1
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Abbass J, Parisi C. Machine learning-based prediction of proteins' architecture using sequences of amino acids and structural alphabets. J Biomol Struct Dyn 2024:1-16. [PMID: 38505995 DOI: 10.1080/07391102.2024.2328736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/05/2024] [Indexed: 03/21/2024]
Abstract
In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creation of a much larger database of protein structures. Annotating such a vast number of structures has become an increasingly challenging task. CATH is widely recognized as one the most common platforms for addressing this challenge, as it classifies proteins based on their structural and evolutionary relationships, offering the scientific community an invaluable resource for uncovering various properties, including functional annotations. While CATH annotation involves - to some extent - human intervention, keeping up with the classification of the rapidly expanding repositories of protein structures has become exceedingly difficult. Therefore, there is a pressing need for a fully automated approach. On the other hand, the abundance of protein sequences stemming from next generation sequencing technologies, lacking structural annotations, presents an additional challenge to the scientific community. Consequently, 'pre-annotating' protein sequences with structural features, ensuring a high level of precision, could prove highly advantageous. In this paper, after a thorough investigation, we introduce a novel machine-learning model capable of classifying any protein domain, whether it has a known structure or not, into one of the 40 main CATH Architectures. We achieve an F1 Score of 0.92 using only the amino acid sequence and a score of 0.94 using both the sequence of amino acids and the sequence of structural alphabets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jad Abbass
- School of Computer Science and Mathematics, Kingston University, London, UK
| | - Charles Parisi
- School of Computer Science and Mathematics, Kingston University, London, UK
- Telecom Physique Strasbourg, Strasbourg University, Strasbourg, France
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2
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Floch A, Galochkina T, Pirenne F, Tournamille C, de Brevern AG. Molecular dynamics of the human RhD and RhAG blood group proteins. Front Chem 2024; 12:1360392. [PMID: 38566898 PMCID: PMC10985258 DOI: 10.3389/fchem.2024.1360392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Blood group antigens of the RH system (formerly known as "Rhesus") play an important role in transfusion medicine because of the severe haemolytic consequences of antibodies to these antigens. No crystal structure is available for RhD proteins with its partner RhAG, and the precise stoichiometry of the trimer complex remains unknown. Methods: To analyse their structural properties, the trimers formed by RhD and/or RhAG subunits were generated by protein modelling and molecular dynamics simulations were performed. Results: No major differences in structural behaviour were found between trimers of different compositions. The conformation of the subunits is relatively constant during molecular dynamics simulations, except for three large disordered loops. Discussion: This work makes it possible to propose a reasonable stoichiometry and demonstrates the potential of studying the structural behaviour of these proteins to investigate the hundreds of genetic variants relevant to transfusion medicine.
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Affiliation(s)
- Aline Floch
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Tatiana Galochkina
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
| | - France Pirenne
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Christophe Tournamille
- University Paris Est Créteil, INSERM U955 Equipe Transfusion et Maladies du Globule Rouge, IMRB, Créteil, France
- Laboratoire de Biologie Médicale de Référence en Immuno-Hématologie Moléculaire, Etablissement Français du Sang Ile-de-France, Créteil, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, DSIMB Bioinformatics team, Paris, France
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3
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Martins C, Diharce J, Nadaradjane AA, de Brevern AG. Evaluation of the Potential Impact of In Silico Humanization on V HH Dynamics. Int J Mol Sci 2023; 24:14586. [PMID: 37834033 PMCID: PMC10572902 DOI: 10.3390/ijms241914586] [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: 08/21/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 10/15/2023] Open
Abstract
Camelids have the peculiarity of having classical antibodies composed of heavy and light chains as well as single-chain antibodies. They have lost their light chains and one heavy-chain domain. This evolutionary feature means that their terminal heavy-chain domain, VH, called VHH here, has no partner and forms an independent domain. The VHH is small and easy to express alone; it retains thermodynamic and interaction properties. Consequently, VHHs have garnered significant interest from both biotechnological and pharmaceutical perspectives. However, due to their origin in camelids, they cannot be used directly on humans. A humanization step is needed before a possible use. However, changes, even in the constant parts of the antibodies, can lead to a loss of quality. A dedicated tool, Llamanade, has recently been made available to the scientific community. In a previous paper, we already showed the different types of VHH dynamics. Here, we have selected a representative VHH and tested two humanization hypotheses to accurately assess the potential impact of these changes. This example shows that despite the non-negligible change (1/10th of residues) brought about by humanization, the effect is not drastic, and the humanized VHH retains conformational properties quite similar to those of the camelid VHH.
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Affiliation(s)
- Carla Martins
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
| | - Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
| | - Alexandre G. de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-75014 Paris, France; (C.M.); (J.D.)
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, F-97715 Saint Denis Messag, France
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4
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Kranjc A, Narwani TJ, Abby SS, de Brevern AG. Structural Space of the Duffy Antigen/Receptor for Chemokines' Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:13280. [PMID: 37686086 PMCID: PMC10488288 DOI: 10.3390/ijms241713280] [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: 07/27/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Plasmodium vivax malaria affects 14 million people each year. Its invasion requires interactions between the parasitic Duffy-binding protein (PvDBP) and the N-terminal extracellular domain (ECD1) of the host's Duffy antigen/receptor for chemokines (DARC). ECD1 is highly flexible and intrinsically disordered, therefore it can adopt different conformations. We computationally modeled the challenging ECD1 local structure. With T-REMD simulations, we sampled its dynamic behavior and collected its most representative conformations. Our results suggest that most of the DARC ECD1 domain remains in a disordered state during the simulated time. Globular local conformations are found in the analyzed local free-energy minima. These globular conformations share an α-helix spanning residues Ser18 to Ser29 and in many cases they comprise an antiparallel β-sheet, whose β-strands are formed around residues Leu10 and Ala49. The formation of a parallel β-sheet is almost negligible. So far, progress in understanding the mechanisms forming the basis of the P. vivax malaria infection of reticulocytes has been hampered by experimental difficulties, along with a lack of DARC structural information. Our collection of the most probable ECD1 structural conformations will help to advance modeling of the DARC structure and to explore DARC-ECD1 interactions with a range of physiological and pathological ligands.
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Affiliation(s)
- Agata Kranjc
- Université Paris Cité and Université des Antilles and Université de la Réunion, BIGR, UMR_S1134, DSIMB Team, Inserm, F-75014 Paris, France;
- Institut National de la Transfusion Sanguine (INTS), F-75015 Paris, France
- Institute of Neuroscience and Medicine (INM-9)/Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Tarun Jairaj Narwani
- Université Paris Cité and Université des Antilles and Université de la Réunion, BIGR, UMR_S1134, DSIMB Team, Inserm, F-75014 Paris, France;
- Institut National de la Transfusion Sanguine (INTS), F-75015 Paris, France
| | - Sophie S. Abby
- University Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, F-38000 Grenoble, France;
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, BIGR, UMR_S1134, DSIMB Team, Inserm, F-75014 Paris, France;
- Institut National de la Transfusion Sanguine (INTS), F-75015 Paris, France
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5
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General Trends of the Camelidae Antibody V HHs Domain Dynamics. Int J Mol Sci 2023; 24:ijms24054511. [PMID: 36901942 PMCID: PMC10003728 DOI: 10.3390/ijms24054511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Conformational flexibility plays an essential role in antibodies' functional and structural stability. They facilitate and determine the strength of antigen-antibody interactions. Camelidae express an interesting subtype of single-chain antibody, named Heavy Chain only Antibody. They have only one N-terminal Variable domain (VHH) per chain, composed of Frameworks (FRs) and Complementarity Determining regions (CDRs) like their VH and VL counterparts in IgG. Even when expressed independently, VHH domains display excellent solubility and (thermo)stability, which helps them to retain their impressive interaction capabilities. Sequence and structural features of VHH domains contributing to these abilities have already been studied compared to classical antibodies. To have the broadest view and understand the changes in dynamics of these macromolecules, large-scale molecular dynamics simulations for a large number of non-redundant VHH structures have been performed for the first time. This analysis reveals the most prevalent movements in these domains. It reveals the four main classes of VHHs dynamics. Diverse local changes were observed in CDRs with various intensities. Similarly, different types of constraints were observed in CDRs, while FRs close to CDRs were sometimes primarily impacted. This study sheds light on the changes in flexibility in different regions of VHH that may impact their in silico design.
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6
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Nadaradjane AA, Diharce J, Rebehmed J, Cadet F, Gardebien F, Gelly JC, Etchebest C, de Brevern AG. Quality assessment of V HH models. J Biomol Struct Dyn 2023; 41:13287-13301. [PMID: 36752327 DOI: 10.1080/07391102.2023.2172613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Heavy Chain Only Antibodies are specific to Camelid species. Despite the lack of the light chain variable domain, their heavy chain variable domain (VH) domain, named VHH or nanobody, has promising potential applications in research and therapeutic fields. The structural study of VHH is therefore of great interest. Unfortunately, considering the huge amount of sequences that might be produced, only about one thousand of VHH experimental structures are publicly available in the Protein Data Bank, implying that structural model prediction of VHH is a necessary alternative to obtaining 3D information besides its sequence. The present study aims to assess and compare the quality of predictions from different modelling methodologies. Established comparative & homology modelling approaches to recent Deep Learning-based modelling strategies were applied, i.e. Modeller using single or multiple structural templates, ModWeb, SwissModel (with two evaluation schema), RoseTTAfold, AlphaFold 2 and NanoNet. The prediction accuracy was evaluated using RMSD, TM-score, GDT-TS, GDT-HA and Protein Blocks distance metrics. Besides the global structure assessment, we performed specific analyses of Frameworks and CDRs structures. We observed that AlphaFold 2 and especially NanoNet performed better than the other evaluated softwares. Importantly, we performed molecular dynamics simulations of an experimental structure and a NanoNet predicted model of a VHH in order to compare the global structural flexibility and local conformations using Protein Blocks. Despite rather similar structures, substantial differences in dynamical properties were observed, which underlies the complexity of the task of model evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aravindan Arun Nadaradjane
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Julien Diharce
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Frédéric Cadet
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
- Artificial Intelligence Department, PEACCEL, Paris, France
| | - Fabrice Gardebien
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
| | - Jean-Christophe Gelly
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Catherine Etchebest
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
| | - Alexandre G de Brevern
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Paris, France
- Université Paris Cité and Université de la Réunion and Université des Antilles, INSERM, BIGR, DSIMB, Saint Denis Messag, France
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7
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Zea DJ, Teppa E, Marino-Buslje C. Easy Not Easy: Comparative Modeling with High-Sequence Identity Templates. Methods Mol Biol 2023; 2627:83-100. [PMID: 36959443 DOI: 10.1007/978-1-0716-2974-1_5] [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: 03/25/2023]
Abstract
Homology modeling is the most common technique to build structural models of a target protein based on the structure of proteins with high-sequence identity and available high-resolution structures. This technique is based on the idea that protein structure shows fewer changes than sequence through evolution. While in this scenario single mutations would minimally perturb the structure, experimental evidence shows otherwise: proteins with high conformational diversity impose a limit of the paradigm of comparative modeling as the same protein sequence can adopt dissimilar three-dimensional structures. These cases present challenges for modeling; at first glance, they may seem to be easy cases, but they have a complexity that is not evident at the sequence level. In this chapter, we address the following questions: Why should we care about conformational diversity? How to consider conformational diversity when doing template-based modeling in a practical way?
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Affiliation(s)
- Diego Javier Zea
- Laboratory of Computational and Quantitative Biology, LCQB, UMR 7238 CNRS, IBPS, Sorbonne Université, Paris, France
| | - Elin Teppa
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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8
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Craveur P, Narwani TJ, Srinivasan N, Gelly JC, Rebehmed J, de Brevern AG. Shaking the β-Bulges. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:14-18. [PMID: 34115590 DOI: 10.1109/tcbb.2021.3088444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
β-bulges are irregularities inside the β-sheets. They represent more than 3 percent of the protein residues, i.e., they are as frequent as 3.10 helices. In terms of evolution, β-bulges are not more conserved than any other local protein conformations within homologous protein structures. In a first of its kind study, we have investigated the dynamical behaviour of β-bulges using the largest known set of protein molecular dynamics simulations. We observed that more than 50 percent of the existing β-bulges in protein crystal structures remained stable during dynamics while more than1/6th were not stable at all and disappeared entirely. Surprisingly, 1.1 percent of β-bulges that appeared remained stable. β-bulges have been categorized in different subtypes. The most common β-bulges' types are the smallest insertion in β-strands (namely AC and AG); they are found as stable as the whole β-bulges dataset. Low occurring types (namely PC and AS), that have the largest insertions, are significantly more stable than expected. Thus, this pioneer study allowed to precisely quantify the stability of the β-bulges, demonstrating their structural robustness, with few unexpected cases raising structural questions.
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9
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Karuppasamy MP, Venkateswaran S, Subbiah P. PDB-2-PBv3.0: An updated protein block database. J Bioinform Comput Biol 2021; 18:2050009. [PMID: 32404014 DOI: 10.1142/s0219720020500092] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Our protein block (PB) sequence database PDB-2-PBv1.0 provides PB sequences and dihedral angles for 74,297 protein structures comprising of 103,252 protein chains of Protein Data Bank (PDB) as on 2011. Since there are a lot of practical applications of PB and also as the size of PDB database increases, it becomes necessary to provide the PB sequences for all PDB protein structures. The current updated PDB-2-PBv3.0 contains PB sequences for 147,602 PDB structures comprising of 400,355 protein chains as on October 2019. When compared to our previous version PDB-2-PBv1.0, the current PDB-2-PBv3.0 contains 2- and 4-fold increase in the number of protein structures and chains, respectively. Notably, it provides PB information for any protein chain, regardless of the missing atom records of protein structure data in PDB. It includes protein interaction information with DNA and RNA along with their corresponding functional classes from Nucleic Acid Database (NDB) and PDB. Now, the updated version allows the user to download multiple PB records by parameter search and/or by a given list. This database is freely accessible at http://bioinfo.bdu.ac.in/pb3.
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Affiliation(s)
- Muthuvel Prasath Karuppasamy
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Suresh Venkateswaran
- Department of Paediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, GA, USA
| | - Parthasarathy Subbiah
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
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10
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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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11
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de Brevern AG. Analysis of Protein Disorder Predictions in the Light of a Protein Structural Alphabet. Biomolecules 2020; 10:biom10071080. [PMID: 32698546 PMCID: PMC7408373 DOI: 10.3390/biom10071080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Intrinsically-disordered protein (IDP) characterization was an amazing change of paradigm in our classical sequence-structure-function theory. Moreover, IDPs are over-represented in major disease pathways and are now often targeted using small molecules for therapeutic purposes. This has had created a complex continuum from order-that encompasses rigid and flexible regions-to disorder regions; the latter being not accessible through classical crystallographic methodologies. In X-ray structures, the notion of order is dictated by access to resolved atom positions, providing rigidity and flexibility information with low and high experimental B-factors, while disorder is associated with the missing (non-resolved) residues. Nonetheless, some rigid regions can be found in disorder regions. Using ensembles of IDPs, their local conformations were analyzed in the light of a structural alphabet. An entropy index derived from this structural alphabet allowed us to propose a continuum of states from rigidity to flexibility and finally disorder. In this study, the analysis was extended to comparing these results to disorder predictions, underlying a limited correlation, and so opening new ideas to characterize and predict disorder.
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Affiliation(s)
- Alexandre G de Brevern
- INSERM, UMR_S 1134, DSIMB, Univ Paris, INTS, Laboratoire d'Excellence GR-Ex, 75015 Paris, France
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12
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Akhila MV, Narwani TJ, Floch A, Maljković M, Bisoo S, Shinada NK, Kranjc A, Gelly JC, Srinivasan N, Mitić N, de Brevern AG. A structural entropy index to analyse local conformations in intrinsically disordered proteins. J Struct Biol 2020; 210:107464. [DOI: 10.1016/j.jsb.2020.107464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022]
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13
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Narwani TJ, Craveur P, Shinada NK, Floch A, Santuz H, Vattekatte AM, Srinivasan N, Rebehmed J, Gelly JC, Etchebest C, de Brevern AG. Discrete analyses of protein dynamics. J Biomol Struct Dyn 2019; 38:2988-3002. [PMID: 31361191 DOI: 10.1080/07391102.2019.1650112] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein structures are highly dynamic macromolecules. This dynamics is often analysed through experimental and/or computational methods only for an isolated or a limited number of proteins. Here, we explore large-scale protein dynamics simulation to observe dynamics of local protein conformations using different perspectives. We analysed molecular dynamics to investigate protein flexibility locally, using classical approaches such as RMSf, solvent accessibility, but also innovative approaches such as local entropy. First, we focussed on classical secondary structures and analysed specifically how β-strand, β-turns, and bends evolve during molecular simulations. We underlined interesting specific bias between β-turns and bends, which are considered as the same category, while their dynamics show differences. Second, we used a structural alphabet that is able to approximate every part of the protein structures conformations, namely protein blocks (PBs) to analyse (i) how each initial local protein conformations evolve during dynamics and (ii) if some exchange can exist among these PBs. Interestingly, the results are largely complex than simple regular/rigid and coil/flexible exchange. AbbreviationsNeqnumber of equivalentPBProtein BlocksPDBProtein DataBankRMSfroot mean square fluctuationsCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tarun Jairaj Narwani
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Pierrick Craveur
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicolas K Shinada
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Discngine, SAS, Paris, France
| | - Aline Floch
- Laboratoire D'Excellence GR-Ex, Paris, France.,Etablissement Français du Sang Ile de France, Créteil, France.,IMRB - INSERM U955 Team 2 « Transfusion et Maladies du Globule Rouge », Paris Est- Créteil Univ, Créteil, France.,UPEC, Université Paris Est-Créteil, Créteil, France
| | - Hubert Santuz
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Akhila Melarkode Vattekatte
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France
| | | | - Joseph Rebehmed
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Department of Computer Science and Mathematics, Lebanese American University, Byblos, Lebanon
| | - Jean-Christophe Gelly
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France.,IBL, Paris, France
| | - Catherine Etchebest
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France
| | - Alexandre G de Brevern
- Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France.,Laboratoire D'Excellence GR-Ex, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France.,IBL, Paris, France
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14
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Dong R, Peng Z, Zhang Y, Yang J. mTM-align: an algorithm for fast and accurate multiple protein structure alignment. Bioinformatics 2019; 34:1719-1725. [PMID: 29281009 DOI: 10.1093/bioinformatics/btx828] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022] Open
Abstract
Motivation As protein structure is more conserved than sequence during evolution, multiple structure alignment can be more informative than multiple sequence alignment, especially for distantly related proteins. With the rapid increase of the number of protein structures in the Protein Data Bank, it becomes urgent to develop efficient algorithms for multiple structure alignment. Results A new multiple structure alignment algorithm (mTM-align) was proposed, which is an extension of the highly efficient pairwise structure alignment program TM-align. The algorithm was benchmarked on four widely used datasets, HOMSTRAD, SABmark_sup, SABmark_twi and SISY-multiple, showing that mTM-align consistently outperforms other algorithms. In addition, the comparison with the manually curated alignments in the HOMSTRAD database shows that the automated alignments built by mTM-align are in general more accurate. Therefore, mTM-align may be used as a reliable complement to construct multiple structure alignments for real-world applications. Availability and implementation http://yanglab.nankai.edu.cn/mTM-align. Contact zhng@umich.edu or yangjy@nankai.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Runze Dong
- School of Mathematical Sciences, Nankai University, Tianjin 300071, China
| | - Zhenling Peng
- Center for Applied Mathematics, Tianjin University, Tianjin 300072, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA
| | - Jianyi Yang
- School of Mathematical Sciences, Nankai University, Tianjin 300071, China
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15
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A minimum set of stable blocks for rational design of polypeptide chains. Biochimie 2019; 160:88-92. [DOI: 10.1016/j.biochi.2019.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
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16
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de Brevern AG, Floch A, Barrault A, Martret J, Bodivit G, Djoudi R, Pirenne F, Tournamille C. Alloimmunization risk associated with amino acid 223 substitution in the RhD protein: analysis in the light of molecular modeling. Transfusion 2018; 58:2683-2692. [DOI: 10.1111/trf.14809] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/09/2018] [Accepted: 04/21/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Alexandre G. de Brevern
- INSERM UMR_S 1134; Univ. Paris Diderot, Sorbonne Paris Cité, Univ. de la Réunion, Univ. Antilles; Paris
- Laboratory of Excellence GR-Ex; Paris
- Institut National de la Transfusion Sanguine (INTS); Paris
| | - Aline Floch
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
- UPEC; Université Paris Est-Créteil; Créteil France
| | | | | | - Gwellaouen Bodivit
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
| | - Rachid Djoudi
- Etablissement Français du Sang Ile de France; Créteil France
| | - France Pirenne
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
- UPEC; Université Paris Est-Créteil; Créteil France
| | - Christophe Tournamille
- Laboratory of Excellence GR-Ex; Paris
- Etablissement Français du Sang Ile de France; Créteil France
- IMRB-INSERM U955 Team 2 “Transfusion et Maladies du Globule Rouge”; Créteil France
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17
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MIP diversity from Trichoderma: Structural considerations and transcriptional modulation during mycoparasitic association with Fusarium solani olive trees. PLoS One 2018; 13:e0193760. [PMID: 29543834 PMCID: PMC5854309 DOI: 10.1371/journal.pone.0193760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/17/2018] [Indexed: 11/19/2022] Open
Abstract
Major intrinsic proteins (MIP) are characterized by a transmembrane pore-type architecture that facilitates transport across biomembranes of water and a variety of low molecular weight solutes. They are found in all parts of life, with remarkable protein diversity. Very little is known about MIP from fungi. And yet, it can legitimately be stated that MIP are pivotal molecular components in the privileged relationships fungi enjoy with plants or soil fauna in various environments. To date, MIP have never been studied in a mycoparasitism situation. In this study, the diversity, expression and functional prediction of MIP from the genus Trichoderma were investigated. Trichoderma spp. genomes have at least seven aquaporin genes. Based on a phylogenetic analysis of the translated sequences, members were assigned to the AQP, AQGP and XIP subfamilies. In in vitro and in planta assays with T. harzianum strain Ths97, expression analyses showed that four genes were constitutively expressed. In a mycoparasitic context with Fusarium solani, the causative agent of fusarium dieback on olive tree roots, these genes were up-regulated. This response is of particular interest in analyzing the MIP promoter cis-regulatory motifs, most of which are involved in various carbon and nitrogen metabolisms. Structural analyses provide new insights into the possible role of structural checkpoints by which these members transport water, H2O2, glycerol and, more generally, linear polyols across the membranes. Taken together, these results provide the first evidence that MIP may play a key role in Trichoderma mycoparasitism lifestyle.
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18
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Barnoud J, Santuz H, Craveur P, Joseph AP, Jallu V, de Brevern AG, Poulain P. PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks. PeerJ 2017; 5:e4013. [PMID: 29177113 PMCID: PMC5700758 DOI: 10.7717/peerj.4013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/19/2017] [Indexed: 11/20/2022] Open
Abstract
This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.
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Affiliation(s)
- Jonathan Barnoud
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Current affiliation: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Hubert Santuz
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Current affiliation: Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France
| | - Pierrick Craveur
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Current affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Agnel Praveen Joseph
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Current affiliation: Birkbeck College, University of London, London, UK
| | | | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Pierre Poulain
- INSERM, U 1134, DSIMB, Paris, France.,Univ. Paris Diderot, Sorbonne Paris Cité, Univ de la Réunion, Univ des Antilles, UMR-S 1134, Paris, France.,Institut National de la Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France.,Current affiliation: Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod, UMR 7592, Univ. Paris Diderot, CNRS, Sorbonne Paris Cité, Paris, France
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19
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Regad L, Chéron JB, Triki D, Senac C, Flatters D, Camproux AC. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight. PLoS One 2017; 12:e0182972. [PMID: 28817602 PMCID: PMC5560695 DOI: 10.1371/journal.pone.0182972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/27/2017] [Indexed: 11/18/2022] Open
Abstract
Protein flexibility is often implied in binding with different partners and is essential for protein function. The growing number of macromolecular structures in the Protein Data Bank entries and their redundancy has become a major source of structural knowledge of the protein universe. The analysis of structural variability through available redundant structures of a target, called multiple target conformations (MTC), obtained using experimental or modeling methods and under different biological conditions or different sources is one way to explore protein flexibility. This analysis is essential to improve the understanding of various mechanisms associated with protein target function and flexibility. In this study, we explored structural variability of three biological targets by analyzing different MTC sets associated with these targets. To facilitate the study of these MTC sets, we have developed an efficient tool, SA-conf, dedicated to capturing and linking the amino acid and local structure variability and analyzing the target structural variability space. The advantage of SA-conf is that it could be applied to divers sets composed of MTCs available in the PDB obtained using NMR and crystallography or homology models. This tool could also be applied to analyze MTC sets obtained by dynamics approaches. Our results showed that SA-conf tool is effective to quantify the structural variability of a MTC set and to localize the structural variable positions and regions of the target. By selecting adapted MTC subsets and comparing their variability detected by SA-conf, we highlighted different sources of target flexibility such as induced by binding partner, by mutation and intrinsic flexibility. Our results support the interest to mine available structures associated with a target using to offer valuable insight into target flexibility and interaction mechanisms. The SA-conf executable script, with a set of pre-compiled binaries are available at http://www.mti.univ-paris-diderot.fr/recherche/plateformes/logiciels.
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Affiliation(s)
- Leslie Regad
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail: anne-claude.camproux@univ-paris-diderot (ACC); (LR)
| | - Jean-Baptiste Chéron
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Institut de Chimie de Nice, UMR-CNRS 7272, Faculté des Sciences, Université de Nice-Sophia Antipolis, Nice, France
| | - Dhoha Triki
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Caroline Senac
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale (LIB), Paris, France
| | - Delphine Flatters
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Anne-Claude Camproux
- Molécules thérapeutiques in silico (MTi), INSERM UMR-S973, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- * E-mail: anne-claude.camproux@univ-paris-diderot (ACC); (LR)
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20
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Computational Analysis of Gynura bicolor Bioactive Compounds as Dipeptidyl Peptidase-IV Inhibitor. Adv Bioinformatics 2017; 2017:5124165. [PMID: 28932239 PMCID: PMC5591938 DOI: 10.1155/2017/5124165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/11/2017] [Accepted: 06/22/2017] [Indexed: 12/23/2022] Open
Abstract
The inhibition of dipeptidyl peptidase-IV (DPPIV) is a popular route for the treatment of type-2 diabetes. Commercially available gliptin-based drugs such as sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin were specifically developed as DPPIV inhibitors for diabetic patients. The use of Gynura bicolor in treating diabetes had been reported in various in vitro experiments. However, an understanding of the inhibitory actions of G. bicolor bioactive compounds on DPPIV is still lacking and this may provide crucial information for the development of more potent and natural sources of DPPIV inhibitors. Evaluation of G. bicolor bioactive compounds for potent DPPIV inhibitors was computationally conducted using Lead IT and iGEMDOCK software, and the best free-binding energy scores for G. bicolor bioactive compounds were evaluated in comparison with the commercial DPPIV inhibitors, sitagliptin, anagliptin, linagliptin, saxagliptin, and alogliptin. Drug-likeness and absorption, distribution, metabolism, and excretion (ADME) analysis were also performed. Based on molecular docking analysis, four of the identified bioactive compounds in G. bicolor, 3-caffeoylquinic acid, 5-O-caffeoylquinic acid, 3,4-dicaffeoylquinic acid, and trans-5-p-coumaroylquinic acid, resulted in lower free-binding energy scores when compared with two of the commercially available gliptin inhibitors. The results revealed that bioactive compounds in G. bicolor are potential natural inhibitors of DPPIV.
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21
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Noël F, Malpertuy A, de Brevern AG. Global analysis of VHHs framework regions with a structural alphabet. Biochimie 2016; 131:11-19. [PMID: 27613403 DOI: 10.1016/j.biochi.2016.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 02/08/2023]
Abstract
The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models.
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Affiliation(s)
- Floriane Noël
- INSERM, U 1134, DSIMB, F-75739 Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France; Laboratoire d'Excellence GR-Ex, F-75739 Paris, France
| | | | - Alexandre G de Brevern
- INSERM, U 1134, DSIMB, F-75739 Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, F-75739 Paris, France; Institut National de la Transfusion Sanguine (INTS), F-75739 Paris, France; Laboratoire d'Excellence GR-Ex, F-75739 Paris, France.
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22
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Pandini A, Fornili A. Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput 2016; 12:1368-79. [PMID: 26808351 PMCID: PMC5356493 DOI: 10.1021/acs.jctc.5b00992] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Conformational
changes associated with protein function often occur
beyond the time scale currently accessible to unbiased molecular dynamics
(MD) simulations, so that different approaches have been developed
to accelerate their sampling. Here we investigate how the knowledge
of backbone conformations preferentially adopted by protein fragments,
as contained in precalculated libraries known as structural alphabets
(SA), can be used to explore the landscape of protein conformations
in MD simulations. We find that (a) enhancing the sampling of native
local states in both metadynamics and steered MD simulations allows
the recovery of global folded states in small proteins; (b) folded
states can still be recovered when the amount of information on the
native local states is reduced by using a low-resolution version of
the SA, where states are clustered into macrostates; and (c) sequences
of SA states derived from collections of structural motifs can be
used to sample alternative conformations of preselected protein regions.
The present findings have potential impact on several applications,
ranging from protein model refinement to protein folding and design.
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Affiliation(s)
- Alessandro Pandini
- Department of Computer Science, College of Engineering, Design and Physical Sciences and Synthetic Biology Theme, Institute of Environment, Health and Societies, Brunel University London , Uxbridge UB8 3PH, United Kingdom
| | - Arianna Fornili
- School of Biological and Chemical Sciences, Queen Mary University of London , Mile End Road, London E1 4NS, United Kingdom
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23
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Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci 2015; 2:20. [PMID: 26075209 PMCID: PMC4445325 DOI: 10.3389/fmolb.2015.00020] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/30/2015] [Indexed: 01/01/2023] Open
Abstract
Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.
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Affiliation(s)
- Pierrick Craveur
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Agnel P Joseph
- Rutherford Appleton Laboratory, Science and Technology Facilities Council Didcot, UK
| | - Jeremy Esque
- Institut National de la Santé et de la Recherche Médicale U964,7 UMR Centre National de la Recherche Scientifique 7104, IGBMC, Université de Strasbourg Illkirch, France
| | - Tarun J Narwani
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Floriane Noël
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Nicolas Shinada
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Matthieu Goguet
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Sylvain Leonard
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Pierre Poulain
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Ets Poulain Pointe-Noire, Congo
| | - Olivier Bertrand
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Guilhem Faure
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health Bethesda, MD, USA
| | - Joseph Rebehmed
- Centre National de la Recherche Scientifique UMR7590, Sorbonne Universités, Université Pierre et Marie Curie - MNHN - IRD - IUC Paris, France
| | | | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Hospital for Sick Children, and Departments of Biochemistry and Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - Ramachandra M Bhaskara
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore Bangalore, India ; Department of Theoretical Biophysics, Max Planck Institute of Biophysics Frankfurt, Germany
| | - Jonathan Barnoud
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Laboratoire de Physique, École Normale Supérieure de Lyon, Université de Lyon, Centre National de la Recherche Scientifique UMR 5672 Lyon, France
| | - Stéphane Téletchéa
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France ; Faculté des Sciences et Techniques, Université de Nantes, Unité Fonctionnalité et Ingénierie des Protéines, Centre National de la Recherche Scientifique UMR 6286, Université Nantes Nantes, France
| | - Vincent Jallu
- Platelet Unit, Institut National de la Transfusion Sanguine Paris, France
| | - Jiri Cerny
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology, The Czech Academy of Sciences Prague, Czech Republic
| | - Catherine Etchebest
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | | | - Jean-Christophe Gelly
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
| | - Alexandre G de Brevern
- Institut National de la Santé et de la Recherche Médicale U 1134 Paris, France ; UMR_S 1134, DSIMB, Université Paris Diderot, Sorbonne Paris Cite Paris, France ; Institut National de la Transfusion Sanguine, DSIMB Paris, France ; UMR_S 1134, DSIMB, Laboratory of Excellence GR-Ex Paris, France
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24
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Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. A novel approach to represent and compare RNA secondary structures. Nucleic Acids Res 2014; 42:6146-57. [PMID: 24753415 PMCID: PMC4041456 DOI: 10.1093/nar/gku283] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/18/2022] Open
Abstract
Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny.
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Affiliation(s)
- Eugenio Mattei
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Fabrizio Ferrè
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome 'Tor Vergata', Via della Ricerca Scientifica snc, 00133 Rome, Italy
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25
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Li Z, Natarajan P, Ye Y, Hrabe T, Godzik A. POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res 2014; 42:W240-5. [PMID: 24838569 PMCID: PMC4086100 DOI: 10.1093/nar/gku394] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
POSA (Partial Order Structure Alignment), available at http://posa.godziklab.org, is a server for multiple protein structure alignment introduced in 2005 (Ye,Y. and Godzik,A. (2005) Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21, 2362–2369). It is free and open to all users, and there is no login requirement, albeit there is an option to register and store results in individual, password-protected directories. In the updated POSA server described here, we introduce two significant improvements. First is an interface allowing the user to provide additional information by defining segments that anchor the alignment in one or more input structures. This interface allows users to take advantage of their intuition and biological insights to improve the alignment and guide it toward a biologically relevant solution. The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure alignments) or view them individually in a series of synchronized windows with extensive, user-controlled visualization options. The user can rotate structure(s) in any of the windows and study similarities or differences between structures clearly visible in individual windows.
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Affiliation(s)
- Zhanwen Li
- Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Padmaja Natarajan
- Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Yuzhen Ye
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Thomas Hrabe
- Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
| | - Adam Godzik
- Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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