Affiliation(s)
- Samira Fotoohifiroozabadi
- 1 Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai 81310 Johor, Malaysia
| | - Mohd Saberi Mohamad
- 1 Artificial Intelligence and Bioinformatics Research Group, Faculty of Computing, Universiti Teknologi Malaysia, Skudai 81310 Johor, Malaysia
| | - Safaai Deris
- 2 Faculty of Creative Technology & Heritage, Universiti Malaysia Kelantan, Locked Bag 01, 16300 Bachok, Kota Bharu, Kelantan, Malaysia
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42
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Panjkovich A, Svergun DI. Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis. Phys Chem Chem Phys 2017; 18:5707-19. [PMID: 26611321 DOI: 10.1039/c5cp04540a] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Structural flexibility and conformational rearrangements are often related to important functions of biological macromolecules, but the experimental characterization of such transitions with high-resolution techniques is challenging. At a lower resolution, small angle X-ray scattering (SAXS) can be used to obtain information on biomolecular shapes and transitions in solution. Here, we present SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data. The method starts from a given conformation of the protein (which does not agree with the SAXS data). The structure is partitioned into pseudo-domains either using structural classification databases or automatically from the protein dynamics as predicted by the NMA. The algorithm proceeds hierarchically employing NMA to first probe large rearrangements and progresses into smaller and more localized movements. At the large rearrangements stage the pseudo-domains stay as rigid bodies allowing one to avoid structural disruptions inherent to the earlier NMA-based algorithms. To validate the approach, we compiled a representative benchmark set of 88 conformational states known experimentally at high resolution. The performance of the algorithm is demonstrated in the simulated data on the benchmark set and also in a number of experimental examples. SREFLEX is included into the ATSAS program package freely available to the academic users, both for download and in the on-line mode.
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Affiliation(s)
- Alejandro Panjkovich
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, EMBL c/o DESY, Notkestr. 85, Geb. 25a, 22607 Hamburg, Germany.
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43
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Cao H, Lu Y. Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment. J Comput Biol 2017; 24:2-12. [DOI: 10.1089/cmb.2016.0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hu Cao
- School of Information Science and Engineering, Lanzhou University, Gansu 730000, Lanzhou, China
| | - Yonggang Lu
- School of Information Science and Engineering, Lanzhou University, Gansu 730000, Lanzhou, China
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44
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Abstract
Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin Webb
- University of California at San Francisco, San Francisco, California
| | - Andrej Sali
- University of California at San Francisco, San Francisco, California
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45
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Zhou W, Leone V, Krah A, Faraldo-Gómez JD. Predicted Structures of the Proton-Bound Membrane-Embedded Rotor Rings of the Saccharomyces cerevisiae and Escherichia coli ATP Synthases. J Phys Chem B 2016; 121:3297-3307. [PMID: 27715045 DOI: 10.1021/acs.jpcb.6b08051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent years have witnessed a renewed interest in the ATP synthase as a drug target against human pathogens. Indeed, clinical, biochemical, and structural data indicate that hydrophobic inhibitors targeting the membrane-embedded proton-binding sites of the c-subunit ring could serve as last-resort antibiotics against multidrug resistant strains. However, because inhibition of the mitochondrial ATP synthase in humans is lethal, it is essential that these inhibitors be not only potent but also highly selective for the bacterial enzyme. To this end, a detailed understanding of the structure of this protein target is arguably instrumental. Here, we use computational methods to predict the atomic structures of the proton-binding sites in two prototypical c-rings: that of the ATP synthase from Saccharomyces cerevisiae, which is a model system for mitochondrial enzymes, and that from Escherichia coli, which can be pathogenic for humans. Our study reveals the structure of these binding sites loaded with protons and in the context of the membrane, that is, in the state that would mediate the recognition of a potential inhibitor. Both structures reflect a mode of proton coordination unlike those previously observed in other c-ring structures, whether experimental or modeled.
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Affiliation(s)
- Wenchang Zhou
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Vanessa Leone
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Alexander Krah
- Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Section, National Heart, Lung and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.,Theoretical Molecular Biophysics Group, Max Planck Institute of Biophysics , 60438 Frankfurt am Main, Germany
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46
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Costanzo LD, Ghosh S, Zardecki C, Burley SK. Using the Tools and Resources of the RCSB Protein Data Bank. ACTA ACUST UNITED AC 2016; 55:1.9.1-1.9.35. [DOI: 10.1002/cpbi.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Luigi Di Costanzo
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Sutapa Ghosh
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Christine Zardecki
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
| | - Stephen K. Burley
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey Piscataway New Jersey
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego California
- San Diego Supercomputer Center, University of California San Diego California
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47
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Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP11 statistics and the prediction center evaluation system. Proteins 2016; 84 Suppl 1:15-9. [PMID: 26857434 PMCID: PMC5479680 DOI: 10.1002/prot.25005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 01/18/2016] [Accepted: 02/04/2016] [Indexed: 01/10/2023]
Abstract
We outline the role of the Protein Structure Prediction Center (predictioncenter.org) in conducting the CASP11 and CASP ROLL experiments, discuss the experiment statistics, and provide an overview of the present CASP infrastructure. The biggest changes compared to the previous CASPs are the implementation of the evaluation system incorporating practically all evaluation measures, statistical tests, and visualization tools historically used by the CASP assessors, the expansion of the infrastructure to incorporate new categories of contact-assisted and multimeric predictions, and the redesign of the assessors' web-workspace enabling assessments based on multiple measures for different group categories and target sets. Proteins 2016; 84(Suppl 1):15-19. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Bohdan Monastyrskyy
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, California, 95616.
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48
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Gao J, Zhang Q, Liu M, Zhu L, Wu D, Cao Z, Zhu R. bSiteFinder, an improved protein-binding sites prediction server based on structural alignment: more accurate and less time-consuming. J Cheminform 2016; 8:38. [PMID: 27403208 PMCID: PMC4939519 DOI: 10.1186/s13321-016-0149-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/30/2016] [Indexed: 11/10/2022] Open
Abstract
MOTIVATION Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. RESULTS By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset. For 210 bound dataset, bSiteFinder achieved high accuracies up to 94.8 % (MCC 0.95). For another 48 bound/unbound dataset, bSiteFinder achieved high accuracies up to 93.8 % for bound proteins (MCC 0.95) and 85.4 % for unbound proteins (MCC 0.72). Our bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/, and the source code is provided at the methods page. CONCLUSION An online bSiteFinder server is freely available at http://binfo.shmtu.edu.cn/bsitefinder/. Our work lays a foundation for functional annotation of protein and structure-based drug design. With ever increasing numbers of three-dimensional protein-ligand complex structures, our server should be more accurate and less time-consuming.Graphical Abstract bSiteFinder (http://binfo.shmtu.edu.cn/bsitefinder/) as a protein-binding sites prediction server was developed based on the largest database of bound templates so far with stringent quality control. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server have been significantly improved. What's more, the accuracy was approximately 2-10 % higher than that of other algorithms for the test with either bound dataset or unbound dataset.
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Affiliation(s)
- Jun Gao
- Department of Bioinformatics, Tongji University, Shanghai, 200092 People's Republic of China ; School of Information Engineering, Shanghai Maritime University, Shanghai, 201306 People's Republic of China
| | - Qingchen Zhang
- Department of Bioinformatics, Tongji University, Shanghai, 200092 People's Republic of China
| | - Min Liu
- School of Information Engineering, Shanghai Maritime University, Shanghai, 201306 People's Republic of China
| | - Lixin Zhu
- Digestive Diseases and Nutrition Center, Department of Pediatrics, The State University of New York at Buffalo, Buffalo, NY 14260 USA ; Genomics, Environment, and Microbiome Community of Excellence, The State University of New York at Buffalo, Buffalo, NY 14203 USA ; Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032 People's Republic of China
| | - Dingfeng Wu
- Department of Bioinformatics, Tongji University, Shanghai, 200092 People's Republic of China
| | - Zhiwei Cao
- Department of Bioinformatics, Tongji University, Shanghai, 200092 People's Republic of China
| | - Ruixin Zhu
- Department of Bioinformatics, Tongji University, Shanghai, 200092 People's Republic of China
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49
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Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. CURRENT PROTOCOLS IN BIOINFORMATICS 2016; 54:5.6.1-5.6.37. [PMID: 27322406 PMCID: PMC5031415 DOI: 10.1002/cpbi.3] [Citation(s) in RCA: 1880] [Impact Index Per Article: 235.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin Webb
- University of California at San Francisco, San Francisco, California
| | - Andrej Sali
- University of California at San Francisco, San Francisco, California
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50
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Addressing the Role of Conformational Diversity in Protein Structure Prediction. PLoS One 2016; 11:e0154923. [PMID: 27159429 PMCID: PMC4861349 DOI: 10.1371/journal.pone.0154923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2016] [Indexed: 11/19/2022] Open
Abstract
Computational modeling of tertiary structures has become of standard use to study proteins that lack experimental characterization. Unfortunately, 3D structure prediction methods and model quality assessment programs often overlook that an ensemble of conformers in equilibrium populates the native state of proteins. In this work we collected sets of publicly available protein models and the corresponding target structures experimentally solved and studied how they describe the conformational diversity of the protein. For each protein, we assessed the quality of the models against known conformers by several standard measures and identified those models ranked best. We found that model rankings are defined by both the selected target conformer and the similarity measure used. 70% of the proteins in our datasets show that different models are structurally closest to different conformers of the same protein target. We observed that model building protocols such as template-based or ab initio approaches describe in similar ways the conformational diversity of the protein, although for template-based methods this description may depend on the sequence similarity between target and template sequences. Taken together, our results support the idea that protein structure modeling could help to identify members of the native ensemble, highlight the importance of considering conformational diversity in protein 3D quality evaluations and endorse the study of the variability of the native structure for a meaningful biological analysis.
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