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Chailyan A, Marcatili P. Structural Characterization of Peptide Antibodies. Methods Mol Biol 2024; 2821:195-204. [PMID: 38997490 DOI: 10.1007/978-1-0716-3914-6_15] [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] [Indexed: 07/14/2024]
Abstract
The role of proteins as very effective immunogens for the generation of antibodies is indisputable. Nevertheless, cases in which protein usage for antibody production is not feasible or convenient compelled the creation of a powerful alternative consisting of synthetic peptides. Synthetic peptides can be modified to obtain desired properties or conformation, tagged for purification, isotopically labeled for protein quantitation or conjugated to immunogens for antibody production. The antibodies that bind to these peptides represent an invaluable tool for biological research and discovery. To better understand the underlying mechanisms of antibody-antigen interaction, here, we present a pipeline developed by us to structurally classify immunoglobulin antigen binding sites and to infer key sequence residues and other variables that have a prominent role in each structural class.
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Affiliation(s)
- Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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2
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Yan Y, Huang T. The Interactome of Protein, DNA, and RNA. Methods Mol Biol 2023; 2695:89-110. [PMID: 37450113 DOI: 10.1007/978-1-0716-3346-5_6] [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] [Indexed: 07/18/2023]
Abstract
Proteins participate in many processes of the organism and are very important for maintaining the health of the organism. However, proteins cannot function independently in the body. They must interact with proteins, DNA, RNA, and other substances to perform biological functions and maintain the body's health. At present, there are many experimental methods and software tools that can detect and predict the interaction between proteins and other substances. There are also many databases that record the interaction between proteins and other substances. This article mainly describes protein-protein, protein-DNA, and protein-RNA interactions in detail by introducing some commonly used experimental methods, the software tools produced with the accumulation of experimental data and the rapid development of machine learning, and the related databases that record the relationship between proteins and some substances. By this review, we hope that through the analysis and summary of various aspects, it will be convenient for researchers to conduct further research on protein interactions.
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Affiliation(s)
- Yuyao Yan
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
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3
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Bongini P, Niccolai N, Trezza A, Mangiavacchi G, Santucci A, Spiga O, Bianchini M, Gardini S. Structural Bioinformatic Survey of Protein-Small Molecule Interfaces Delineates the Role of Glycine in Surface Pocket Formation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1881-1886. [PMID: 33095703 DOI: 10.1109/tcbb.2020.3033384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
With a structural bioinformatic approach, we have explored amino acid compositions at PISA defined interfaces between small molecules and proteins that are contained in an optimized subset of 11,351 PDB files. The use of a series of restrictions, to prevent redundancy and biases from interactions between amino acids with charged side chains and ions, yielded a final data set of 45,230 protein-small molecule interfaces. We have compared occurrences of natural amino acids in surface exposed regions and binding sites for all the proteins of our data set. From our structural bioinformatic survey, the most relevant signal arose from the unexpected Gly abundance at enzyme catalytic sites. This finding suggested that Gly must have a fundamental role in stabilizing concave protein surface moieties. Subsequently, we have tried to predict the effect of in silico Gly mutations in hen egg white lysozyme to optimize those conditions that can reshape the protein surface with the appearance of new pockets. Replacing amino acids having bulky side chains with Gly in specific protein regions seems a feasible way for designing proteins with additional surface pockets, which can alter protein surface dynamics, therefore, representing controllable switches for protein activity.
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4
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Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. Pharmaceuticals (Basel) 2022; 15:566. [PMID: 35631392 PMCID: PMC9147475 DOI: 10.3390/ph15050566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022] Open
Abstract
Bronchoalveolar lavage of the epithelial lining fluid (BALF) can sample the profound changes in the airway lumen milieu prevalent in chronic obstructive pulmonary disease (COPD). We compared the BALF proteome of ex-smokers with moderate COPD who are not in exacerbation status to non-smoking healthy control subjects and applied proteome-scale translational bioinformatics approaches to identify potential therapeutic protein targets and drugs that modulate these proteins for the treatment of COPD. Proteomic profiles of BALF were obtained from (1) never-smoker control subjects with normal lung function (n = 10) or (2) individuals with stable moderate (GOLD stage 2, FEV1 50−80% predicted, FEV1/FVC < 0.70) COPD who were ex-smokers for at least 1 year (n = 10). After identifying potential crucial hub proteins, drug−proteome interaction signatures were ranked by the computational analysis of novel drug opportunities (CANDO) platform for multiscale therapeutic discovery to identify potentially repurposable drugs. Subsequently, a literature-based knowledge graph was utilized to rank combinations of drugs that most likely ameliorate inflammatory processes. Proteomic network analysis demonstrated that 233 of the >1800 proteins identified in the BALF were significantly differentially expressed in COPD versus control. Functional annotation of the differentially expressed proteins was used to detail canonical pathways containing the differential expressed proteins. Topological network analysis demonstrated that four putative proteins act as central node proteins in COPD. The drugs with the most similar interaction signatures to approved COPD drugs were extracted with the CANDO platform. The drugs identified using CANDO were subsequently analyzed using a knowledge-based technique to determine an optimal two-drug combination that had the most appropriate effect on the central node proteins. Network analysis of the BALF proteome identified critical targets that have critical roles in modulating COPD pathogenesis, for which we identified several drugs that could be repurposed to treat COPD using a multiscale shotgun drug discovery approach.
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Affiliation(s)
- Manoj J. Mammen
- Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA; (C.T.); (J.Q.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Matthew C. Morris
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - Spencer Richman
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA; (C.T.); (J.Q.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - Sanjay Sethi
- WNY VA Healthcare System, Buffalo, NY 14215, USA;
- Department of Medicine, Jacobs School of Medicine and Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
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5
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Halip L, Avram S, Neanu C. The B-factor index for the binding site (BFIbs) to prioritize crystal protein structures for docking. Struct Chem 2021. [DOI: 10.1007/s11224-021-01751-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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A chemical interpretation of protein electron density maps in the worldwide protein data bank. PLoS One 2020; 15:e0236894. [PMID: 32785279 PMCID: PMC7423092 DOI: 10.1371/journal.pone.0236894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022] Open
Abstract
High-quality three-dimensional structural data is of great value for the functional interpretation of biomacromolecules, especially proteins; however, structural quality varies greatly across the entries in the worldwide Protein Data Bank (wwPDB). Since 2008, the wwPDB has required the inclusion of structure factors with the deposition of x-ray crystallographic structures to support the independent evaluation of structures with respect to the underlying experimental data used to derive those structures. However, interpreting the discrepancies between the structural model and its underlying electron density data is difficult, since derived sigma-scaled electron density maps use arbitrary electron density units which are inconsistent between maps from different wwPDB entries. Therefore, we have developed a method that converts electron density values from sigma-scaled electron density maps into units of electrons. With this conversion, we have developed new methods that can evaluate specific regions of an x-ray crystallographic structure with respect to a physicochemical interpretation of its corresponding electron density map. We have systematically compared all deposited x-ray crystallographic protein models in the wwPDB with their underlying electron density maps, if available, and characterized the electron density in terms of expected numbers of electrons based on the structural model. The methods generated coherent evaluation metrics throughout all PDB entries with associated electron density data, which are consistent with visualization software that would normally be used for manual quality assessment. To our knowledge, this is the first attempt to derive units of electrons directly from electron density maps without the aid of the underlying structure factors. These new metrics are biochemically-informative and can be extremely useful for filtering out low-quality structural regions from inclusion into systematic analyses that span large numbers of PDB entries. Furthermore, these new metrics will improve the ability of non-crystallographers to evaluate regions of interest within PDB entries, since only the PDB structure and the associated electron density maps are needed. These new methods are available as a well-documented Python package on GitHub and the Python Package Index under a modified Clear BSD open source license.
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Lübben AV, Sheldrick GM. PDB2INS: bridging the gap between small-molecule and macromolecular refinement. J Appl Crystallogr 2019; 52:669-673. [PMID: 31236096 PMCID: PMC6557183 DOI: 10.1107/s1600576719005478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 04/22/2019] [Indexed: 11/27/2022] Open
Abstract
The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3-8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395-1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213-220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages.
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Affiliation(s)
- Anna V. Lübben
- Abteilung für Strukturchemie, Universität Göttingen, Tammannstrase 4, Göttingen, D-37077, Germany
| | - George M. Sheldrick
- Abteilung für Strukturchemie, Universität Göttingen, Tammannstrase 4, Göttingen, D-37077, Germany
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de Freitas CS, Higa LM, Sacramento CQ, Ferreira AC, Reis PA, Delvecchio R, Monteiro FL, Barbosa-Lima G, James Westgarth H, Vieira YR, Mattos M, Rocha N, Hoelz LVB, Leme RPP, Bastos MM, L. Rodrigues GO, M. Lopes CE, Queiroz-Junior CM, Lima CX, Costa VV, Teixeira MM, Bozza FA, Bozza PT, Boechat N, Tanuri A, Souza TML. Yellow fever virus is susceptible to sofosbuvir both in vitro and in vivo. PLoS Negl Trop Dis 2019; 13:e0007072. [PMID: 30699122 PMCID: PMC6375661 DOI: 10.1371/journal.pntd.0007072] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 02/14/2019] [Accepted: 12/12/2018] [Indexed: 02/05/2023] Open
Abstract
Yellow fever virus (YFV) is a member of the Flaviviridae family. In Brazil, yellow fever (YF) cases have increased dramatically in sylvatic areas neighboring urban zones in the last few years. Because of the high lethality rates associated with infection and absence of any antiviral treatments, it is essential to identify therapeutic options to respond to YFV outbreaks. Repurposing of clinically approved drugs represents the fastest alternative to discover antivirals for public health emergencies. Other Flaviviruses, such as Zika (ZIKV) and dengue (DENV) viruses, are susceptible to sofosbuvir, a clinically approved drug against hepatitis C virus (HCV). Our data showed that sofosbuvir docks onto YFV RNA polymerase using conserved amino acid residues for nucleotide binding. This drug inhibited the replication of both vaccine and wild-type strains of YFV on human hepatoma cells, with EC50 values around 5 μM. Sofosbuvir protected YFV-infected neonatal Swiss mice and adult type I interferon receptor knockout mice (A129-/-) from mortality and weight loss. Because of its safety profile in humans and significant antiviral effects in vitro and in mice, Sofosbuvir may represent a novel therapeutic option for the treatment of YF. Key-words: Yellow fever virus; Yellow fever, antiviral; sofosbuvir Yellow fever virus is transmitted by mosquitoes and its infection may be asymptomatic or lead to a wide clinical spectrum ranging from a mild febrile illness to a potentially lethal viral hemorrhagic fever characterized by liver damage. Although a yellow fever vaccine is available, low coverage allows 80,000–200,000 cases and 30,000–60,000 deaths annually worldwide. There are no specific therapy and treatment relies on supportive care, reinforcing an urgent need for antiviral repourposing. Here, we showed that sofosbuvir, clinically approved against hepatitis C, inhibits yellow fever virus replication in liver cell lines and animal models. In vitro, sofosbuvir inhibits viral RNA replication, decreases the number of infected cells and the production of infectious virus particles. These data is particularly relevante since the liver is the main target of yellow fever infection. Sofosbuvir also protected infected animals from mortality, weight loss and liver injury, especially prophylatically. Our pre-clinical results supports a second use of sofosbuvir against yellow fever.
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Affiliation(s)
- Caroline S. de Freitas
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Luiza M. Higa
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Carolina Q. Sacramento
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C. Ferreira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia A. Reis
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Rodrigo Delvecchio
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Fabio L. Monteiro
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Harrison James Westgarth
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Yasmine Rangel Vieira
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Mayara Mattos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natasha Rocha
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | | | - Mônica M. Bastos
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Gisele Olinto L. Rodrigues
- Center for Research and Development of Pharmaceuticals, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
- Research Group in Arboviral Diseases, Department of Morphology, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Carla Elizabeth M. Lopes
- Center for Research and Development of Pharmaceuticals, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
- Research Group in Arboviral Diseases, Department of Morphology, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Celso Martins Queiroz-Junior
- Cardiac Lab, Department of Morphology, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Cristiano X. Lima
- Departamento de Cirurgia, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vivian V. Costa
- Center for Research and Development of Pharmaceuticals, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
- Research Group in Arboviral Diseases, Department of Morphology, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Mauro M. Teixeira
- Center for Research and Development of Pharmaceuticals, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
- Immunopharmacology Lab, Department of Biochemistry and Immunology, Institute of Biological Sciences (ICB), Universidade Federal de Minas Gerais (UFMG), Minas Gerais, Brazil
| | - Fernando A. Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T. Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Nubia Boechat
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Thiago Moreno L. Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Yakubu RR, Nieves E, Weiss LM. The Methods Employed in Mass Spectrometric Analysis of Posttranslational Modifications (PTMs) and Protein-Protein Interactions (PPIs). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:169-198. [PMID: 31347048 DOI: 10.1007/978-3-030-15950-4_10] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass Spectrometry (MS) has revolutionized the way we study biomolecules, especially proteins, their interactions and posttranslational modifications (PTM). As such MS has established itself as the leading tool for the analysis of PTMs mainly because this approach is highly sensitive, amenable to high throughput and is capable of assigning PTMs to specific sites in the amino acid sequence of proteins and peptides. Along with the advances in MS methodology there have been improvements in biochemical, genetic and cell biological approaches to mapping the interactome which are discussed with consideration for both the practical and technical considerations of these techniques. The interactome of a species is generally understood to represent the sum of all potential protein-protein interactions. There are still a number of barriers to the elucidation of the human interactome or any other species as physical contact between protein pairs that occur by selective molecular docking in a particular spatiotemporal biological context are not easily captured and measured.PTMs massively increase the complexity of organismal proteomes and play a role in almost all aspects of cell biology, allowing for fine-tuning of protein structure, function and localization. There are an estimated 300 PTMS with a predicted 5% of the eukaryotic genome coding for enzymes involved in protein modification, however we have not yet been able to reliably map PTM proteomes due to limitations in sample preparation, analytical techniques, data analysis, and the substoichiometric and transient nature of some PTMs. Improvements in proteomic and mass spectrometry methods, as well as sample preparation, have been exploited in a large number of proteome-wide surveys of PTMs in many different organisms. Here we focus on previously published global PTM proteome studies in the Apicomplexan parasites T. gondii and P. falciparum which offer numerous insights into the abundance and function of each of the studied PTM in the Apicomplexa. Integration of these datasets provide a more complete picture of the relative importance of PTM and crosstalk between them and how together PTM globally change the cellular biology of the Apicomplexan protozoa. A multitude of techniques used to investigate PTMs, mostly techniques in MS-based proteomics, are discussed for their ability to uncover relevant biological function.
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Affiliation(s)
- Rama R Yakubu
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Louis M Weiss
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA. .,Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
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Mode-of-Action-Guided, Molecular Modeling-Based Toxicity Prediction: A Novel Approach for In Silico Predictive Toxicology. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-16443-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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van Beusekom B, Joosten K, Hekkelman ML, Joosten RP, Perrakis A. Homology-based loop modeling yields more complete crystallographic protein structures. IUCRJ 2018; 5:585-594. [PMID: 30224962 PMCID: PMC6126648 DOI: 10.1107/s2052252518010552] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Inherent protein flexibility, poor or low-resolution diffraction data or poorly defined electron-density maps often inhibit the building of complete structural models during X-ray structure determination. However, recent advances in crystallographic refinement and model building often allow completion of previously missing parts. This paper presents algorithms that identify regions missing in a certain model but present in homologous structures in the Protein Data Bank (PDB), and 'graft' these regions of interest. These new regions are refined and validated in a fully automated procedure. Including these developments in the PDB-REDO pipeline has enabled the building of 24 962 missing loops in the PDB. The models and the automated procedures are publicly available through the PDB-REDO databank and webserver. More complete protein structure models enable a higher quality public archive but also a better understanding of protein function, better comparison between homologous structures and more complete data mining in structural bioinformatics projects.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Krista Joosten
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Maarten L. Hekkelman
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Robbie P. Joosten
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, The Netherlands
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12
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Gore S, Sanz García E, Hendrickx PMS, Gutmanas A, Westbrook JD, Yang H, Feng Z, Baskaran K, Berrisford JM, Hudson BP, Ikegawa Y, Kobayashi N, Lawson CL, Mading S, Mak L, Mukhopadhyay A, Oldfield TJ, Patwardhan A, Peisach E, Sahni G, Sekharan MR, Sen S, Shao C, Smart OS, Ulrich EL, Yamashita R, Quesada M, Young JY, Nakamura H, Markley JL, Berman HM, Burley SK, Velankar S, Kleywegt GJ. Validation of Structures in the Protein Data Bank. Structure 2017; 25:1916-1927. [PMID: 29174494 PMCID: PMC5718880 DOI: 10.1016/j.str.2017.10.009] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 09/08/2017] [Accepted: 10/27/2017] [Indexed: 11/01/2022]
Abstract
The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.
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Affiliation(s)
- Swanand Gore
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eduardo Sanz García
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pieter M S Hendrickx
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - John D Westbrook
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Huanwang Yang
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zukang Feng
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kumaran Baskaran
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Brian P Hudson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yasuyo Ikegawa
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Naohiro Kobayashi
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Catherine L Lawson
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steve Mading
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lora Mak
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas J Oldfield
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ezra Peisach
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monica R Sekharan
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sanchayita Sen
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Chenghua Shao
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Oliver S Smart
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eldon L Ulrich
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Reiko Yamashita
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Martha Quesada
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Y Young
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Haruki Nakamura
- PDBj, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - John L Markley
- BMRB, BioMagResBank, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helen M Berman
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stephen K Burley
- RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; RCSB Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Sameer Velankar
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gerard J Kleywegt
- Protein Data Bank in Europe (PDBe), European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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13
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LeBlanc RM, Longhini AP, Le Grice SF, Johnson BA, Dayie TK. Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment. Nucleic Acids Res 2017; 45:e146. [PMID: 28934505 PMCID: PMC5766159 DOI: 10.1093/nar/gkx591] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 01/08/2023] Open
Abstract
Although ∼98% of the human genomic output is transcribed as non-protein coding RNA, <2% of the protein data bank structures comprise RNA. This huge structural disparity stems from combined difficulties of crystallizing RNA for X-ray crystallography along with extensive chemical shift overlap and broadened linewidths associated with NMR of RNA. While half of the deposited RNA structures in the PDB were solved by NMR methods, the usefulness of NMR is still limited by the high cost of sample preparation and challenges of resonance assignment. Here we propose a novel strategy for resonance assignment that combines new strategic 13C labeling technologies with filter/edit type NOESY experiments to greatly reduce spectral complexity and crowding. This new strategy allowed us to assign important non-exchangeable resonances of proton and carbon (1', 2', 2, 5, 6 and 8) nuclei using only one sample and <24 h of NMR instrument time for a 27 nt model RNA. The method was further extended to assigning a 6 nt bulge from a 61 nt viral RNA element justifying its use for a wide range RNA chemical shift resonance assignment problems.
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Affiliation(s)
- Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
- Basic Research Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Andrew P. Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | | - Bruce A. Johnson
- One Moon Scientific, Inc., Westfield, NJ 07090, USA
- Structural Biology Initiative, Advanced Science Research Center at the Graduate Center of the City University of New York, New York, NY 10031, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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14
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Stepanenko OV, Stepanenko OV, Bublikov G, Kuznetsova I, Verkhusha V, Turoverov K. Stabilization of structure in near-infrared fluorescent proteins by binding of biliverdin chromophore. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.095] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Sacramento CQ, de Melo GR, de Freitas CS, Rocha N, Hoelz LVB, Miranda M, Fintelman-Rodrigues N, Marttorelli A, Ferreira AC, Barbosa-Lima G, Abrantes JL, Vieira YR, Bastos MM, de Mello Volotão E, Nunes EP, Tschoeke DA, Leomil L, Loiola EC, Trindade P, Rehen SK, Bozza FA, Bozza PT, Boechat N, Thompson FL, de Filippis AMB, Brüning K, Souza TML. The clinically approved antiviral drug sofosbuvir inhibits Zika virus replication. Sci Rep 2017; 7:40920. [PMID: 28098253 PMCID: PMC5241873 DOI: 10.1038/srep40920] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/13/2016] [Indexed: 12/18/2022] Open
Abstract
Zika virus (ZIKV) is a member of the Flaviviridae family, along with other agents of clinical significance such as dengue (DENV) and hepatitis C (HCV) viruses. Since ZIKV causes neurological disorders during fetal development and in adulthood, antiviral drugs are necessary. Sofosbuvir is clinically approved for use against HCV and targets the protein that is most conserved among the members of the Flaviviridae family, the viral RNA polymerase. Indeed, we found that sofosbuvir inhibits ZIKV RNA polymerase, targeting conserved amino acid residues. Sofosbuvir inhibited ZIKV replication in different cellular systems, such as hepatoma (Huh-7) cells, neuroblastoma (SH-Sy5y) cells, neural stem cells (NSC) and brain organoids. In addition to the direct inhibition of the viral RNA polymerase, we observed that sofosbuvir also induced an increase in A-to-G mutations in the viral genome. Together, our data highlight a potential secondary use of sofosbuvir, an anti-HCV drug, against ZIKV.
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Affiliation(s)
- Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Gabrielle R de Melo
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Caroline S de Freitas
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natasha Rocha
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Milene Miranda
- Laboratório de Vírus Respiratório e do Sarampo, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil.,Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andressa Marttorelli
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Giselle Barbosa-Lima
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juliana L Abrantes
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Yasmine Rangel Vieira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Mônica M Bastos
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | | | - Diogo A Tschoeke
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil.,Núcleo em Ecologia e Desenvolvimento Sócio-Ambiental de Macaé (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, Rio de Janeiro, Brazil
| | - Luciana Leomil
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil
| | | | - Pablo Trindade
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil
| | - Stevens K Rehen
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil
| | - Fernando A Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Nubia Boechat
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Fabiano L Thompson
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.,SAGE -COPPE, UFRJ, Rio de Janeiro, RJ, Brazil
| | | | - Karin Brüning
- BMK Consortium: Blanver Farmoquímica Ltda; Microbiológica Química e FarmacêuticaLtda; Karin Bruning &Cia, Ltda, Brazil
| | - Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Infectologia (INI), Fiocruz, Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
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16
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Neuwald AF, Altschul SF. Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations. PLoS Comput Biol 2016; 12:e1005294. [PMID: 28002465 PMCID: PMC5225019 DOI: 10.1371/journal.pcbi.1005294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/10/2017] [Accepted: 12/08/2016] [Indexed: 11/25/2022] Open
Abstract
Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes’ theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu). Protein sequence data, when gathered in great quantity, contain important but implicit biological information manifest as statistical correlations. Here we describe an approach to access this information by comprehensively modeling and characterizing the distribution of sequences belonging to a major protein superfamily. This approach takes as input a large set of unaligned sequences belonging to the superfamily. By applying the minimum description length principle, it seeks the statistical model that best explains the sequences while avoiding over-fitting the data. It concurrently aligns the sequences and, to model evolutionary divergence, partitions them into subgroups that are hierarchically-arranged based upon correlated residue patterns. Auxiliary routines create PyMOL scripts to visualize the locations of correlated residues within available structures. Because these correlations likely arise from structural and biochemical constraints, they can help elucidate protein properties important for functional specificity. Comparing and contrasting sequence and structural features in this way may therefore suggest, in the light of published studies, plausible biological hypotheses for experimental investigation. We illustrate this approach with N-acetyltransferases.
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Affiliation(s)
- Andrew F. Neuwald
- Institute for Genome Sciences and Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, BioPark II, Room 617, Baltimore, MD, United States of America
- * E-mail:
| | - Stephen F. Altschul
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America
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17
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Dong X, Su X, Yu J, Liu J, Shi X, Pan Q, Yang J, Chen J, Li L, Cao H. Homology modeling and molecular dynamics simulation of the HIF2α degradation-related HIF2α-VHL complex. J Mol Graph Model 2016; 71:116-123. [PMID: 27902963 DOI: 10.1016/j.jmgm.2016.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 11/07/2016] [Accepted: 11/18/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Hypoxia-inducible factor 2 alpha (HIF2α), prolyl hydroxylase domain protein 2 (PHD2), and the von Hippel Lindau tumor suppressor protein (pVHL) are three principal proteins in the oxygen-sensing pathway. Under normoxic conditions, a conserved proline in HIF2α is hydroxylated by PHD2 in an oxygen-dependent manner, and then pVHL binds and promotes the degradation of HIF2α. However, the crystal structure of the HIF2α-pVHL complex has not yet been established, and this has limited research on the interaction between HIF and pVHL. Here, we constructed a structural model of a 23-residue HIF2α peptide (528-550)-pVHL-ElonginB-ElonginC complex by using homology modeling and molecular dynamics simulations. We also applied these methods to HIF2α mutants (HYP531PRO, F540L, A530 V, A530T, and G537R) to reveal structural defects that explain how these mutations weaken the interaction with pVHL. METHODS Homology modeling and molecular dynamics simulations were used to construct a three-dimensional (3D) structural model of the HIF2α-VHL complex. Subsequently, MolProbity, an active validation tool, was used to analyze the reliability of the model. Molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) and solvated interaction energy (SIE) methods were used to calculate the binding free energy between HIF2a and pVHL, and the stability of the simulation system was evaluated by using root mean square deviation (RMSD) analysis. We also determined the secondary structure of the system by using the definition of secondary structure of proteins (DSSP) algorithm. Finally, we investigated the structural significance of specific point mutations known to have clinical implications. RESULTS We established a reliable structural model of the HIF2α-pVHL complex, which is similar to the crystal structure of HIF1α in 1LQB. Furthermore, we compared the structural model of the HIF2α-pVHL complex and the HIF2α (HYP531P, F540L, A530V, A530T, and G537R)-pVHL mutants on the basis of RMSD, DSSP, binding free energy, and hydrogen bonding. The experimental data indicate that the stability of the structural model of the HIF2α-pVHL complex is higher than that of the mutants, consistently with clinical observations. CONCLUSIONS The structural model of the HIF2α-pVHL complex presented in this study enhances understanding of how HIF2α is captured by pVHL. Moreover, the important contact amino acids that we identified may be useful in the development of drugs to treat HIF2a-related diseases.
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Affiliation(s)
- Xiaotian Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Xiaoru Su
- Department of Laboratory Medicine, the Affiliated Hospital of Hangzhou Normal University, Hangzhou City 310015, China.
| | - Jiong Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Jingqi Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Xiaowei Shi
- Chu Kochen Honors College, Zhejiang University, 866 Yuhangtang Rd., Hangzhou City 310058, China.
| | - Qiaoling Pan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Jinfeng Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Jiajia Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
| | - Hongcui Cao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 79 Qingchun Road, Hangzhou City 310003, China.
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18
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Chiu SH, Xie L. Toward High-Throughput Predictive Modeling of Protein Binding/Unbinding Kinetics. J Chem Inf Model 2016; 56:1164-74. [PMID: 27159844 DOI: 10.1021/acs.jcim.5b00632] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One of the unaddressed challenges in drug discovery is that drug potency determined in vitro is not a reliable indicator of drug activity in vivo. Accumulated evidence suggests that in vivo activity is more strongly correlated with the binding/unbinding kinetics than the equilibrium thermodynamics of protein-ligand interactions (PLIs). However, existing experimental and computational techniques are insufficient in studying the molecular details of kinetics processes of PLIs on a large scale. Consequently, we not only have limited mechanistic understanding of the kinetic processes but also lack a practical platform for high-throughput screening and optimization of drug leads on the basis of their kinetic properties. For the first time, we address this unmet need by integrating coarse-grained normal mode analysis with multitarget machine learning (MTML). To test our method, HIV-1 protease is used as a model system. We find that computational models based on the residue normal mode directionality displacement of PLIs can not only recapitulate the results from all-atom molecular dynamics simulations but also predict protein-ligand binding/unbinding kinetics accurately. When this is combined with energetic features, the accuracy of combined kon and koff prediction reaches 74.35%. Furthermore, our integrated model provides us with new insights into the molecular determinants of the kinetics of PLIs. We propose that the coherent coupling of conformational dynamics and thermodynamic interactions between the receptor and the ligand may play a critical role in determining the kinetic rate constants of PLIs. In conclusion, we demonstrate that residue normal mode directionality displacement can serve as a kinetic fingerprint to capture long-time-scale conformational dynamics of the binding/unbinding kinetics. When this is coupled with MTML, it is possible to screen and optimize compounds on the basis of their binding/unbinding kinetics in a high-throughput fashion. The further development of such computational tools will bridge one of the critical missing links between in vitro compound screening and in vivo drug activity.
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Affiliation(s)
- See Hong Chiu
- Department of Computer Science, The Graduate Center, The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States
| | - Lei Xie
- Department of Computer Science, The Graduate Center, The City University of New York , 365 Fifth Avenue, New York, New York 10016, United States.,Department of Computer Science, Hunter College, The City University of New York , 695 Park Avenue, New York, New York 10065, United States
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19
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Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016. [PMID: 24018324 DOI: 10.1016/b978-0-12-416596-0.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.
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20
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Stepanenko OV, Roginskii DO, Stepanenko OV, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and stability of recombinant bovine odorant-binding protein: III. Peculiarities of the wild type bOBP unfolding in crowded milieu. PeerJ 2016; 4:e1642. [PMID: 27114858 PMCID: PMC4841217 DOI: 10.7717/peerj.1642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/08/2016] [Indexed: 11/23/2022] Open
Abstract
Contrary to the majority of the members of the lipocalin family, which are stable monomers with the specific OBP fold (a β-barrel consisting of a 8-stranded anti-parallel β-sheet followed by a short α-helical segment, a ninth β-strand, and a disordered C-terminal tail) and a conserved disulfide bond, bovine odorant-binding protein (bOBP) does not have such a disulfide bond and forms a domain-swapped dimer that involves crossing the α-helical region from each monomer over the β-barrel of the other monomer. Furthermore, although natural bOBP isolated from bovine tissues exists as a stable domain-swapped dimer, recombinant bOBP has decreased dimerization potential and therefore exists as a mixture of monomeric and dimeric variants. In this article, we investigated the effect model crowding agents of similar chemical nature but different molecular mass on conformational stability of the recombinant bOBP. These experiments were conducted in order to shed light on the potential influence of model crowded environment on the unfolding-refolding equilibrium. To this end, we looked at the influence of PEG-600, PEG-4000, and PEG-12000 in concentrations of 80, 150, and 300 mg/mL on the equilibrium unfolding and refolding transitions induced in the recombinant bOBP by guanidine hydrochloride. We are showing here that the effect of crowding agents on the structure and conformational stability of the recombinant bOBP depends on the size of the crowder, with the smaller crowding agents being more effective in the stabilization of the bOBP native dimeric state against the guanidine hydrochloride denaturing action. This effect of the crowding agents is concentration dependent, with the high concentrations of the agents being more effective.
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Affiliation(s)
- Olga V. Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Denis O. Roginskii
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Olesya V. Stepanenko
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Irina M. Kuznetsova
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir N. Uversky
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine, University of South Florida, United States
| | - Konstantin K. Turoverov
- Laboratory of structural dynamics, stability and folding of proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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21
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Stepanenko OV, Roginskii DO, Stepanenko OV, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and stability of recombinant bovine odorant-binding protein: II. Unfolding of the monomeric forms. PeerJ 2016; 4:e1574. [PMID: 27114857 PMCID: PMC4841237 DOI: 10.7717/peerj.1574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/16/2015] [Indexed: 01/27/2023] Open
Abstract
In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities of the recombinant bOBP and its monomeric variants, the bOBP-Gly121+ mutant containing an additional glycine residue after the residue 121 of the bOBP, and the GCC-bOBP mutant obtained from the bOBP-Gly121+ form by introduction of the Trp64Cys/His155Cys double mutation to restore the canonical disulfide bond. We also analyzed the effect of the natural ligand binding on the conformational stabilities of these bOBP variants. Our data are consistent with the conclusion that the unfolding-refolding pathways of the recombinant bOBP and its mutant monomeric forms bOBP-Gly121+ and GCC-bOBP are similar and do not depend on the oligomeric status of the protein. This clearly shows that the information on the unfolding-refolding mechanism is encoded in the structure of the bOBP monomers. However, the process of the bOBP unfolding is significantly complicated by the formation of the domain-swapped dimer, and the rates of the unfolding-refolding reactions essentially depend on the conditions in which the protein is located.
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Affiliation(s)
- Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Denis O. Roginskii
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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22
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Stepanenko OV, Roginskii DO, Stepanenko OV, Kuznetsova IM, Uversky VN, Turoverov KK. Structure and stability of recombinant bovine odorant-binding protein: I. Design and analysis of monomeric mutants. PeerJ 2016; 4:e1933. [PMID: 27114880 PMCID: PMC4841250 DOI: 10.7717/peerj.1933] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/23/2016] [Indexed: 02/02/2023] Open
Abstract
Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and for being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and to understand the role of the domain swapping on maintaining the native structure of the protein, structural properties of the recombinant wild type bOBP and its mutant that cannot dimerize via the domain swapping were analyzed. We also looked at the effect of the disulfide bond by designing a monomeric bOBPs with restored disulfide bond which is conserved in other lipocalins. Finally, to understand which features in the microenvironment of the bOBP tryptophan residues play a role in the defining peculiarities of the intrinsic fluorescence of this protein we designed and investigated single-tryptophan mutants of the monomeric bOBP. Our analysis revealed that the insertion of the glycine after the residue 121 of the bOBP prevents domain swapping and generates a stable monomeric protein bOBP-Gly121+. We also show that the restored disulfide bond in the GCC-bOBP mutant leads to the noticeable stabilization of the monomeric structure. Structural and functional analysis revealed that none of the amino acid substitutions introduced to the bOBP affected functional activity of the protein and that the ligand binding leads to the formation of a more compact and stable state of the recombinant bOBP and its mutant monomeric forms. Finally, analysis of the single-tryptophan mutants of the monomeric bOBP gave us a unique possibility to find peculiarities of the microenvironment of tryptophan residues which were not previously described.
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Affiliation(s)
- Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Denis O Roginskii
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science , St. Petersburg , Russia
| | - Vladimir N Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Science, St. Petersburg, Russia; Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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23
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Modulation of Erythrocyte Plasma Membrane Redox System Activity by Curcumin. Biochem Res Int 2016; 2016:6025245. [PMID: 26904287 PMCID: PMC4745374 DOI: 10.1155/2016/6025245] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/31/2023] Open
Abstract
Plasma membrane redox system (PMRS) is an electron transport chain system ubiquitously present throughout all cell types. It transfers electron from intracellular substrates to extracellular acceptors for regulation of redox status. Curcumin, isolated from Curcuma longa, has modulatory effects on cellular physiology due to its membrane interaction ability and antioxidant potential. The present study investigates the effect of curcumin on PMRS activity of erythrocytes isolated from Wistar rats in vitro and in vivo and validated through an in silico docking simulation study using Molegro Virtual Docker (MVD). Effects of curcumin were also evaluated on level of glutathione (GSH) and the oxidant potential of plasma measured in terms of plasma ferric equivalent oxidative potentials (PFEOP). Results show that curcumin significantly (p < 0.01) downregulated the PMRS activity in a dose-dependent manner. Molecular docking results suggest that curcumin interacts with amino acids at the active site cavity of cytochrome b 5 reductase, a key constituent of PMRS. Curcumin also increased the GSH level in erythrocytes and plasma while simultaneously decreasing the oxidant potential (PFEOP) of plasma. Altered PMRS activity and redox status are associated with the pathophysiology of several health complications including aging and diabetes; hence, the above finding may explain part of the role of curcumin in health beneficial effects.
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24
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Stepanenko OV, Baloban M, Bublikov GS, Shcherbakova DM, Stepanenko OV, Turoverov KK, Kuznetsova IM, Verkhusha VV. Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes. Sci Rep 2016; 6:18750. [PMID: 26725513 PMCID: PMC4698714 DOI: 10.1038/srep18750] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/25/2015] [Indexed: 01/02/2023] Open
Abstract
Fluorescent proteins (FPs) engineered from bacterial phytochromes attract attention as probes for in vivo imaging due to their near-infrared (NIR) spectra and use of available in mammalian cells biliverdin (BV) as chromophore. We studied spectral properties of the iRFP670, iRFP682 and iRFP713 proteins and their mutants having Cys residues able to bind BV either in both PAS (Cys15) and GAF (Cys256) domains, in one of these domains, or without these Cys residues. We show that the absorption and fluorescence spectra and the chromophore binding depend on the location of the Cys residues. Compared with NIR FPs in which BV covalently binds to Cys15 or those that incorporate BV noncovalently, the proteins with BV covalently bound to Cys256 have blue-shifted spectra and higher quantum yield. In dimeric NIR FPs without Cys15, the covalent binding of BV to Сys256 in one monomer allosterically inhibits the covalent binding of BV to the other monomer, whereas the presence of Cys15 allosterically promotes BV binding to Cys256 in both monomers. The NIR FPs with both Cys residues have the narrowest blue-shifted spectra and the highest quantum yield. Our analysis resulted in the iRFP713/Val256Cys protein with the highest brightness in mammalian cells among available NIR FPs.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Mikhail Baloban
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Grigory S Bublikov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation.,Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, St. Petersburg 194064, Russian Federation
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
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25
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Abstract
The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.
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Affiliation(s)
- Bart van Beusekom
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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26
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Kim JK, Won CI, Cha J, Lee K, Kim DS. Optimal ligand descriptor for pocket recognition based on the Beta-shape. PLoS One 2015; 10:e0122787. [PMID: 25835497 PMCID: PMC4383629 DOI: 10.1371/journal.pone.0122787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Structure-based virtual screening is one of the most important and common computational methods for the identification of predicted hit at the beginning of drug discovery. Pocket recognition and definition is frequently a prerequisite of structure-based virtual screening, reducing the search space of the predicted protein-ligand complex. In this paper, we present an optimal ligand shape descriptor for a pocket recognition algorithm based on the beta-shape, which is a derivative structure of the Voronoi diagram of atoms. We investigate six candidates for a shape descriptor for a ligand using statistical analysis: the minimum enclosing sphere, three measures from the principal component analysis of atoms, the van der Waals volume, and the beta-shape volume. Among them, the van der Waals volume of a ligand is the optimal shape descriptor for pocket recognition and best tunes the pocket recognition algorithm based on the beta-shape for efficient virtual screening. The performance of the proposed algorithm is verified by a benchmark test.
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Affiliation(s)
- Jae-Kwan Kim
- Voronoi Diagram Research Center, Hanyang University, Seoul, Korea
| | - Chung-In Won
- Voronoi Diagram Research Center, Hanyang University, Seoul, Korea
| | - Jehyun Cha
- School of Mechanical Engineering, Hanyang University, Seoul, Korea
| | - Kichun Lee
- Department of Industrial Engineering, Hanyang University, Seoul, Korea
| | - Deok-Soo Kim
- Voronoi Diagram Research Center, Hanyang University, Seoul, Korea
- School of Mechanical Engineering, Hanyang University, Seoul, Korea
- * E-mail:
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27
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Abstract
The role of proteins as very effective immunogens for the generation of antibodies is indisputable. Nevertheless, cases in which protein usage for antibody production is not feasible or convenient compelled the creation of a powerful alternative consisting of synthetic peptides. Synthetic peptides can be modified to obtain desired properties or conformation, tagged for purification, isotopically labeled for protein quantitation or conjugated to immunogens for antibody production. The antibodies that bind to these peptides represent an invaluable tool for biological research and discovery. To better understand the underlying mechanisms of antibody-antigen interaction here we present a pipeline developed by us to structurally classify immunoglobulin antigen binding sites and to infer key sequence residues and other variables that have a prominent role in each structural class.
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Affiliation(s)
- Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
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28
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Stepanenko OV, Fonin AV, Stepanenko OV, Staiano M, D'Auria S, Kuznetsova IM, Turoverov KK. Tryptophan residue of the D-galactose/D-glucose-binding protein from E. Coli localized in its active center does not contribute to the change in intrinsic fluorescence upon glucose binding. J Fluoresc 2014; 25:87-94. [PMID: 25501855 DOI: 10.1007/s10895-014-1483-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/25/2014] [Indexed: 11/24/2022]
Abstract
Changes of the characteristics of intrinsic tryptophan fluorescence of the wild type of D-galactose/D-glucose-binding protein from Escherichia coli (GGBPwt) induced by D-glucose binding were examined by the intrinsic UV-fluorescence of proteins, circular dyhroism in the near-UV region, and acrylamide-induced fluorescence quenching. The analysis of the different characteristics of GGBPwt and its mutant form GGBP-W183A together with the analysis of the microenvironment of tryptophan residues of GGBPwt revealed that Trp 183, which is directly involved in sugar binding, has the least influence on the provoked by D-glucose blue shift and increase in the intensity of protein intrinsic fluorescence in comparison with other tryptophan residues of GGBP.
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Affiliation(s)
- Olga V Stepanenko
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky ave., 4, 194064, St. Petersburg, Russia
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29
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Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA. Small molecule annotation for the Protein Data Bank. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau116. [PMID: 25425036 PMCID: PMC4243272 DOI: 10.1093/database/bau116] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors.
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Affiliation(s)
- Sanchayita Sen
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Jasmine Young
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - John M Berrisford
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Minyu Chen
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Matthew J Conroy
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Shuchismita Dutta
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Luigi Di Costanzo
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Guanghua Gao
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Sutapa Ghosh
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Brian P Hudson
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Reiko Igarashi
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Yumiko Kengaku
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Yuhe Liang
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Ezra Peisach
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Irina Persikova
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Abhik Mukhopadhyay
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Buvaneswari Coimbatore Narayanan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Gaurav Sahni
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Junko Sato
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Monica Sekharan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Chenghua Shao
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Lihua Tan
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
| | - Marina A Zhuravleva
- Protein Data Bank in Europe (PDBe), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, RCSB Protein Data Bank (RCSB PDB), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA and Protein Data Bank Japan (PDBj), Osaka University, Osaka, Japan
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30
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Fazio VJ, Peat TS, Newman J. A drunken search in crystallization space. Acta Crystallogr F Struct Biol Commun 2014; 70:1303-11. [PMID: 25286930 PMCID: PMC4188070 DOI: 10.1107/s2053230x1401841x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/12/2014] [Indexed: 11/10/2022] Open
Abstract
The REMARK280 field of the Protein Data Bank is the richest open source of successful crystallization information. The REMARK280 field is optional and currently uncurated, so significant effort needs to be applied to extract reliable data. There are well over 15 000 crystallization conditions available commercially from 12 different vendors. After putting the PDB crystallization information and the commercial cocktail data into a consistent format, these data are used to extract information about the overlap between the two sets of crystallization conditions. An estimation is made as to which commercially available conditions are most appropriate for producing well diffracting crystals by looking at which commercial conditions are found unchanged (or almost unchanged) in the PDB. Further analyses include which commercial kits are the most appropriate for shotgun or more traditional approaches to crystallization screening. This analysis suggests that almost 40% of the crystallization conditions found currently in the PDB are identical or very similar to a commercial condition.
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Affiliation(s)
- Vincent J. Fazio
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S. Peat
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Janet Newman
- Manufacturing Flagship, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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31
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Gallina AM, Bork P, Bordo D. Structural analysis of protein-ligand interactions: the binding of endogenous compounds and of synthetic drugs. J Mol Recognit 2014; 27:65-72. [PMID: 24436123 DOI: 10.1002/jmr.2332] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 08/23/2013] [Accepted: 10/07/2013] [Indexed: 01/30/2023]
Abstract
The large number of macromolecular structures deposited with the Protein Data Bank (PDB) describing complexes between proteins and either physiological compounds or synthetic drugs made it possible a systematic analysis of the interactions occurring between proteins and their ligands. In this work, the binding pockets of about 4000 PDB protein-ligand complexes were investigated and amino acid and interaction types were analyzed. The residues observed with lowest frequency in protein sequences, Trp, His, Met, Tyr, and Phe, turned out to be the most abundant in binding pockets. Significant differences between drug-like and physiological compounds were found. On average, physiological compounds establish with respect to drugs about twice as many hydrogen bonds with protein atoms, whereas drugs rely more on hydrophobic interactions to establish target selectivity. The large number of PDB structures describing homologous proteins in complex with the same ligand made it possible to analyze the conservation of binding pocket residues among homologous protein structures bound to the same ligand, showing that Gly, Glu, Arg, Asp, His, and Thr are more conserved than other amino acids. Also in the cases in which the same ligand is bound to unrelated proteins, the binding pockets showed significant conservation in the residue types. In this case, the probability of co-occurrence of the same amino acid type in the binding pockets could be up to thirteen times higher than that expected on a random basis. The trends identified in this study may provide an useful guideline in the process of drug design and lead optimization.
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Affiliation(s)
- Anna M Gallina
- IRCCS Az. Ospedaliera Universitaria S. Martino - IST, National Cancer Research Institute, Largo R. Benzi, 10, 16132, Genova, Italy
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32
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Povarova OI, Uversky VN, Kuznetsova IM, Turoverov KK. Actinous enigma or enigmatic actin: Folding, structure, and functions of the most abundant eukaryotic protein. INTRINSICALLY DISORDERED PROTEINS 2014; 2:e34500. [PMID: 28232879 PMCID: PMC5314930 DOI: 10.4161/idp.34500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 02/06/2023]
Abstract
Being the most abundant protein of the eukaryotic cell, actin continues to keep its secrets for more than 60 years. Everything about this protein, its structure, functions, and folding, is mysteriously counterintuitive, and this review represents an attempt to solve some of the riddles and conundrums commonly found in the field of actin research. In fact, actin is a promiscuous binder with a wide spectrum of biological activities. It can exist in at least three structural forms, globular, fibrillar, and inactive (G-, F-, and I-actin, respectively). G-actin represents a thermodynamically instable, quasi-stationary state, which is formed in vivo as a result of the energy-intensive, complex posttranslational folding events controlled and driven by cellular folding machinery. The G-actin structure is dependent on the ATP and Mg2+ binding (which in vitro is typically substituted by Ca2+) and protein is easily converted to the I-actin by the removal of metal ions and by action of various denaturing agents (pH, temperature, and chemical denaturants). I-actin cannot be converted back to the G-form. Foldable and “natively folded” forms of actin are always involved in interactions either with the specific protein partners, such as Hsp70 chaperone, prefoldin, and the CCT chaperonin during the actin folding in vivo or with Mg2+ and ATP as it takes place in the G-form. We emphasize that the solutions for the mysteries of actin multifunctionality, multistructurality, and trapped unfolding can be found in the quasi-stationary nature of this enigmatic protein, which clearly possesses many features attributed to both globular and intrinsically disordered proteins.
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Affiliation(s)
- Olga I Povarova
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia
| | - Vladimir N Uversky
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa, FL USA; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino, Russia; Biology Department; Faculty of Science; King Abdulaziz University; Jeddah, Kingdom of Saudi Arabia
| | - Irina M Kuznetsova
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; St. Petersburg State Polytechnical University; St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of structural dynamics, stability, and folding of proteins; Institute of Cytology; Russian Academy of Sciences; St. Petersburg, Russia; St. Petersburg State Polytechnical University; St. Petersburg, Russia
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33
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Wiederstein M, Gruber M, Frank K, Melo F, Sippl MJ. Structure-based characterization of multiprotein complexes. Structure 2014; 22:1063-70. [PMID: 24954616 PMCID: PMC4087271 DOI: 10.1016/j.str.2014.05.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 01/22/2023]
Abstract
Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.
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Affiliation(s)
- Markus Wiederstein
- Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria.
| | - Markus Gruber
- Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Karl Frank
- Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - Francisco Melo
- Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Alameda 340, 8320000 Santiago, Chile; Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotherapy, 8320000 Santiago, Chile
| | - Manfred J Sippl
- Division of Structural Biology & Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
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34
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Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 116:187-93. [PMID: 24931138 DOI: 10.1016/j.pbiomolbio.2014.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 05/17/2014] [Indexed: 11/16/2022]
Abstract
Protein interactions have evolved into highly precise and regulated networks adding an immense layer of complexity to cellular systems. The most accurate atomistic description of protein binding sites can be obtained directly from structures of protein complexes. The availability of structurally characterized protein interfaces significantly improves our understanding of interactomes, and the progress in structural characterization of protein-protein interactions (PPIs) can be measured by calculating the structural coverage of protein domain families. We analyze the coverage of protein domain families (defined according to CDD and Pfam databases) by structures, structural protein-protein complexes and unique protein binding sites. Structural PPI coverage of currently available protein families is about 30% without any signs of saturation in coverage growth dynamics. Given the current growth rates of domain databases and structural PPI deposition, complete domain coverage with PPIs is not expected in the near future. As a result of this study we identify families without any protein-protein interaction evidence (listed on a supporting website http://www.ncbi.nlm.nih.gov/Structure/ibis/coverage/) and propose them as potential targets for structural studies with a focus on protein interactions.
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Affiliation(s)
- Alexander Goncearenco
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Benjamin A Shoemaker
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Dachuan Zhang
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Alexey Sarychev
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States
| | - Anna R Panchenko
- Computational Biology Branch of the National Center for Biotechnology Information in Bethesda, Maryland, United States.
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35
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Stepanenko OV, Bublikov GS, Stepanenko OV, Shcherbakova DM, Verkhusha VV, Turoverov KK, Kuznetsova IM. A knot in the protein structure - probing the near-infrared fluorescent protein iRFP designed from a bacterial phytochrome. FEBS J 2014; 281:2284-98. [PMID: 24628916 DOI: 10.1111/febs.12781] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/18/2014] [Accepted: 03/11/2014] [Indexed: 11/30/2022]
Abstract
The possibility of engineering near-infrared fluorescent proteins and biosensors from bacterial phytochrome photoreceptors (BphPs) has led to substantial interest in this family of proteins. The near-infrared fluorescent proteins have allowed non-invasive bio-imaging of deep tissues and whole organs in living animals. BphPs and derived near-infrared fluorescent proteins contain a structural element, called a knot, in their polypeptide chains. The formation of knot structures in proteins was refuted for a long time. Here, we studied the denaturation and renaturation processes of the near-infrared fluorescent probe iRFP, engineered from RpBphP2, which utilizes a heme-derived tetrapyrrole compound biliverdin as a chromophore. iRFP contains a unique figure-of-eight knot. The denaturation and renaturation curves of the iRFP apoform coincided well, suggesting efficient refolding. However, the iRFP holoform exhibited irreversible unfolding and aggregation associated with the bound chromophore. The knot structure in the apoform did not prevent subsequent binding of biliverdin, resulting in the functional iRFP holoform. We suggest that the irreversibility of protein unfolding is caused by post-translational protein modifications, such as chromophore binding, rather than the presence of the knot. These results are essential for future design of BphP-based near-infrared probes, and add important features to our knowledge of protein folding.
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Affiliation(s)
- Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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36
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Dasgupta B, Dey S, Chakrabarti P. Water and side-chain embedded π-turns. Biopolymers 2014; 101:441-53. [PMID: 23996674 DOI: 10.1002/bip.22401] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/24/2013] [Accepted: 08/26/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Bhaskar Dasgupta
- Department of Biochemistry; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata West Bengal 700 054 India
| | - Sucharita Dey
- Bioinformatics Centre; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata West Bengal 700 054 India
| | - Pinak Chakrabarti
- Department of Biochemistry; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata West Bengal 700 054 India
- Bioinformatics Centre; Bose Institute; P-1/12 CIT Scheme VIIM Kolkata West Bengal 700 054 India
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37
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Stepanenko OV, Stepanenko OV, Staiano M, Kuznetsova IM, Turoverov KK, D’Auria S. The quaternary structure of the recombinant bovine odorant-binding protein is modulated by chemical denaturants. PLoS One 2014; 9:e85169. [PMID: 24409322 PMCID: PMC3883677 DOI: 10.1371/journal.pone.0085169] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/22/2013] [Indexed: 11/30/2022] Open
Abstract
A large group of odorant-binding proteins (OBPs) has attracted great scientific interest as promising building blocks in constructing optical biosensors for dangerous substances, such as toxic and explosive molecules. Native tissue-extracted bovine OBP (bOBP) has a unique dimer folding pattern that involves crossing the α-helical domain in each monomer over the other monomer’s β-barrel. In contrast, recombinant bOBP maintaining the high level of stability inherent to native tissue bOBP is produced in a stable native-like state with a decreased tendency for dimerization and is a mixture of monomers and dimers in a buffered solution. This work is focused on the study of the quaternary structure and the folding-unfolding processes of the recombinant bOBP in the absence and in the presence of guanidine hydrochloride (GdnHCl). Our results show that the recombinant bOBP native dimer is only formed at elevated GdnHCl concentrations (1.5 M). This process requires re-organizing the protein structure by progressing through the formation of an intermediate state. The bOBP dimerization process appears to be irreversible and it occurs before the protein unfolds. Though the observed structural changes for recombinant bOBP at pre-denaturing GdnHCl concentrations show a local character and the overall protein structure is maintained, such changes should be considered where the protein is used as a sensitive element in a biosensor system.
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Affiliation(s)
- Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Olesya V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Maria Staiano
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia
- St. Petersburg State Polytechnical University, St. Petersburg, Russia
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology of the Russian Academy of Sciences, St. Petersburg, Russia
- * E-mail: (KKT); (SD)
| | - Sabato D’Auria
- Laboratory for Molecular Sensing, IBP-CNR, Naples, Italy
- * E-mail: (KKT); (SD)
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38
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Fatima M, Kesharwani RK, Misra K, Rizvi SI. Protective effect of theaflavin on erythrocytes subjected to in vitro oxidative stress. Biochem Res Int 2013; 2013:649759. [PMID: 24455262 PMCID: PMC3880739 DOI: 10.1155/2013/649759] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/01/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
Antioxidant and free radical scavenging effect of black tea theaflavins has been shown in many epidemiological studies. In the present work we report the protective mechanism of tea theaflavins on biomarkers of oxidative stress, which are elevated during stress conditions. We hereby report the in vitro effect of theaflavins on erythrocyte malondialdehyde (MDA), intracellular reduced glutathione (GSH), and plasma membrane redox system (PMRS) of rats. The effect of theaflavin on PMRS has also been validated through an in silico docking simulation study using Molegro Virtual Docker (MVD). We report that theaflavins show significant protection to erythrocyte against oxidative stress induced by tert-butyl hydroperoxide (t-BHP). The findings suggest a possible protective role of theaflavins as antioxidant.
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Affiliation(s)
- Mahejabeen Fatima
- Department of Biochemistry, University of Allahabad, Allahabad 211002, India
| | - Rajesh Kumar Kesharwani
- Division of Applied Science & Indo-Russian Center for Biotechnology (IRCB), Indian Institute of Information Technology, Allahabad 211012, India
| | - Krishna Misra
- Division of Applied Science & Indo-Russian Center for Biotechnology (IRCB), Indian Institute of Information Technology, Allahabad 211012, India
| | - Syed Ibrahim Rizvi
- Department of Biochemistry, University of Allahabad, Allahabad 211002, India
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39
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Kizjakina K, Tanner JJ, Sobrado P. Targeting UDP-galactopyranose mutases from eukaryotic human pathogens. Curr Pharm Des 2013; 19:2561-73. [PMID: 23116395 PMCID: PMC3624792 DOI: 10.2174/1381612811319140007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 10/30/2012] [Indexed: 12/19/2022]
Abstract
UDP-Galactopyranose mutase (UGM) is a unique flavin-dependent enzyme that catalyzes the conversion of UDP-galactopyranose(UDP-Galp) to UDP-galactofuranose (UDP-Galf). The product of this reaction is the precursor to Galf, a major component of the cell wall and of cell surface glycoproteins and glycolipids in many eukaryotic and prokaryotic human pathogens. The function of UGM is important in the virulence of fungi, parasites, and bacteria. Its role in virulence and its absence in humans suggest that UGM is an ideal drug target. Significant structural and mechanistic information has been accumulated on the prokaryotic UGMs; however, in the past few years the research interest has shifted to UGMs from eukaryotic human pathogens such as fungi and protozoan parasites. It has become clear that UGMs from prokaryotic and eukaryotic organisms have different structural and mechanistic features. The amino acid sequence identity between these two classes of enzymes is low, resulting in differences in oligomeric states, substrate binding, active site flexibility, and interaction with redox partners. However, the unique role of the flavin cofactor in catalysis is conserved among this enzyme family. In this review, recent findings on eukaryotic UGMs are discussed and presented in comparison with prokaryotic UGMs.
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Affiliation(s)
- Karina Kizjakina
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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40
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Janda JO, Meier A, Merkl R. CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. ACTA ACUST UNITED AC 2013; 29:3029-35. [PMID: 24048358 DOI: 10.1093/bioinformatics/btt519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The precise identification of functionally and structurally important residues of a protein is still an open problem, and state-of-the-art classifiers predict only one or at most two different categories. RESULT We have implemented the classifier CLIPS-4D, which predicts in a mutually exclusively manner a role in catalysis, ligand-binding or protein stability for each residue-position of a protein. Each prediction is assigned a P-value, which enables the statistical assessment and the selection of predictions with similar quality. CLIPS-4D requires as input a multiple sequence alignment and a 3D structure of one protein in PDB format. A comparison with existing methods confirmed state-of-the-art prediction quality, even though CLIPS-4D classifies more specifically than other methods. CLIPS-4D was implemented as a multiclass support vector machine, which exploits seven sequence-based and two structure-based features, each of which was shown to contribute to classification quality. The classification of ligand-binding sites profited most from the 3D features, which were the assessment of the solvent accessible surface area and the identification of surface pockets. In contrast, five additionally tested 3D features did not increase the classification performance achieved with evolutionary signals deduced from the multiple sequence alignment.
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Affiliation(s)
- Jan-Oliver Janda
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040 Regensburg, Germany and Faculty of Mathematics and Computer Science, University of Hagen, D-58084 Hagen, Germany
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41
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Barba M, Glansdorff N, Labedan B. Evolution of Cyclic Amidohydrolases: A Highly Diversified Superfamily. J Mol Evol 2013; 77:70-80. [DOI: 10.1007/s00239-013-9580-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/16/2013] [Indexed: 11/29/2022]
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42
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Woollett B, Whitmore L, Janes RW, Wallace BA. ValiDichro: a website for validating and quality control of protein circular dichroism spectra. Nucleic Acids Res 2013; 41:W417-21. [PMID: 23625965 PMCID: PMC3977657 DOI: 10.1093/nar/gkt287] [Citation(s) in RCA: 11] [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: 01/21/2013] [Revised: 03/26/2013] [Accepted: 03/31/2013] [Indexed: 11/13/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is widely used in structural biology as a technique for examining the structure, folding and conformational changes of proteins. A new server, ValiDichro, has been developed for checking the quality and validity of CD spectral data and metadata, both as an aid to data collection and processing and as a validation procedure for spectra to be included in publications. ValiDichro currently includes 25 tests for data completeness, consistency and quality. For each test that is done, not only is a validation report produced, but the user is also provided with suggestions for correcting or improving the data. The ValiDichro server is freely available at http://valispec.cryst.bbk.ac.uk/circularDichroism/ValiDichro/upload.html.
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Affiliation(s)
- Benjamin Woollett
- Institute of Structural and Molecular Biology, Birkbeck
College, University of London, London WC1E 7HX, UK and School of Biological and
Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Lee Whitmore
- Institute of Structural and Molecular Biology, Birkbeck
College, University of London, London WC1E 7HX, UK and School of Biological and
Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Robert W. Janes
- Institute of Structural and Molecular Biology, Birkbeck
College, University of London, London WC1E 7HX, UK and School of Biological and
Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology, Birkbeck
College, University of London, London WC1E 7HX, UK and School of Biological and
Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
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43
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Affiliation(s)
- S Parasuraman
- Department of Pharmacology, Jawaharlal Institute of Postgradute Medical Education and Research, Pondicherry, India
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Stepanenko OV, Stepanenko OV, Kuznetsova IM, Verkhusha VV, Turoverov KK. Beta-barrel scaffold of fluorescent proteins: folding, stability and role in chromophore formation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 302:221-78. [PMID: 23351712 DOI: 10.1016/b978-0-12-407699-0.00004-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review focuses on the current view of the interaction between the β-barrel scaffold of fluorescent proteins and their unique chromophore located in the internal helix. The chromophore originates from the polypeptide chain and its properties are influenced by the surrounding protein matrix of the β-barrel. On the other hand, it appears that a chromophore tightens the β-barrel scaffold and plays a crucial role in its stability. Furthermore, the presence of a mature chromophore causes hysteresis of protein unfolding and refolding. We survey studies measuring protein unfolding and refolding using traditional methods as well as new approaches, such as mechanical unfolding and reassembly of truncated fluorescent proteins. We also analyze models of fluorescent protein unfolding and refolding obtained through different approaches, and compare the results of protein folding in vitro to co-translational folding of a newly synthesized polypeptide chain.
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Affiliation(s)
- Olesya V Stepanenko
- Institute of Cytology of Russian Academy of Sciences, St. Petersburg, Russia
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45
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Designing, synthesis, and characterization of some novel coumarin derivatives as probable anticancer drugs. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0299-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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46
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Gallina AM, Bisignano P, Bergamino M, Bordo D. PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures. Bioinformatics 2012. [PMID: 23196990 DOI: 10.1093/bioinformatics/bts691] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. RESULTS The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database. AVAILABILITY Freely accessible at http://bioinformatics.istge.it/pli/.
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Affiliation(s)
- Anna Maria Gallina
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST-Istituto Nazionale Ricerca sul Cancro, 16132 Genova, Italy
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Distinct effects of guanidine thiocyanate on the structure of superfolder GFP. PLoS One 2012; 7:e48809. [PMID: 23144981 PMCID: PMC3492234 DOI: 10.1371/journal.pone.0048809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/05/2012] [Indexed: 11/22/2022] Open
Abstract
Having a high folding efficiency and a low tendency to aggregate, the superfolder GFP (sfGFP) offers a unique opportunity to study the folding of proteins that have a β-barrel topology. Here, we studied the unfolding–refolding of sfGFP that was induced by guanidine thiocyanate (GTC), which is a stronger denaturing agent than GdnHCl or urea. Structural perturbations of sfGFP were studied by spectroscopic methods (absorbance, fluorescence, and circular dichroism), by acrylamide quenching of tryptophan and green chromophore fluorescence, and by size-exclusion chromatography. Low concentrations of GTC (up to 0.1 M) induce subtle changes in the sfGFP structure. The pronounced changes in the visible absorption spectrum of sfGFP which are accompanied by a dramatic decrease in tryptophan and green chromophore fluorescence was recorded in the range 0–0.7 M GNC. These alterations of sfGFP characteristics that erroneously can be mixed up with appearance of intermediate state in fact have pure spectroscopic but not structural nature. Higher concentrations of GTC (from 0.7 to 1.7 M), induce a disruption of the sfGFP structure, that is manifested in simultaneous changes of all of the detected parameters. Full recovery of native properties of denaturated sfGFP was observed after denaturant removal. The refolding of sfGFP passes through the accumulation of the off-pathway intermediate state, in which inner alpha-helix and hence green chromophore and Trp57 are still not tuned up to (properly integrated into) the already formed β-barrel scaffold of protein. Incorporation of the chromophore in the β-barrel in the pathway of refolding and restoration of its ability to fluoresce occur in a narrow range of GTC concentrations from 1.0 to 0.7 M, and a correct insertion of Trp 57 occurs at concentrations ranging from 0.7 to 0 M GTC. These two processes determine the hysteresis of protein unfolding and refolding.
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Bernhardt J, Michalik S, Wollscheid B, Völker U, Schmidt F. Proteomics approaches for the analysis of enriched microbial subpopulations and visualization of complex functional information. Curr Opin Biotechnol 2012; 24:112-9. [PMID: 23141770 DOI: 10.1016/j.copbio.2012.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 09/28/2012] [Accepted: 10/09/2012] [Indexed: 02/05/2023]
Abstract
Advances in the separation of microbial subpopulations and in proteomics technologies have paved the way for the global molecular characterization of microbial cells that share common functional characteristics. Quantitative characterization of the dynamics of microbial proteomes enables an unprecedented view of the adaptive responses of microbes to environmental stimuli or during interaction with other species or host cells. However, the intrinsic complexity of such data requires sophisticated visualization methods for the display, mining, interpretation and efficient exploitation of these data resources. In this review, we discuss how new approaches in data visualization such as streamgraphs, network graphs or Voronoi treemaps are being used in the field to provide new insights into the functional complexity of microbial cells, populations and multispecies consortia.
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Affiliation(s)
- Jörg Bernhardt
- Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, D-17487 Greifswald, Germany
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Pérez-Cano L, Jiménez-García B, Fernández-Recio J. A protein-RNA docking benchmark (II): Extended set from experimental and homology modeling data. Proteins 2012; 80:1872-82. [DOI: 10.1002/prot.24075] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/28/2012] [Accepted: 03/30/2012] [Indexed: 12/13/2022]
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50
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Kesharwani RK, Singh DV, Misra K, Rizvi SI. Plant polyphenols as electron donors for erythrocyte plasma membrane redox system: validation through in silico approach. Org Med Chem Lett 2012; 2:12. [PMID: 22475026 PMCID: PMC3355021 DOI: 10.1186/2191-2858-2-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Accepted: 04/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background The plasma membrane redox system (PMRS) has extensively been studied in erythrocytes. The PMRS plays an important role in maintaining plasma redox balance and provides a protective mechanism against oxidative stress. Earlier it was proposed that only NADH or NADPH provided reducing equivalents to PMRS; however, now it is acknowledged that some polyphenols also have the ability to donate reducing equivalents to PMRS. Methods Two different docking simulation softwares, Molegro Virtual Docker and Glide were used to study the interaction of certain plant polyphenols viz. quercetin, epigallocatechin gallate, catechin epicatechin and resveratrol with human erythroyte NADH-cytochrome b5 reductase, which is a component of PMRS and together with the identification of minimum pharmacophoric feature using Pharmagist. Results The derived common minimum pharmacophoric features show the presence of minimum bioactive component in all the selected polyphenols. Our results confirm wet lab findings which show that these polyphenols have the ability to interact and donate protons to the Human NADH-cytochrome b5 reductase. Conclusion With the help of these comparative results of docking simulation and pharmacophoric features, novel potent molecules can be designed with higher efficacy for activation of the PMRS system.
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