1
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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2
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Carugo OI. Chalcogen bonds formed by protein sulfur atoms in proteins. A survey of high-resolution structures deposited in the protein data bank. J Biomol Struct Dyn 2023; 41:9576-9582. [PMID: 36342326 DOI: 10.1080/07391102.2022.2143427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/30/2022] [Indexed: 11/09/2022]
Abstract
The presence of chalcogen bonds in native proteins was investigated on a non-redundant and high-resolution (≤ 1 Angstrom) set of protein crystal structures deposited in the Protein Data Bank. It was observed that about one half of the sulfur atoms of methionines and disulfide bridges from chalcogen bonds with nucleophiles (oxygen and sulfur atoms, and aromatic rings). This suggests that chalcogen bonds are a non-bonding interaction important for protein stability. Quite numerous chalcogen bonds involve water molecules. Interestingly, in the case of disulfide bridges, chalcogen bonds have a marked tendency to occur along the S-S bond extension rather than along the C-S bond extension. Additionally, it has been observed that closer residues have a higher probability of being connected by a chalcogen bonds, while the secondary structure of the two residues connected by a chalcogen bond do not correlate with its formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oliviero Italo Carugo
- Department of Chemistry, University of Pavia, Pavia, Italy
- Department of Structural and Computational Biology, Max Perutz Labs University of Vienna, Vienna, Austria
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3
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Crine SL, Acharya KR. Molecular basis of C-mannosylation - a structural perspective. FEBS J 2022; 289:7670-7687. [PMID: 34741587 DOI: 10.1111/febs.16265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/22/2021] [Accepted: 11/04/2021] [Indexed: 01/14/2023]
Abstract
The structural and functional diversity of proteins can be enhanced by numerous post-translational modifications. C-mannosylation is a rare form of glycosylation consisting of a single alpha or beta D-mannopyranose forming a carbon-carbon bond with the pyrrole ring of a tryptophan residue. Despite first being discovered in 1994, C-mannosylation is still poorly understood and 3D structures are available for only a fraction of the total predicted C-mannosylated proteins. Here, we present the first comprehensive review of C-mannosylated protein structures by analysing the data for all 10 proteins with C-mannosylation/s deposited in the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB). We analysed in detail the WXXW/WXXWXXW consensus motif and the highly conserved pair of arginine residues in thrombospondin type 1 repeat C-mannosylation sites or homologous arginine residues in other domains. Furthermore, we identified a conserved PXP sequence C-terminal of the C-mannosylation site. The PXP motif forms a tight turn region in the polypeptide chain and its universal conservation in C-mannosylated protein is worthy of further experimental study. The stabilization of C-mannopyranosyl groups was demonstrated through hydrogen bonding with arginine and other charged or polar amino acids. Where possible, the structural findings were linked to other functional studies demonstrating the role of C-mannosylation in protein stability, secretion or function. With the current technological advances in structural biology, we hope to see more progress in the study of C-mannosylation that may correspond to discoveries of novel C-mannosylation pathways and functions with implications for human health and biotechnology.
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Affiliation(s)
- Samuel L Crine
- Department of Biology and Biochemistry, University of Bath, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, UK
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4
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Varadi M, Anyango S, Appasamy SD, Armstrong D, Bage M, Berrisford J, Choudhary P, Bertoni D, Deshpande M, Leines GD, Ellaway J, Evans G, Gaborova R, Gupta D, Gutmanas A, Harrus D, Kleywegt GJ, Bueno WM, Nadzirin N, Nair S, Pravda L, Afonso MQL, Sehnal D, Tanweer A, Tolchard J, Abrams C, Dunlop R, Velankar S. PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education. Protein Sci 2022; 31:e4439. [PMID: 36173162 PMCID: PMC9517934 DOI: 10.1002/pro.4439] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe‐KB; pdbekb.org), we provide data, data‐access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
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Affiliation(s)
- Mihaly Varadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Stephen Anyango
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sri Devan Appasamy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - David Armstrong
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Marcus Bage
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - John Berrisford
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Preeti Choudhary
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Damian Bertoni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Mandar Deshpande
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Grisell Diaz Leines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Joseph Ellaway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Genevieve Evans
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Romana Gaborova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Deepti Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Aleksandras Gutmanas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Deborah Harrus
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | | | - Nurul Nadzirin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sreenath Nair
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Lukas Pravda
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | | | - David Sehnal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton.,CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ahsan Tanweer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - James Tolchard
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Charlotte Abrams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Roisin Dunlop
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
| | - Sameer Velankar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton
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5
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Wang G, Zhai YJ, Xue ZZ, Xu YY. Improving Protein Subcellular Location Classification by Incorporating Three-Dimensional Structure Information. Biomolecules 2021; 11:biom11111607. [PMID: 34827605 PMCID: PMC8615982 DOI: 10.3390/biom11111607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
The subcellular locations of proteins are closely related to their functions. In the past few decades, the application of machine learning algorithms to predict protein subcellular locations has been an important topic in proteomics. However, most studies in this field used only amino acid sequences as the data source. Only a few works focused on other protein data types. For example, three-dimensional structures, which contain far more functional protein information than sequences, remain to be explored. In this work, we extracted various handcrafted features to describe the protein structures from physical, chemical, and topological aspects, as well as the learned features obtained by deep neural networks. We then used these features to classify the protein subcellular locations. Our experimental results demonstrated that some of these structural features have a certain effect on the protein location classification, and can help improve the performance of sequence-based location predictors. Our method provides a new view for the analysis of protein spatial distribution, and is anticipated to be used in revealing the relationships between protein structures and functions.
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Affiliation(s)
- Ge Wang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; (G.W.); (Z.-Z.X.)
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
| | - Yu-Jia Zhai
- Guangzhou Women and Children’s Medical Center, Department of Pharmacy, Guangzhou Medical University, Guangzhou 510623, China;
| | - Zhen-Zhen Xue
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; (G.W.); (Z.-Z.X.)
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
- Paul C. Lauterbur Research Center for Biomedical Imaging, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ying-Ying Xu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China; (G.W.); (Z.-Z.X.)
- Guangdong Provincial Key Laboratory of Medical Imaging Processing, Southern Medical University, Guangzhou 510515, China
- Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
- Correspondence: ; Tel.: +86-020-62789343
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6
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Abstract
Our protein block (PB) sequence database PDB-2-PBv1.0 provides PB sequences and dihedral angles for 74,297 protein structures comprising of 103,252 protein chains of Protein Data Bank (PDB) as on 2011. Since there are a lot of practical applications of PB and also as the size of PDB database increases, it becomes necessary to provide the PB sequences for all PDB protein structures. The current updated PDB-2-PBv3.0 contains PB sequences for 147,602 PDB structures comprising of 400,355 protein chains as on October 2019. When compared to our previous version PDB-2-PBv1.0, the current PDB-2-PBv3.0 contains 2- and 4-fold increase in the number of protein structures and chains, respectively. Notably, it provides PB information for any protein chain, regardless of the missing atom records of protein structure data in PDB. It includes protein interaction information with DNA and RNA along with their corresponding functional classes from Nucleic Acid Database (NDB) and PDB. Now, the updated version allows the user to download multiple PB records by parameter search and/or by a given list. This database is freely accessible at http://bioinfo.bdu.ac.in/pb3.
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Affiliation(s)
- Muthuvel Prasath Karuppasamy
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Suresh Venkateswaran
- Department of Paediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, GA, USA
| | - Parthasarathy Subbiah
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
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7
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Carugo O. Lithium-Protein Interactions: Analysis of Lithium-Containing Protein Crystal Structures Deposited in the Protein Data Bank. Protein Pept Lett 2020; 27:763-769. [PMID: 32133946 DOI: 10.2174/0929866527666200305144447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/19/2019] [Accepted: 01/09/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Despite the fact that lithium is not a biologically essential metallic element, its pharmacological properties are well known and human exposure to lithium is increasingly possible because of its used in aerospace industry and in batteries. OBJECTIVE Lithium-protein interactions are therefore interesting and the surveys of the structures of lithium-protein complexes is described in this paper. METHODS A high quality non-redundant set of lithium containing protein crystal structures was extracted from the Protein Data Bank and the stereochemistry of the lithium first coordination sphere was examined in detail. RESULTS Four main observations were reported: (i) lithium interacts preferably with oxygen atoms; (ii) preferably with side-chain atoms; (iii) preferably with Asp or Glu carboxylates; (iv) the coordination number tends to be four with stereochemical parameters similar to those observed in small molecules containing lithium. CONCLUSION Although structural information on lithium-protein, available from the Protein Data Bank, is relatively scarce, these trends appears to be so clear that one may suppose that they will be confirmed by further data that will join the Protein Data Bank in the future.
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8
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Basati G, Saffari-Chaleshtori J, Abbaszadeh S, Asadi-Samani M, Ashrafi-Dehkordi K. Molecular Dynamics Mechanisms of the Inhibitory Effects of Abemaciclib, Hymenialdisine, and Indirubin on CDK-6. Curr Drug Res Rev 2019; 11:135-141. [PMID: 31875784 DOI: 10.2174/2589977511666191018180001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/21/2019] [Accepted: 09/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cyclin-Dependent Kinases-6 (CDK-6) is a serine/threonine protein kinase with regular activity in the cell cycle. Some inhibitors, such as abemaciclib, hymenialdisine, and indirubin, cause cell arrest by decreasing its activity. OBJECTIVES The purpose of this study was to evaluate the Molecular Dynamic (MD) effects of abemaciclib, hymenialdisine, and indirubin on the structure of CDK-6. METHODS The PDB file of CDK-6 was obtained from the Protein Data Bank (http://www.rcsb.org). After the simulation of CDK-6 in the Gromacs software, 200 stages of molecular docking were run on CDK-6 in the presence of the inhibitors using AutoDock 4.2. The simulation of CDK-6 in the presence of inhibitors was performed after docking. RESULTS Abemaciclib showed the greatest tendency to bind CDK-6 via binding 16 residues in the binding site with hydrogen bonds and hydrophobic bonding. CDK-6 docked to hymenialdisine and indirubin increased the Total Energy (TE) and decreased the radius of gyration (Rg). CDK-6 docked to hymenialdisine significantly decreased the coil secondary structure. CONCLUSION CDK-6 is inhibited via high binding affinity to abemaciclib, hymenialdisine, and indirubin inhibitors and induces variation in the secondary structure and Rg in the CDK-6 docked to the three inhibitors. It seems that developing a drug with a binding tendency to CDK6 that is similar to those of abemaciclib, indirubin, and hymenialdisine can change the secondary structure of CDK6, possibly more potently, and can be used to develop anticancer drugs. However, additional studies are needed to confirm this argument.
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Affiliation(s)
- Gholam Basati
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Saber Abbaszadeh
- Student Research Committee, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Majid Asadi-Samani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Korosh Ashrafi-Dehkordi
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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9
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Sobhia ME, Ghosh K, Singh A, Sul K, Singh M, Kumar R, Sandeep, Merugu S, Donempudi S. A Multi-Perspective Review on Dengue Research. Curr Drug Targets 2019; 20:1550-1562. [PMID: 31339068 DOI: 10.2174/1389450120666190724145937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/03/2019] [Accepted: 07/17/2019] [Indexed: 11/22/2022]
Abstract
Dengue fever is a disease which is caused by a family of viruses named Flaviviridae which are transmitted by female Aedes mosquitoes. Today, this is endemic in more than 100 nations in the World Health Organization's African, Americas, Eastern Mediterranean, South-East Asia and Western Pacific locales. The treatment of typical dengue is focused on relieving the symptoms and signs. Carica papaya is a very common plant whose leaf extract is used in the treatment of this disease. Despite extensive research on Dengue, not a single vaccine or anti-viral drug was available until 2016 (a partially effective Chimeric Yellow fever virus treated by DENV-Tetravalent Dengue Vaccine for dengue fever made by Sanofi Pasteur). This review highlights dengue fever's current situation and explains the importance of Natural chemical moieties like methionine-proline anilides, tetrapeptide aldehyde uncovered via Structure Activity Relationship studies. Also, we have reviewed the drug candidates currently in the clinical trials that have the potential to solve these issues. Important patents in the past 20 years have been outlined in this review. An in depth Protein Data Bank analysis of the different possible target proteins that can potentially have a major role in curing Dengue fever has been conducted.
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Affiliation(s)
- M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ketan Ghosh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ajeet Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Komal Sul
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Monica Singh
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Ravi Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Sandeep
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Satti Merugu
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
| | - Sunilchand Donempudi
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Mohali, India
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10
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Abstract
Structure-based drug design starts with the collection, preparation, and initial analysis of protein structures. With more than 115,000 structures publically available in the Protein Data Bank (PDB), fully automated processes reliably performing these important preprocessing steps are needed. Several tools are available for these tasks, however, most of them do not address the special needs of scientists interested in protein-ligand interactions. In this paper, we summarize our research activities towards an automated processing pipeline from raw PDB data towards ready-to-use protein binding site ensembles. Starting from a single protein structure, the pipeline covers the following phases: Extracting structurally related binding sites from the PDB, aligning disconnected binding site sequences, resolving tautomeric forms and protonation, orienting hydrogens and flippable side-chains, structurally aligning the multitude of binding sites, and performing a reasonable reduction of ensemble structures. The pipeline, named SIENA, creates protein-structural ensembles for the analysis of protein flexibility, molecular design efforts like docking or de novo design within seconds. For the first time, we are able to process the whole PDB in order to create a large collection of protein binding site ensembles. SIENA is available as part of the ZBH ProteinsPlus webserver under http://proteinsplus.zbh.uni-hamburg.de.
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Affiliation(s)
- Stefan Bietz
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Rainer Fährrolfes
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
| | - Matthias Rarey
- University of Hamburg, ZBH -, Center for Bioinformatics, Bundesstraße 43, 20146, Hamburg, Germany
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11
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DeForte S, Uversky VN. Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree. Protein Sci 2016; 25:676-88. [PMID: 26683124 DOI: 10.1002/pro.2864] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 12/25/2022]
Abstract
Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612.,Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah, Jeddah 21589, Saudi Arabia.,Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation.,Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russian Federation
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12
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Djinovic-Carugo K, Carugo O. Missing strings of residues in protein crystal structures. Intrinsically Disord Proteins 2015; 3:e1095697. [PMID: 28232893 DOI: 10.1080/21690707.2015.1095697] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 10/22/2022]
Abstract
A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.
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Affiliation(s)
- Kristina Djinovic-Carugo
- Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Biochemistry; Faculty of Chemistry and Chemical Technology, University of Ljubljana; Ljubljana, Slovenia
| | - Oliviero Carugo
- Department of Structural and Computational Biology; Max F. Perutz Laboratories, Vienna University, Vienna Biocenter (VBC); Vienna, Austria; Department of Chemistry; Pavia University; Pavia, Italy
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13
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Hughes TJ, Cardamone S, Popelier PLA. Realistic sampling of amino acid geometries for a multipolar polarizable force field. J Comput Chem 2015; 36:1844-57. [PMID: 26235784 PMCID: PMC4973712 DOI: 10.1002/jcc.24006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/19/2015] [Accepted: 06/20/2015] [Indexed: 12/19/2022]
Abstract
The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X-ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF.
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Affiliation(s)
- Timothy J Hughes
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - Salvatore Cardamone
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology (MIB), 131 Princess Street, Manchester, M1 7DN, Great Britain
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, Great Britain
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14
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Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AMJJ, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CAM, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 2015; 23:1156-67. [PMID: 26095030 PMCID: PMC4933300 DOI: 10.1016/j.str.2015.05.013] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 05/11/2015] [Accepted: 05/18/2015] [Indexed: 01/20/2023]
Abstract
Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Methods Task Force Workshop held at the European Bioinformatics Institute in Hinxton, UK, on October 6 and 7, 2014. At the workshop, experts in various experimental fields of structural biology, experts in integrative modeling and visualization, and experts in data archiving addressed a series of questions central to the future of structural biology. How should integrative models be represented? How should the data and integrative models be validated? What data should be archived? How should the data and models be archived? What information should accompany the publication of integrative models?
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Affiliation(s)
- Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall Room 503B, University of California, San Francisco, 1700 4(th) Street, San Francisco, CA 94158-2330, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Torsten Schwede
- Swiss Institute of Bioinformatics Biozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
| | - Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, NSW 2006, Australia
| | - Gerard Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - John Markley
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Haruki Nakamura
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Paul Adams
- Physical Biosciences Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720-8235, USA; Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Wah Chiu
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL) and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frank Di Maio
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7370, USA
| | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry and Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2517, USA
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre of Human Genetics, University of Oxford, OX3 7BN Oxford, UK
| | - Aleksandras Gutmanas
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Graham Johnson
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, 600 16(th) Street, San Francisco, CA 94158-2330, USA
| | - Catherine L Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Marc A Marti-Renom
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG) and Institució Catalana de Recerca i Estudis Avançats (ICREA), 08028 Barcelona, Spain
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Michael Nilges
- Département de Biologie Structurale et Chimie, Unité de Bioinformatique Structurale, Institut Pasteur, F-75015 Paris, France; Unité Mixte de Recherche 3258, Centre National de la Recherche Scientifique, F-75015 Paris, France
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ardan Patwardhan
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Helen Saibil
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gunnar F Schröder
- Institute of Complex Systems (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Claus A M Seidel
- Chair for Molecular Physical Chemistry, Heinrich-Heine-Universität, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Eldon L Ulrich
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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15
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Abstract
The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.
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Affiliation(s)
- Helen M Berman
- RCSB PDB, Department of Chemistry and Chemical Biology and Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA,
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16
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Negahdar M, Aukrust I, Molnes J, Solheim MH, Johansson BB, Sagen JV, Dahl-Jørgensen K, Kulkarni RN, Søvik O, Flatmark T, Njølstad PR, Bjørkhaug L. GCK-MODY diabetes as a protein misfolding disease: the mutation R275C promotes protein misfolding, self-association and cellular degradation. Mol Cell Endocrinol 2014; 382:55-65. [PMID: 24001579 DOI: 10.1016/j.mce.2013.08.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 11/28/2022]
Abstract
GCK-MODY, dominantly inherited mild hyperglycemia, is associated with more than 600 mutations in the glucokinase gene. Different molecular mechanisms have been shown to explain GCK-MODY. Here, we report a Pakistani family harboring the glucokinase mutation c.823C>T (p.R275C). The recombinant and in cellulo expressed mutant pancreatic enzyme revealed slightly increased enzyme activity (kcat) and normal affinity for α-D-glucose, and resistance to limited proteolysis by trypsin comparable with wild-type. When stably expressed in HEK293 cells and MIN6 β-cells (at different levels), the mutant protein appeared misfolded and unstable with a propensity to form dimers and aggregates. Its degradation rate was increased, involving the lysosomal and proteasomal quality control systems. On mutation, a hydrogen bond between the R275 side-chain and the carbonyl oxygen of D267 is broken, destabilizing the F260-L271 loop structure and the protein. This promotes the formation of dimers/aggregates and suggests that an increased cellular degradation is the molecular mechanism by which R275C causes GCK-MODY.
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Affiliation(s)
- Maria Negahdar
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway; Section of Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Janne Molnes
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Marie H Solheim
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Bente B Johansson
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Jørn V Sagen
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Institute of Medicine, University of Bergen, Bergen, Norway; Hormone Laboratory, Haukeland University Hospital, Bergen, Norway
| | - Knut Dahl-Jørgensen
- Pediatric Department Ullevaal, Oslo University Hospital, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rohit N Kulkarni
- Section of Islet Cell Biology and Regenerative Medicine, Joslin Diabetes Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Oddmund Søvik
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Pål R Njølstad
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway.
| | - Lise Bjørkhaug
- KG Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway; Department of Biomedicine, University of Bergen, Bergen, Norway
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17
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Bhattacharya S, Das A, Ghosh S, Dasgupta R, Bagchi A. Hypoglycosylation of dystroglycan due to T192M mutation: a molecular insight behind the fact. Gene 2013; 537:108-14. [PMID: 24361964 DOI: 10.1016/j.gene.2013.11.071] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/22/2013] [Accepted: 11/23/2013] [Indexed: 01/11/2023]
Abstract
Abnormal glycosylation of dystroglycan (DG), a transmembrane glycoprotein, results in a group of diseases known as dystroglycanopathy. A severe dystroglycanopathy known as the limb girdle disease MDDGC9 [OMIM: 613818] occurs as a result of hypoglycosylation of alpha subunit of DG. Reasons behind this has been traced back to a point mutation (T192M) in DG that leads to weakening of interactions of DG protein with laminin and subsequent loss of signal flow through the DG protein. In this work we have tried to analyze the molecular details of the interactions between DG and laminin1 in order to propose a mechanism about the onset of the disease MDDGC9. We have observed noticeable changes between the modeled structures of wild type and mutant DG proteins. We also have employed molecular docking techniques to study and compare the binding interactions between laminin1 and both the wild type and mutant DG proteins. The docking simulations have revealed that the mutant DG has weaker interactions with laminin1 as compared to the wild type DG. Till date there are no previous reports that deal with the elucidation of the interactions of DG with laminin1 from the molecular level. Our study is therefore the first of its kind which analyzes the differences in binding patterns of laminin1 with both the wild type and mutant DG proteins. Our work would therefore facilitate analysis of the molecular mechanism of the disease MDDGC9. Future work based on our results may be useful for the development of suitable drugs against this disease.
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Affiliation(s)
- Simanti Bhattacharya
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia - 741235 WB, India
| | - Amit Das
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia - 741235 WB, India
| | - Semanti Ghosh
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia - 741235 WB, India
| | - Rakhi Dasgupta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia - 741235 WB, India.
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, Nadia - 741235 WB, India.
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18
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Desphande A, Xia G, Boerma LJ, Vines KK, Atigadda VR, Lobo-Ruppert S, Grubbs CJ, Moeinpour FL, Smith CD, Christov K, Brouillette WJ, Muccio DD. Methyl-substituted conformationally constrained rexinoid agonists for the retinoid X receptors demonstrate improved efficacy for cancer therapy and prevention. Bioorg Med Chem 2014; 22:178-85. [PMID: 24359708 DOI: 10.1016/j.bmc.2013.11.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 11/11/2013] [Accepted: 11/20/2013] [Indexed: 11/20/2022]
Abstract
(2E,4E,6Z,8Z)-8-(3',4'-Dihydro-1'(2H)-naphthalen-1'-ylidene)-3,7-dimethyl-2,3,6-octatrienoinic acid, 9cUAB30, is a selective rexinoid for the retinoid X nuclear receptors (RXR). 9cUAB30 displays substantial chemopreventive capacity with little toxicity and is being translated to the clinic as a novel cancer prevention agent. To improve on the potency of 9cUAB30, we synthesized 4-methyl analogs of 9cUAB30, which introduced chirality at the 4-position of the tetralone ring. The syntheses and biological evaluations of the racemic homolog and enantiomers are reported. We demonstrate that the S-enantiomer is the most potent and least toxic even though these enantiomers bind in a similar conformation in the ligand binding domain of RXR.
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19
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Ramteke MP, Shelke P, Ramamoorthy V, Somavarapu AK, Gautam AKS, Nanaware PP, Karanam S, Mukhopadhyay S, Venkatraman P. Identification of a novel ATPase activity in 14-3-3 proteins--evidence from enzyme kinetics, structure guided modeling and mutagenesis studies. FEBS Lett 2013; 588:71-8. [PMID: 24269678 DOI: 10.1016/j.febslet.2013.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/16/2013] [Accepted: 11/05/2013] [Indexed: 12/21/2022]
Abstract
14-3-3 Proteins bind phosphorylated sequences in proteins and regulate multiple cellular functions. For the first time, we show that pure recombinant human 14-3-3 ζ, γ, ε and τ isofoms hydrolyze ATP with similar Km and kcat values. In sharp contrast the sigma isoform has no detectable activity. Docking studies identify two putative binding pockets in 14-3-3 zeta. Mutation of D124A in the amphipathic pocket enhances binding affinity and catalysis. Mutation of a critical Arg (R55A) at the dimer interface in zeta reduces binding and decreases catalysis. These experimental results coincide with a binding pose at the dimer interface. This newly identified function could be a moon lighting function in some of these isoforms.
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Affiliation(s)
- Manoj P Ramteke
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Pradnya Shelke
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Vidhya Ramamoorthy
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Arun Kumar Somavarapu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Amit Kumar Singh Gautam
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Padma P Nanaware
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Sudheer Karanam
- Vlife Sciences Technologies Pvt. Ltd., 2nd Floor, Plot No-05, Ram Indu Park, Baner Road, Pune 411045, India
| | - Sami Mukhopadhyay
- Vlife Sciences Technologies Pvt. Ltd., 2nd Floor, Plot No-05, Ram Indu Park, Baner Road, Pune 411045, India
| | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India.
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20
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Dal Ben D, Buccioni M, Lambertucci C, Thomas A, Klotz KN, Federico S, Cacciari B, Spalluto G, Volpini R. 8-(2-Furyl)adenine derivatives as A₂A adenosine receptor ligands. Eur J Med Chem 2013; 70:525-35. [PMID: 24189496 DOI: 10.1016/j.ejmech.2013.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022]
Abstract
Selective adenosine receptor modulators are potential tools for numerous therapeutic applications, including cardiovascular, inflammatory, and neurodegenerative diseases. In this work, the synthesis and biological evaluation at the four human adenosine receptor subtypes of a series of 9-substituted 8-(2-furyl)adenine derivatives are reported. Results show that 8-(2-furyl)-9-methyladenine is endowed with high affinity at the A₂A subtype. Further modification of this compound with introduction of arylacetyl or arylcarbamoyl groups in N(6)-position takes to different effects on the A₂A affinity and in particular on the selectivity versus the other three adenosine receptor subtypes. A molecular modelling analysis at three different A₂A receptor crystal structures provides an interpretation of the obtained biological results.
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Affiliation(s)
- Diego Dal Ben
- School of Pharmacy, Medicinal Chemistry Unit, University of Camerino, Via S. Agostino 1, I-62032 Camerino, MC, Italy
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21
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Gacche RN, Meshram RJ. Targeting tumor micro-environment for design and development of novel anti-angiogenic agents arresting tumor growth. Prog Biophys Mol Biol. 2013;113:333-354. [PMID: 24139944 DOI: 10.1016/j.pbiomolbio.2013.10.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 12/12/2022]
Abstract
Angiogenesis: a process of generation of new blood vessels has been proved to be necessary for sustained tumor growth and cancer progression. Inhibiting angiogenesis pathway has long been remained a significant hope for the development of novel, effective and target orientated antitumor agents arresting the tumor proliferation and metastasis. The process of neoangiogenesis as a biological process is regulated by several pro- and anti-angiogenic factors, especially vascular endothelial growth factor, fibroblast growth factor, epidermal growth factor, hypoxia inducible factor 1 and transforming growth factor. Every endothelial cell destined for vessel formation is equipped with receptors for these angiogenic peptides. Moreover, numerous other angiogenic cytokines such as platelet derived growth factor (PGDF), placenta growth factor (PGF), nerve growth factor (NGF), stem-cell factor (SCF), and interleukins-2, 4, 6 etc. These molecular players performs critical role in regulating the angiogenic switch. Couple of decade's research in molecular aspects of tumor biology has unraveled numerous structural and functional mysteries of these angiogenic peptides. In present article, a detailed update on the functional and structural peculiarities of the various angiogenic peptides is described focusing on structural opportunities made available that has potential to be used to modulate function of these angiogenic peptides in developing therapeutic agents targeting neoplastic angiogenesis. The data may be useful in the mainstream of developing novel anticancer agents targeting tumor angiogenesis. We also discuss major therapeutic agents that are currently used in angiogenesis associated therapies as well as those are subject of active research or are in clinical trials.
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22
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Li J, Hua Z, Miao L, Jian T, Wei Y, Shasha Z, Shaocheng Z, Zhen G, Hongpeng Z, Ailong H, Deqiang W. The crystal structure and biochemical properties of DHBPS from Streptococcus pneumoniae, a potential anti-infective target for Gram-positive bacteria. Protein Expr Purif 2013; 91:161-8. [PMID: 23954596 DOI: 10.1016/j.pep.2013.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 11/30/2022]
Abstract
The enzymes involved in riboflavin biosynthesis are considered to be potential anti-bacterial drug targets because these proteins are essential in bacterial pathogens but are absent in humans. 3,4-dihydroxy-2-butanone-4-phosphate synthase (DHBPS) is one of the key enzymes in the biosynthesis of riboflavin. DHBPS catalyzes the conversion of ribulose-5-phosphate (Ru5P) to 3,4-Dihydroxy-2-butanone-4-phosphate (DHBP) and formate. The purified SpDHBPS enzyme, in the presence of Mg(2+) ion, catalyzed the conversion of Ru5P to DHBP at a rate of 109nmolmin(-1)mg(-1) with an apparent Km value of 181μM at 37°C. Surprisingly, our experiments first revealed that DHBPS showed activity in the presence of the trivalent metal ion, Fe(3+). Furthermore, we determined the crystal structure of DHBPS from Gram-positive bacteria, Streptococcus pneumoniae, with 2.0Å resolution. The overall architecture of SpDHBPS was similar to its homologs, which comprise one β-sheet (five-stranded) and eight α-helices, adopting a three-layered α-β-α sandwich fold. Similar to the homologs, gel-filtration experiments verified that the enzyme was arranged as a dimer. Although the overall fold of DHBPS was similar, the significant structural differences between the species at the active site region may be utilized to develop antibacterial agents that are species-specific.
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Affiliation(s)
- Jin Li
- Key Laboratory of Molecular Biology on Infectious Disease, Chongqing Medical University, YiXueYuanlu-1, Chongqing 400016, People's Republic of China; Department of Laboratory Medicine, Chongqing Medical University, YiXueYuanlu-1, Chongqing 400016, People's Republic of China
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Martin KR, Narang P, Medina-Franco JL, Meurice N, MacKeigan JP. Integrating virtual and biochemical screening for protein tyrosine phosphatase inhibitor discovery. Methods 2014; 65:219-28. [PMID: 23969317 DOI: 10.1016/j.ymeth.2013.08.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 12/14/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) represent an important class of enzymes that mediate signal transduction and control diverse aspects of cell behavior. The importance of their activity is exemplified by their significant contribution to disease etiology with over half of all human PTP genes implicated in at least one disease. Small molecule inhibitors targeting individual PTPs are important biological tools, and are needed to fully characterize the function of these enzymes. Moreover, potent and selective PTP inhibitors hold the promise to transform the treatment of many diseases. While numerous methods exist to develop PTP-directed small molecules, we have found that complimentary use of both virtual (in silico) and biochemical (in vitro) screening approaches expedite compound identification and drug development. Here, we summarize methods pertinent to our work and others. Focusing on specific challenges and successes we have experienced, we discuss the considerable caution that must be taken to avoid enrichment of inhibitors that function by non-selective oxidation. We also discuss the utility of using "open" PTP structures to identify active-site directed compounds, a rather unconventional choice for virtual screening. When integrated closely, virtual and biochemical screening can be used in a productive workflow to identify small molecules targeting PTPs.
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24
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Gorham RD, Forest DL, Tamamis P, López de Victoria A, Kraszni M, Kieslich CA, Banna CD, Bellows-Peterson ML, Larive CK, Floudas CA, Archontis G, Johnson LV, Morikis D. Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures. Exp Eye Res 2013; 116:96-108. [PMID: 23954241 DOI: 10.1016/j.exer.2013.07.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/06/2013] [Accepted: 07/20/2013] [Indexed: 11/19/2022]
Abstract
We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide inhibitors of the complement system. The peptides belong to the compstatin family and, compared to existing compstatin analogs, have been optimized to promote binding to their target, complement protein C3, and to enhance solubility by improving their polarity/hydrophobicity ratios. Based on analysis of molecular dynamics simulation data of peptide-C3 complexes, novel binding features were designed by introducing intermolecular salt bridge-forming arginines at the N-terminus and at position -1 of N-terminal dipeptide extensions. Our study demonstrates that the RPE cell assay has discriminatory capability for measuring the efficacy and potency of inhibitory peptides in a macular disease environment.
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Affiliation(s)
- Ronald D Gorham
- Department of Bioengineering, University of California, Riverside, CA 92521, USA
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25
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Cross PJ, Parker EJ. Allosteric inhibitor specificity of Thermotoga maritima 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase. FEBS Lett 2013; 587:3063-8. [PMID: 23916814 DOI: 10.1016/j.febslet.2013.07.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/22/2013] [Accepted: 07/22/2013] [Indexed: 10/26/2022]
Abstract
3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first step of the shikimate pathway for the biosynthesis of aromatic amino acids. Allosteric regulation of Thermotoga maritima DAH7PS is mediated by L-Tyr binding to a discrete ACT regulatory domain appended to a core catalytic (β/α)8 barrel. Variants of T. maritima DAH7PS (TmaDAH7PS) were created to probe the role of key residues in inhibitor selection. Substitution Ser31Gly severely reduced inhibition by L-Tyr. In contrast both L-Tyr and L-Phe inhibited the TmaHis29Ala variant, while the variant where Ser31 and His29 were interchanged (His29Ser/Ser31His), was inhibited to a greater extent by L-Phe than L-Tyr. These studies highlight the role and importance of His29 and Ser31 for determining both inhibitory ligand selectivity and the potency of allosteric response by TmaDAH7PS.
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Affiliation(s)
- Penelope J Cross
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, Christchurch, New Zealand
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26
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Blundell CD, Packer MJ, Almond A. Quantification of free ligand conformational preferences by NMR and their relationship to the bioactive conformation. Bioorg Med Chem 2013; 21:4976-87. [PMID: 23886813 PMCID: PMC3744816 DOI: 10.1016/j.bmc.2013.06.056] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 12/22/2022]
Abstract
Accurate unbound solution 3D-structures of ligands provide unique opportunities for medicinal chemistry and, in particular, a context to understand binding thermodynamics and kinetics. Previous methods of deriving these 3D-structures have had neither the accuracy nor resolution needed for drug design and have not yet realized their potential. Here, we describe and apply a NMR methodology to the aminoglycoside streptomycin that can accurately quantify accessible 3D-space and rank the occupancy of observed conformers to a resolution that enables medicinal chemistry understanding and design. Importantly, it is based upon conventional small molecule NMR techniques and can be performed in physiologically-relevant solvents. The methodology uses multiple datasets, an order of magnitude more experimental data than previous NMR approaches and a dynamic model during refinement, is independent of computational chemistry and avoids the problem of virtual conformations. The refined set of solution 3D-shapes for streptomycin can be grouped into two major families, of which the most populated is almost identical to the 30S ribosomal subunit bioactive shape. We therefore propose that accurate unbound ligand solution conformations may, in some cases, provide a subsidiary route to bioactive shape without crystallography. This experimental technique opens up new opportunities for drug design and more so when complemented with protein co-crystal structures, SAR data and pharmacophore modeling.
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Affiliation(s)
- Charles D Blundell
- C4X Discovery Ltd, Unit 310 Ducie House, Ducie Street, Manchester M1 2JW, UK
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27
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Singh VK, Ghosh I. Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Lett 2013; 587:2806-17. [PMID: 23816706 DOI: 10.1016/j.febslet.2013.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 06/14/2013] [Accepted: 06/17/2013] [Indexed: 11/19/2022]
Abstract
The methylerythritol phosphate (MEP) pathway of Plasmodium falciparum (P. falciparum) has become an attractive target for anti-malarial drug discovery. This study describes a kinetic model of this pathway, its use in validating 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR) as drug target from the systemic perspective, and additional target identification, using metabolic control analysis and in silico inhibition studies. In addition to DXR, 1-deoxy-d-xylulose 5-phosphate synthase (DXS) can be targeted because it is the first enzyme of the pathway and has the highest flux control coefficient followed by that of DXR. In silico inhibition of both enzymes caused large decrement in the pathway flux. An added advantage of targeting DXS is its influence on vitamin B1 and B6 biosynthesis. Two more potential targets, 2-C-methyl-d-erythritol 2,4-cyclodiphosphate synthase and 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase, were also identified. Their inhibition caused large accumulation of their substrates causing instability of the system. This study demonstrates that both types of enzyme targets, one acting via flux reduction and the other by metabolite accumulation, exist in P. falciparum MEP pathway. These groups of targets can be exploited for independent anti-malarial drugs.
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Affiliation(s)
- Vivek Kumar Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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Blayney L, Beck K, MacDonald E, D'Cruz L, Nomikos M, Griffiths J, Thanassoulas A, Nounesis G, Lai FA. ATP interacts with the CPVT mutation-associated central domain of the cardiac ryanodine receptor. Biochim Biophys Acta Gen Subj 2013; 1830:4426-32. [PMID: 23747301 DOI: 10.1016/j.bbagen.2013.05.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 02/03/2023]
Abstract
BACKGROUND This study was designed to determine whether the cardiac ryanodine receptor (RyR2) central domain, a region associated with catecholamine polymorphic ventricular tachycardia (CPVT) mutations, interacts with the RyR2 regulators, ATP and the FK506-binding protein 12.6 (FKBP12.6). METHODS Wild-type (WT) RyR2 central domain constructs (G(2236)to G(2491)) and those containing the CPVT mutations P2328S and N2386I, were expressed as recombinant proteins. Folding and stability of the proteins were examined by circular dichroism (CD) spectroscopy and guanidine hydrochloride chemical denaturation. RESULTS The far-UV CD spectra showed a soluble stably-folded protein with WT and mutant proteins exhibiting a similar secondary structure. Chemical denaturation analysis also confirmed a stable protein for both WT and mutant constructs with similar two-state unfolding. ATP and caffeine binding was measured by fluorescence spectroscopy. Both ATP and caffeine bound with an EC50 of ~200-400μM, and the affinity was the same for WT and mutant constructs. Sequence alignment with other ATP binding proteins indicated the RyR2 central domain contains the signature of an ATP binding pocket. Interaction of the central domain with FKBP12.6 was tested by glutaraldehyde cross-linking and no association was found. CONCLUSIONS The RyR2 central domain, expressed as a 'correctly' folded recombinant protein, bound ATP in accord with bioinformatics evidence of conserved ATP binding sequence motifs. An interaction with FKBP12.6 was not evident. CPVT mutations did not disrupt the secondary structure nor binding to ATP. GENERAL SIGNIFICANCE Part of the RyR2 central domain CPVT mutation cluster, can be expressed independently with retention of ATP binding.
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Affiliation(s)
- Lynda Blayney
- Institute of Molecular and Experimental Medicine, Cardiff University, Cardiff, UK.
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29
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Saif Hasan S, Yamashita E, Cramer WA. Transmembrane signaling and assembly of the cytochrome b6f-lipidic charge transfer complex. Biochim Biophys Acta 2013; 1827:1295-308. [PMID: 23507619 DOI: 10.1016/j.bbabio.2013.03.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/27/2013] [Accepted: 03/06/2013] [Indexed: 12/30/2022]
Abstract
Structure-function properties of the cytochrome b6f complex are sufficiently unique compared to those of the cytochrome bc1 complex that b6f should not be considered a trivially modified bc1 complex. A unique property of the dimeric b6f complex is its involvement in transmembrane signaling associated with the p-side oxidation of plastoquinol. Structure analysis of lipid binding sites in the cyanobacterial b6f complex prepared by hydrophobic chromatography shows that the space occupied by the H transmembrane helix in the cytochrome b subunit of the bc1 complex is mostly filled by a lipid in the b6f crystal structure. It is suggested that this space can be filled by the domain of a transmembrane signaling protein. The identification of lipid sites and likely function defines the intra-membrane conserved central core of the b6f complex, consisting of the seven trans-membrane helices of the cytochrome b and subunit IV polypeptides. The other six TM helices, contributed by cytochrome f, the iron-sulfur protein, and the four peripheral single span subunits, define a peripheral less conserved domain of the complex. The distribution of conserved and non-conserved domains of each monomer of the complex, and the position and inferred function of a number of the lipids, suggests a model for the sequential assembly in the membrane of the eight subunits of the b6f complex, in which the assembly is initiated by formation of the cytochrome b6-subunit IV core sub-complex in a monomer unit. Two conformations of the unique lipidic chlorophyll a, defined in crystal structures, are described, and functions of the outlying β-carotene, a possible 'latch' in supercomplex formation, are discussed. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Ramraj V, Evans G, Diprose JM, Esnouf RM. Nearest-cell: a fast and easy tool for locating crystal matches in the PDB. Acta Crystallogr D Biol Crystallogr 2012; 68:1697-700. [PMID: 23151636 PMCID: PMC3498934 DOI: 10.1107/s0907444912040590] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 09/25/2012] [Indexed: 12/02/2022]
Abstract
When embarking upon X-ray diffraction data collection from a potentially novel macromolecular crystal form, it can be useful to ascertain whether the measured data reflect a crystal form that is already recorded in the Protein Data Bank and, if so, whether it is part of a large family of related structures. Providing such information to crystallographers conveniently and quickly, as soon as the first images have been recorded and the unit cell characterized at an X-ray beamline, has the potential to save time and effort as well as pointing to possible search models for molecular replacement. Given an input unit cell, and optionally a space group, Nearest-cell rapidly scans the Protein Data Bank and retrieves near-matches.
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Affiliation(s)
- V Ramraj
- The Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, England.
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31
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Xia D, Esser L, Tang WK, Zhou F, Zhou Y, Yu L, Yu CA. Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. Biochim Biophys Acta 2012. [PMID: 23201476 DOI: 10.1016/j.bbabio.2012.11.008] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The cytochrome bc1 complex (bc1) is the mid-segment of the cellular respiratory chain of mitochondria and many aerobic prokaryotic organisms; it is also part of the photosynthetic apparatus of non-oxygenic purple bacteria. The bc1 complex catalyzes the reaction of transferring electrons from the low potential substrate ubiquinol to high potential cytochrome c. Concomitantly, bc1 translocates protons across the membrane, contributing to the proton-motive force essential for a variety of cellular activities such as ATP synthesis. Structural investigations of bc1 have been exceedingly successful, yielding atomic resolution structures of bc1 from various organisms and trapped in different reaction intermediates. These structures have confirmed and unified results of decades of experiments and have contributed to our understanding of the mechanism of bc1 functions as well as its inactivation by respiratory inhibitors. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Di Xia
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
Computational virtual screening is useful and powerful strategy for rapid discovery of small biologically active molecules in the early stage of drug discovery. The discovery of a broad range of important biological processes involved by RNA has increased the importance of RNA as a new drug target. To apply structure-based virtual screening methods to the discovery of RNA-binding ligands, many RNA 3D structure prediction programs and optimized docking algorithms have been developed. In this chapter, a number of successful cases of virtual screening targeting RNA will be introduced.
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Affiliation(s)
- Jonathan D. Dinman
- College Park, Cell Biology and Molecular Genetics, University of Maryland, Rm. 2135 Microbiology Building, College Park, 20742-4451 Maryland USA
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33
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Iwaoka M, Isozumi N. Hypervalent nonbonded interactions of a divalent sulfur atom. Implications in protein architecture and the functions. Molecules 2012; 17:7266-83. [PMID: 22695232 PMCID: PMC6269016 DOI: 10.3390/molecules17067266] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/06/2012] [Accepted: 06/08/2012] [Indexed: 12/30/2022] Open
Abstract
In organic molecules a divalent sulfur atom sometimes adopts weak coordination to a proximate heteroatom (X). Such hypervalent nonbonded S···X interactions can control the molecular structure and chemical reactivity of organic molecules, as well as their assembly and packing in the solid state. In the last decade, similar hypervalent interactions have been demonstrated by statistical database analysis to be present in protein structures. In this review, weak interactions between a divalent sulfur atom and an oxygen or nitrogen atom in proteins are highlighted with several examples. S···O interactions in proteins showed obviously different structural features from those in organic molecules (i.e., π(o) → σ(s)* versus n(o) → σ(s)* directionality). The difference was ascribed to the HOMO of the amide group, which expands in the vertical direction (π(o)) rather than in the plane (n(o)). S···X interactions in four model proteins, phospholipase A₂ (PLA₂), ribonuclease A (RNase A), insulin, and lysozyme, have also been analyzed. The results suggested that S···X interactions would be important factors that control not only the three-dimensional structure of proteins but also their functions to some extent. Thus, S···X interactions will be useful tools for protein engineering and the ligand design.
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Affiliation(s)
- Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan.
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Abstract
Atomic structures of biomolecules have provided the experimental evidence for many of the major discoveries in molecular biology, including the basic principles of protein folding and function, modes of biological information and energy flow, and mechanisms of molecular evolution. These experimental data are freely available in online structural databases.
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Afonine PV, Grosse-Kunstleve RW, Chen VB, Headd JJ, Moriarty NW, Richardson JS, Richardson DC, Urzhumtsev A, Zwart PH, Adams PD. phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. J Appl Crystallogr 2010; 43:669-676. [PMID: 20648263 PMCID: PMC2906258 DOI: 10.1107/s0021889810015608] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 04/27/2010] [Indexed: 12/03/2022] Open
Abstract
phenix.model_vs_data is a high-level command-line tool for the computation of crystallographic model and data statistics, and the evaluation of the fit of the model to data. Analysis of all Protein Data Bank structures that have experimental data available shows that in most cases the reported statistics, in particular R factors, can be reproduced within a few percentage points. However, there are a number of outliers where the recomputed R values are significantly different from those originally reported. The reasons for these discrepancies are discussed.
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Affiliation(s)
- Pavel V. Afonine
- Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | | | - Vincent B. Chen
- Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
| | - Jeffrey J. Headd
- Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
| | - Nigel W. Moriarty
- Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Jane S. Richardson
- Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
| | - David C. Richardson
- Biochemistry Department, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexandre Urzhumtsev
- IGBMC, CNRS-INSERM-UdS, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Université Nancy: Département de Physique – Nancy 1, BP 239, Faculté des Sciences et des Technologies, 54506 Vandoeuvre-lès-Nancy, France
| | - Peter H. Zwart
- Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Paul D. Adams
- Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, CA 94720, USA
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Abstract
A method for the identification of alpha-helices in electron-density maps at low resolution followed by interpretation at moderate to high resolution is presented. Rapid identification is achieved at low resolution, where alpha-helices appear as tubes of density. The positioning and direction of the alpha-helices is obtained at moderate to high resolution, where the positions of side chains can be seen. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. An average of 63% of the alpha-helical residues in these proteins were built and an average of 76% of the residues built matched helical residues in the refined models of the proteins. The overall average r.m.s.d. between main-chain atoms in the modeled alpha-helices and the nearest atom with the same name in the refined models of the proteins was 1.3 A.
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Abstract
A method for rapidly building beta-sheets into electron-density maps is presented. beta-Strands are identified as tubes of high density adjacent to and nearly parallel to other tubes of density. The alignment and direction of each strand are identified from the pattern of high density corresponding to carbonyl and C(beta) atoms along the strand averaged over all repeats present in the strand. The beta-strands obtained are then assembled into a single atomic model of the beta-sheet regions. The method was tested on a set of 42 experimental electron-density maps at resolutions ranging from 1.5 to 3.8 A. The beta-sheet regions were nearly completely built in all but two cases, the exceptions being one structure at 2.5 A resolution in which a third of the residues in beta-sheets were built and a structure at 3.8 A in which under 10% were built. The overall average r.m.s.d. of main-chain atoms in the residues built using this method compared with refined models of the structures was 1.5 A.
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Abstract
We have analyzed the interstitial water (ISW) structures in 1500 protein crystal structures deposited in the Protein Data Bank that have greater than 1.5 A resolution with less than 90% sequence similarity with each other. We observed varieties of polygonal water structures composed of three to eight water molecules. These polygons may represent the time- and space-averaged structures of "stable" water oligomers present in liquid water, and their presence as well as relative population may be relevant in understanding physical properties of liquid water at a given temperature. On an average, 13% of ISWs are localized enough to be visible by X-ray diffraction. Of those, averages of 78% are water molecules in the first water layer on the protein surface. Of the localized ISWs beyond the first layer, almost half of them form water polygons such as trigons, tetragons, as well as expected pentagons, hexagons, higher polygons, partial dodecahedrons, and disordered networks. Most of the octagons and nanogons are formed by fusion of smaller polygons. The trigons are most commonly observed. We suggest that our observation provides an experimental basis for including these water polygon structures in correlating and predicting various water properties in liquid state.
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Affiliation(s)
- Jonas Lee
- Department of Chemistry, University of CaliforniaBerkeley, California 94720-5230
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, California 94720
| | - Sung-Hou Kim
- Department of Chemistry, University of CaliforniaBerkeley, California 94720-5230
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, California 94720
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39
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Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund AC, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle IJ, Vriend G. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J Appl Crystallogr 2009; 42:376-384. [PMID: 22477769 PMCID: PMC3246819 DOI: 10.1107/s0021889809008784] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 03/10/2009] [Indexed: 11/24/2022] Open
Abstract
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
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Affiliation(s)
- Robbie P. Joosten
- Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jean Salzemann
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Vincent Bloch
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Heinz Stockinger
- Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland
| | | | - Christophe Blanchet
- IBCP, CNRS Université de Lyon1, IFR128 BioSciences Lyon-Gerland, Lyon, France
| | | | - Christophe Combet
- IBCP, CNRS Université de Lyon1, IFR128 BioSciences Lyon-Gerland, Lyon, France
| | - Ana L. Da Costa
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Gilbert Deleage
- IBCP, CNRS Université de Lyon1, IFR128 BioSciences Lyon-Gerland, Lyon, France
| | - Matteo Diarena
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Roberto Fabbretti
- Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland
| | - Géraldine Fettahi
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Volker Flegel
- Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland
| | - Andreas Gisel
- Institute for Biomedical Technologies Bari, CNR, Bari, Italy
| | - Vinod Kasam
- Fraunhofer-Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany
| | - Timo Kervinen
- CSC – The Finnish IT Center for Science, Espoo, Finland
| | | | - Kimmo Mattila
- CSC – The Finnish IT Center for Science, Espoo, Finland
| | - Marco Pagni
- Swiss Institute of Bioinformatics, Vital-IT Group, Lausanne, Switzerland
| | - Matthieu Reichstadt
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | - Vincent Breton
- CNRS/IN2P3, Laboratoire de Physique Corpusculaire, Université Blaize Pascal, Clermont-Ferrand, France
| | | | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, NCMLS, Radboud University Medical Center, Nijmegen, The Netherlands
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40
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Lawson CL, Dutta S, Westbrook JD, Henrick K, Berman HM. Representation of viruses in the remediated PDB archive. Acta Crystallogr D Biol Crystallogr 2008; D64:874-82. [PMID: 18645236 PMCID: PMC2677383 DOI: 10.1107/s0907444908017393] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Accepted: 06/09/2008] [Indexed: 11/24/2022]
Abstract
A new scheme has been devised to represent viruses and other biological assemblies with regular noncrystallographic symmetry in the Protein Data Bank (PDB). The scheme describes existing and anticipated PDB entries of this type using generalized descriptions of deposited and experimental coordinate frames, symmetry and frame transformations. A simplified notation has been adopted to express the symmetry generation of assemblies from deposited coordinates and matrix operations describing the required point, helical or crystallographic symmetry. Complete correct information for building full assemblies, subassemblies and crystal asymmetric units of all virus entries is now available in the remediated PDB archive.
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Affiliation(s)
- Catherine L Lawson
- RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA.
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Terwilliger TC, Grosse-Kunstleve RW, Afonine PV, Adams PD, Moriarty NW, Zwart P, Read RJ, Turk D, Hung LW. Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models. Acta Crystallogr D Biol Crystallogr 2007; 63:597-610. [PMID: 17452785 PMCID: PMC2483474 DOI: 10.1107/s0907444907009791] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 02/28/2007] [Indexed: 11/10/2022]
Abstract
Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ;perfect' structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models.
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Janin J, Rodier F, Chakrabarti P, Bahadur RP. Macromolecular recognition in the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2007; 63:1-8. [PMID: 17164520 PMCID: PMC2483476 DOI: 10.1107/s090744490603575x] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 09/04/2006] [Indexed: 11/10/2022]
Abstract
Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein-protein and protein-DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200-2000 A2 of protein surface occur in protease-inhibitor and antigen-antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.
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Affiliation(s)
- Joël Janin
- Laboratoire d'Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette, France.
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Iwaoka M, Isozumi N. Possible roles of S···O and S···N interactions in the functions and evolution of phospholipase A 2. Biophysics (Nagoya-shi) 2006; 2:23-34. [PMID: 27857557 PMCID: PMC5036642 DOI: 10.2142/biophysics.2.23] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 01/30/2006] [Indexed: 12/01/2022] Open
Abstract
To investigate possible roles of S···X (X= O, N, S) interactions in the functions and evolution of a protein, two types of database analyses were carried out for a vertebrate phospholipase A2 (PLA2) family. A comprehensive search for close S···X contacts in the structures retrieved from protein data bank (PDB) revealed that there are four common S···O interactions and one common S···N interaction for the PLA2 domain group (PLA2-DG), while an additional three S···O interactions were found for the snake PLA2 domain group (sPLA2-DG). On the other hand, a phylogenetic analysis on the conservation of the observed S···O and S···N interactions over various amino acid sequences of sPLA2-DG demonstrated probable clustering of the interactions on the dendrogram. Most of the interactions characterized for PLA2 were found to reside in the vicinity of the active site and to be able to tolerate the conformational changes due to the substrate binding. These observations suggested that the S···X interactions play some role in the functions and evolution of the PLA2 family.
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Affiliation(s)
- Michio Iwaoka
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
| | - Noriyoshi Isozumi
- Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
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