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Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022; 299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein phase separation is thought to be a primary driving force for the formation of membrane-less organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. Among phase-separating (PS) proteins, many have intrinsically disordered regions (IDRs) that are needed for phase separation to occur. Accurate identification of IDRs that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and PS ID sequences. We then used these sequence sets to examine how broadly existing amino acid property scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving protein phase separation. Collectively, our findings provide further insight into the classification of IDRs and the elements involved in protein phase separation.
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Affiliation(s)
- Ayyam Y. Ibrahim
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | | | - John J. Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Loren E. Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA,For correspondence: Steven T. Whitten; Loren E. Hough
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA,For correspondence: Steven T. Whitten; Loren E. Hough
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2
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Wan X, Tan X. A protein structural study based on the centrality analysis of protein sequence feature networks. PLoS One 2021; 16:e0248861. [PMID: 33780482 PMCID: PMC8006989 DOI: 10.1371/journal.pone.0248861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/05/2021] [Indexed: 11/19/2022] Open
Abstract
In this paper, we use network approaches to analyze the relations between protein sequence features for the top hierarchical classes of CATH and SCOP. We use fundamental connectivity measures such as correlation (CR), normalized mutual information rate (nMIR), and transfer entropy (TE) to analyze the pairwise-relationships between the protein sequence features, and use centrality measures to analyze weighted networks constructed from the relationship matrices. In the centrality analysis, we find both commonalities and differences between the different protein 3D structural classes. Results show that all top hierarchical classes of CATH and SCOP present strong non-deterministic interactions for the composition and arrangement features of Cystine (C), Methionine (M), Tryptophan (W), and also for the arrangement features of Histidine (H). The different protein 3D structural classes present different preferences in terms of their centrality distributions and significant features.
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Affiliation(s)
- Xiaogeng Wan
- College of Mathematics and Physics, Beijing University of Chemical Technology, Beijing, China
- * E-mail:
| | - Xinying Tan
- The Fourth Center of PLA General Hospital, Beijing, China
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3
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Schaduangrat N, Nantasenamat C, Prachayasittikul V, Shoombuatong W. ACPred: A Computational Tool for the Prediction and Analysis of Anticancer Peptides. Molecules 2019; 24:E1973. [PMID: 31121946 PMCID: PMC6571645 DOI: 10.3390/molecules24101973] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/07/2019] [Accepted: 05/17/2019] [Indexed: 01/01/2023] Open
Abstract
Anticancer peptides (ACPs) have emerged as a new class of therapeutic agent for cancer treatment due to their lower toxicity as well as greater efficacy, selectivity and specificity when compared to conventional small molecule drugs. However, the experimental identification of ACPs still remains a time-consuming and expensive endeavor. Therefore, it is desirable to develop and improve upon existing computational models for predicting and characterizing ACPs. In this study, we present a bioinformatics tool called the ACPred, which is an interpretable tool for the prediction and characterization of the anticancer activities of peptides. ACPred was developed by utilizing powerful machine learning models (support vector machine and random forest) and various classes of peptide features. It was observed by a jackknife cross-validation test that ACPred can achieve an overall accuracy of 95.61% in identifying ACPs. In addition, analysis revealed the following distinguishing characteristics that ACPs possess: (i) hydrophobic residue enhances the cationic properties of α-helical ACPs resulting in better cell penetration; (ii) the amphipathic nature of the α-helical structure plays a crucial role in its mechanism of cytotoxicity; and (iii) the formation of disulfide bridges on β-sheets is vital for structural maintenance which correlates with its ability to kill cancer cells. Finally, for the convenience of experimental scientists, the ACPred web server was established and made freely available online.
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Affiliation(s)
- Nalini Schaduangrat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Chanin Nantasenamat
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Virapong Prachayasittikul
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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4
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Tomar K, Soni S, Bhadauriya P, Parihar R, Ganesh S, Nair NN, Ramanathan G. Mercuric Ion Sensing by an Overlapping β-turn Containing Peptide. ChemistrySelect 2017. [DOI: 10.1002/slct.201701058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kalpana Tomar
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Satyendra Soni
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Pratibha Bhadauriya
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Rashmi Parihar
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Subramaniam Ganesh
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Nisanth N. Nair
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
| | - Gurunath Ramanathan
- Department of Chemistry; Indian Institute of Technology Kanpur; Kanpur, Uttar Pradesh INDIA -208016
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5
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mRNA/protein sequence complementarity and its determinants: The impact of affinity scales. PLoS Comput Biol 2017; 13:e1005648. [PMID: 28750009 PMCID: PMC5549747 DOI: 10.1371/journal.pcbi.1005648] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/08/2017] [Accepted: 06/26/2017] [Indexed: 11/22/2022] Open
Abstract
It has recently been demonstrated that the nucleobase-density profiles of mRNA coding sequences are related in a complementary manner to the nucleobase-affinity profiles of their cognate protein sequences. Based on this, it has been proposed that cognate mRNA/protein pairs may bind in a co-aligned manner, especially if unstructured. Here, we study the dependence of mRNA/protein sequence complementarity on the properties of the nucleobase/amino-acid affinity scales used. Specifically, we sample the space of randomly generated scales by employing a Monte Carlo strategy with a fitness function that depends directly on the level of complementarity. For model organisms representing all three domains of life, we show that even short searches reproducibly converge upon highly optimized scales, implying that the topology of the underlying fitness landscape is decidedly funnel-like. Furthermore, the optimized scales, generated without any consideration of the physicochemical attributes of nucleobases or amino acids, resemble closely the nucleobase/amino-acid binding affinity scales obtained from experimental structures of RNA-protein complexes. This provides support for the claim that mRNA/protein sequence complementarity may indeed be related to binding between the two. Finally, we characterize suboptimal scales and show that intermediate-to-high complementarity can be reached by substantially diverse scales, but with select amino acids contributing disproportionally. Our results expose the dependence of cognate mRNA/protein sequence complementarity on the properties of the underlying nucleobase/amino-acid affinity scales and provide quantitative constraints that any physical scales need to satisfy for the complementarity to hold. Messenger RNAs and proteins, two essential types of biopolymers, have recently been shown to exhibit closely related, complementary physicochemical properties. Specifically, density profiles of certain groups in messenger RNA sequences directly match the affinity profiles for precisely those groups in protein sequences they encode. Based on this, it has been suggested that these molecules may interact with each other specifically and in a co-aligned fashion, especially when unstructured. Here, we explore different amino-acid scales used in the above analysis to assess which of their properties dictate the observed matching. Specifically, we define the constraints that need to be satisfied by physical scales for the complementarity to hold and show that the previously derived nucleobase/amino-acid affinity scales indeed satisfy these constraints. As a whole, our work provides a quantitative foundation for understanding the putative messenger RNA/protein complementarity with implications in different areas of RNA/protein biology including transcription, translation, splicing and viral assembly.
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6
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Artymiuk PJ, Rice DW, Mitchell EM, Willett P. Searching techniques for databases of protein secondary structures. J Inf Sci 2016. [DOI: 10.1177/016555158901500411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This paper summarizes the findings of a recent, British Library-funded research project into computer techniques for searching the three-dimensional protein structures that occur in the Protein Data Bank. The work focuses on the secondary structures of proteins and utilizes both angular and distance geometric information. Algorithms are presented for the auto matic identification of secondary structure elements, of sec ondary structure motifs and of proteins with similar secondary structures.
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Affiliation(s)
- Peter J. Artymiuk
- Department of Biochemistry, University of Sheffield, Sheffield S10 2TN, UK
| | - David W. Rice
- Department of Biochemistry, University of Sheffield, Sheffield S10 2TN, UK
| | - Eleanor M. Mitchell
- Department of Information Studies, University of Sheffield, Sheffield S10 2TN, UK
| | - Peter Willett
- Department of Information Studies, University of Sheffield, Sheffield S10 2TN, UK
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7
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Bolognesi B, Lorenzo Gotor N, Dhar R, Cirillo D, Baldrighi M, Tartaglia GG, Lehner B. A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression. Cell Rep 2016; 16:222-231. [PMID: 27320918 PMCID: PMC4929146 DOI: 10.1016/j.celrep.2016.05.076] [Citation(s) in RCA: 182] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/14/2016] [Accepted: 05/18/2016] [Indexed: 11/17/2022] Open
Abstract
Multiple human diseases are associated with a liquid-to-solid phase transition resulting in the formation of amyloid fibers or protein aggregates. Here, we present an alternative mechanism for cellular toxicity based on a concentration-dependent liquid-liquid demixing. Analyzing proteins that are toxic when their concentration is increased in yeast reveals that they share physicochemical properties with proteins that participate in physiological liquid-liquid demixing in the cell. Increasing the concentration of one of these proteins indeed results in the formation of cytoplasmic foci with liquid properties. Demixing occurs at the onset of toxicity and titrates proteins and mRNAs from the cytoplasm. Focus formation is reversible, and resumption of growth occurs as the foci dissolve as protein concentration falls. Preventing demixing abolishes the dosage sensitivity of the protein. We propose that triggering inappropriate liquid phase separation may be an important cause of dosage sensitivity and a determinant of human disease.
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Affiliation(s)
- Benedetta Bolognesi
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Nieves Lorenzo Gotor
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Riddhiman Dhar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Davide Cirillo
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Marta Baldrighi
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
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8
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Sun M, Wang X, Zou C, He Z, Liu W, Li H. Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors. BMC Bioinformatics 2016; 17:231. [PMID: 27266516 PMCID: PMC4897909 DOI: 10.1186/s12859-016-1110-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 06/02/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins. Newly developed discriminative descriptors will help to improve the prediction accuracy of these prediction methods and provide further meaningful information for researchers. RESULTS In this work, we designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the two features were powerful for identifying RNA-binding protein residues. Using these two features and other excellent structure- and sequence-based features, a random forest classifier was constructed to predict RNA-binding residues. The area under the receiver operating characteristic curve (AUC) of five-fold cross-validation for our method on training set RBP195 was 0.900, and when applied to the test set RBP68, the prediction accuracy (ACC) was 0.868, and the F-score was 0.631. CONCLUSIONS The good prediction performance of our method revealed that the two newly designed descriptors could be discriminative for inferring protein residues interacting with RNAs. To facilitate the use of our method, a web-server called RNAProSite, which implements the proposed method, was constructed and is freely available at http://lilab.ecust.edu.cn/NABind .
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Affiliation(s)
- Meijian Sun
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xia Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Chuanxin Zou
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Zenghui He
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Wei Liu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Honglin Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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9
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Optimal secretion of alkali-tolerant xylanase in Bacillus subtilis by signal peptide screening. Appl Microbiol Biotechnol 2016; 100:8745-56. [DOI: 10.1007/s00253-016-7615-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/26/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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10
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl 2015; 54:8896-927. [PMID: 26119925 PMCID: PMC4557054 DOI: 10.1002/anie.201412070] [Citation(s) in RCA: 496] [Impact Index Per Article: 55.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) are involved at all levels of cellular organization, thus making the development of PPI inhibitors extremely valuable. The identification of selective inhibitors is challenging because of the shallow and extended nature of PPI interfaces. Inhibitors can be obtained by mimicking peptide binding epitopes in their bioactive conformation. For this purpose, several strategies have been evolved to enable a projection of side chain functionalities in analogy to peptide secondary structures, thereby yielding molecules that are generally referred to as peptidomimetics. Herein, we introduce a new classification of peptidomimetics (classes A-D) that enables a clear assignment of available approaches. Based on this classification, the Review summarizes strategies that have been applied for the structure-based design of PPI inhibitors through stabilizing or mimicking turns, β-sheets, and helices.
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Affiliation(s)
- Marta Pelay-Gimeno
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Adrian Glas
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
| | - Oliver Koch
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
| | - Tom N Grossmann
- Chemical Genomics Centre of the Max Planck SocietyOtto-Hahn-Strasse 15, 44227 Dortmund (Germany) E-mail:
- TU Dortmund University, Department of Chemistry and Chemical BiologyOtto-Hahn-Strasse 6, 44227 Dortmund (Germany)
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Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Strukturbasierte Entwicklung von Protein-Protein-Interaktionsinhibitoren: Stabilisierung und Nachahmung von Peptidliganden. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412070] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Klus P, Bolognesi B, Agostini F, Marchese D, Zanzoni A, Tartaglia GG. The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. ACTA ACUST UNITED AC 2014; 30:1601-8. [PMID: 24493033 PMCID: PMC4029037 DOI: 10.1093/bioinformatics/btu074] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Motivation: The recent shift towards high-throughput screening is posing new challenges for the interpretation of experimental results. Here we propose the cleverSuite approach for large-scale characterization of protein groups. Description: The central part of the cleverSuite is the cleverMachine (CM), an algorithm that performs statistics on protein sequences by comparing their physico-chemical propensities. The second element is called cleverClassifier and builds on top of the models generated by the CM to allow classification of new datasets. Results: We applied the cleverSuite to predict secondary structure properties, solubility, chaperone requirements and RNA-binding abilities. Using cross-validation and independent datasets, the cleverSuite reproduces experimental findings with great accuracy and provides models that can be used for future investigations. Availability: The intuitive interface for dataset exploration, analysis and prediction is available at http://s.tartaglialab.com/clever_suite. Contact:gian.tartaglia@crg.es Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Petr Klus
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Benedetta Bolognesi
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Federico Agostini
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Domenica Marchese
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Andreas Zanzoni
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Gene Function and Evolution, Centre for Genomic Regulation (CRG), Dr. Aiguader 88 and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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13
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Bozek K, Lengauer T, Sierra S, Kaiser R, Domingues FS. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage. PLoS Comput Biol 2013; 9:e1002977. [PMID: 23555214 PMCID: PMC3605109 DOI: 10.1371/journal.pcbi.1002977] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 01/23/2013] [Indexed: 11/18/2022] Open
Abstract
The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/. Human Immunodeficiency Virus (HIV) requires one of the chemokine coreceptors CCR5 or CXCR4 for entry into the host cell. The capacity of the virus to use one or both of these coreceptors is termed tropism. Monitoring HIV tropism is of high importance due to the relationship of the emergence of CXCR4-tropic virus with the progression of immunodeficiency and for patient treatment with the recently developed CCR5 antagonists. Computational methods for predicting HIV tropism are based on sequence and on structure of the third variable region (V3 loop) of the viral gp120 protein — the major determinant of the HIV tropism. Limitations of the existing methods include the limited insights they provide into the biochemical determinants of coreceptor usage, high computational load of the structure-based methods and low prediction accuracy on clinically derived patient samples. Here we propose a numerical descriptor of the V3 loop encoding the physicochemical and structural properties of the loop. The new descriptor allows for server-based prediction of viral tropism with accuracy comparable to that of established sequence-based methods both on clonal and clinically derived patient data as well as for the interpretation of the properties of the loop relevant for tropism. The server is available under http://structure.bioinf.mpi-inf.mpg.de/.
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Affiliation(s)
- Katarzyna Bozek
- Max Planck Institute for Computer Science, Saarbrucken, Germany.
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14
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Tian S. A 20 Residues Motif Delineates the Furin Cleavage Site and its Physical Properties May Influence Viral Fusion. BIOCHEMISTRY INSIGHTS 2009. [DOI: 10.4137/bci.s2049] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Furin is a proprotein convertase that proteolytically cleaves protein precursors to yield functional proteins. Efficient cleavage depends on the presence of a specific sequence motif on the substrate. Currently, the cleavage site motif is described as a four amino acid pattern: R-X-[K/R]-R⇓. However, not all furin cleavage recognition sites can be described by this pattern and not all R-X-[K/R]-R⇓ sites are cleaved by furin. Since many furin substrates are involved in the pathogenesis of viral infection and human diseases, it is important to accurately characterize the furin cleavage site motif. In this study, the furin cleavage site motif was characterized using statistical analysis. The data were interpreted within the 3D crystal structure of the furin catalytic domain. The results indicate that the furin cleavage site motif is comprised of about 20 residues, P14-P6′. Specific physical properties such as volume, charge, and hydrophilicity are required at specific positions. The furin cleavage site motif is divided into two parts: 1) one core region (8 amino acids, positions P6-P2′) packed inside the furin binding pocket; 2) two polar regions (8 amino acids, positions P7–P14; and 4 amino acids, positions P3′-P6′) located outside the furin binding pocket. The physical properties of the core region contribute to the binding strength of the furin substrate, while the polar regions provide a solvent accessible environment and facilitate the accessibility of the core region to the furin binding pocket. This furin cleavage site motif also revealed a dynamic relationship linking the evolution of physical properties in region P1′-P6′ of viral fusion peptides, furin cleavage efficacy, and viral infectivity.
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Affiliation(s)
- Sun Tian
- Institute of Biomechanics, South China University of Technology, Guangzhou, Guangdong, 510640, China
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15
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Andrianov AM. Modeling of the spatial structure of an HIV-haiti immunodominant epitope. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Taylor T, Rivera M, Wilson G, Vaisman II. New method for protein secondary structure assignment based on a simple topological descriptor. Proteins 2005; 60:513-24. [PMID: 15887224 DOI: 10.1002/prot.20471] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond length, angles, and areas. Rules based on this descriptor can be used for accurate, robust, and computationally efficient secondary structure assignment that correlates well with the existing methods.
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Affiliation(s)
- Todd Taylor
- Laboratory for Structural Bioinformatics, School of Computational Sciences, George Mason University, Manassas, Virginia 20110, USA
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17
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Gromiha MM, Parry DAD. Characteristic features of amino acid residues in coiled-coil protein structures. Biophys Chem 2004; 111:95-103. [PMID: 15381307 DOI: 10.1016/j.bpc.2004.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2004] [Revised: 05/06/2004] [Accepted: 05/06/2004] [Indexed: 11/21/2022]
Abstract
Detailed analyses of protein structures provide an opportunity to understand conformation and function in terms of amino acid sequence and composition. In this work, we have systematically analyzed the characteristic features of the amino acid residues found in alpha-helical coiled-coils and, in so doing, have developed indices for their properties, conformational parameters, surrounding hydrophobicity and flexibility. As expected, there is preference for hydrophobic (Ala, Leu), positive (Lys, Arg) and negatively (Glu) charged residues in coiled-coil domains. However, the surrounding hydrophobicity of residues in coiled-coil domains is significantly less than that for residues in other regions of coiled-coil proteins. The analysis of temperature factors in coiled-coil proteins shows that the residues in these domains are more stable than those in other regions. Further, we have delineated the medium- and long-range contacts in coiled-coil domains and compared the results with those obtained for other (non-coiled-coil) parts of the same proteins and non-coiled-coil helical segments of globular proteins. The residues in coiled-coil domains are largely influenced by medium-range contacts, whereas long-range interactions play a dominant role in other regions of these same proteins as well as in non-coiled-coil helices. We have also revealed the preference of amino acid residues to form cation-pi interactions and we found that Arg is more likely to form such interactions than Lys. The parameters developed in this work can be used to understand the folding and stability of coiled-coil proteins in general.
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Affiliation(s)
- M Michael Gromiha
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Aomi Frontier Building 17F, 2-43 Aomi, Koto, Tokyo 135-0064, Japan.
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18
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Neuberger G, Maurer-Stroh S, Eisenhaber B, Hartig A, Eisenhaber F. Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol 2003; 328:567-79. [PMID: 12706717 DOI: 10.1016/s0022-2836(03)00318-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eukaryote peroxisomes, plant glyoxysomes and trypanosomal glycosomes belong to the microbody family of organelles that compartmentalise a variety of biochemical processes. The interaction between the PTS1 signal and its cognate receptor Pex5 initiates the major import mechanism for proteins into the matrix of these organelles. Relying on the analysis of amino acid sequence variability of known PTS1-targeted proteins and PTS1-containing peptides that interact with Pex5 in the yeast two-hybrid assay, on binding site studies of the Pex5-ligand complex crystal structure, 3D models and sequences of Pex5 proteins from various taxa, we derived the requirements for a C-terminal amino acid sequence to interact productively with Pex5. We found evidence that, at least the 12 C-terminal residues of a given substrate protein are implicated in PTS1 signal recognition. This motif can be structurally and functionally divided into three regions: (i) the C-terminal tripeptide, (ii) a region interacting with the surface of Pex5 (about four residues further upstream), and (iii) a polar, solvent-accessible and unstructured region with linker function (the remaining five residues). Specificity differences are confined to taxonomic subgroups (metazoa and fungi) and are connected with amino acid type preferences in region 1 and deviating hydrophobicity patterns in region 2.
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Affiliation(s)
- Georg Neuberger
- Research Institute of Molecular Pathology, Dr. Bohrgasse 7, A-1030 Vienna, Austria.
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19
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Andrianov AM, Sokalov YA. Structure and polymorphism of the principal neutralization site of Thailand HIV-1 isolate. J Biomol Struct Dyn 2003; 20:603-13. [PMID: 12529159 DOI: 10.1080/07391102.2003.10506877] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Refining the geometric parameters for the ensemble of conformers, derived earlier in terms of NMR-spectroscopy data for the immunogenic tip of Thailand HIV-1 isolate, was carried out by quantum chemical methods. As a result, (i) the energy characteristics of initial structures were significantly improved, (ii) their relative locations on the scale of formation heats were determined, and (iii) the energy barriers between conformers under study were computed. On the basis of all data obtained, the high resolution 3D structure model, describing the set of stable conformers and containing the biologically active conformation, was proposed for neutralizing epitope of Thailand HIV-1 isolate. The following major conclusions were made based on the analysis of simulated conformations: i) the Gly-Pro-Gly-Gln-Val-Phe stretch forming the immunogenic crown of Thailand HIV-1 isolate exhibits the properties characteristic for metastable oligopeptide that constitutes in solution the dominant structure with other conformations admissible; (ii) three structures out of five NMR-based starting models form the cluster of conformers which adequately describes general conformational features of this functionally important site of gp120; (iii) two structures residing in this cluster are found to be well-ground for implementing the function of immunoreactive conformation of the stretch of interest; (iv) in spite of this observation, the "global" structure which gives rise to inverse gamma-turn in the central Gly-Pro-Gly crest of Thailand HIV-1 gp120 is proposed to be the most probable conformation responsible for the formation of viral antigen-antibody complex in particular case under study.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, Belarus Academy of Sciences, Kuprevich St., 5/2, 220141 Minsk, Republic of Belarus.
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20
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Abstract
The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of the fragment under study was carried out using the published sequential d connectivity data and values of spin-spin coupling constants. As a result, (i) the local structure for the V3 loop from Thailand isolate was determined, (ii) the conformations of its irregular segments were analyzed, and the secondary structure elements identified, (iii) the ensemble of conformers matching the experimental and theoretical data was derived for the stretch forming the neutralizing epitope of the HIV-Thailand PND, (iv) to estimate the probability of realizing each of these conformers in solution, the results obtained were collated with the X-ray data for corresponding segments in synthetic molecules imitating the central region of the HIV-MN PND as well as for homologous segments 39-44 in Bence-Jonce REI protein (BJRP), 41-46 in immunoglobulin lambda (Ig lambda), and 50-55 in beta-chain of horse hemoglobin (HH), (v) to find the conserved structural motifs inside diverse HIV-1 isolates, the structure determined was compared with the one derived earlier for the HIV-MN PND from NMR spectroscopy data, (vi) on the basis of all data obtained, the 3D structure model describing the set of biologically relevant conformations, which may present different antigenic determinants to the immune system in various HIV-1 isolates, was proposed for the immunogenic crown of the V3 loop. The results obtained are discussed in conjunction with the data on the structure for the HIV-1 PND reported in literature.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, Belarus Academy of Sciences, Kuprevich St., 5/2, 220141 Minsk, Republic of Belarus.
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21
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Guruprasad K, Prasad MS, Kumar GR. Analysis of gammabeta, betagamma, gammagamma, betabeta continuous turns in proteins. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2001; 57:292-300. [PMID: 11328486 DOI: 10.1046/j.1397-002x.2000.00822.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the observation of continuous turns in proteins which comprise individual gamma-turns or beta-turns or both that are situated immediately one after the other along the polypeptide chain. The continuous turns were identified from a representative data set of three-dimensional protein crystal structures. The gammabeta/betagamma, gammagamma and betabeta continuous turns represent peptides of varying amino acid residue lengths and conformations. The continuous turns frequently observed in proteins were: gammabeta, between a coil and a strand; betagamma, between a helix and a strand; gammagamma, between coils; and betabeta, either between a strand and a coil or between strands or coils. We determined the statistically significant amino acid residue preferences at individual positions in the turn, calculated amino acid positional potentials and analyzed main chain hydrogen bonds and side-chain interactions likely to stabilize the continuous turns. The data on continuous turns have been integrated in the database of structural motifs in proteins (DSMP) on our web server at (http://www.cdfd.org.in/dsmp.html). This is useful to make queries on sequences compatible with different continuous turns.
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Affiliation(s)
- K Guruprasad
- Center for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India.
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22
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Guruprasad K, Prasad MS, Kumar GR. Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2000; 56:250-63. [PMID: 11083064 DOI: 10.1034/j.1399-3011.2000.00739.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The number of gamma-turns in a representative protein dataset selected from the current Protein Data Bank has increased almost seven times during the past decade. Eighty percent classic gamma-turns and 57% inverse gamma-turns are associated as multiple turns with either another y-turn or a beta-turn. We refer to these as multiple turns of the (gammabeta)1,2,3 or (betagamma)1,2,3 type, depending upon whether the gamma-turn is before or after the beta-turn along the protein chain, respectively. However, for multiple turns involving only gamma-turns, we follow the nomenclature analogous to that proposed earlier for the multiple (or double) beta-turns. Fifty-eight per cent beta-turns are associated as multiple turns with another beta-turn. We extracted multiple turns from the protein dataset and classified them on the basis of individual gamma- or beta-turn types and the number of overlapping residues. Furthermore, we evaluated the amino acid positional potentials and determined the statistically significant amino acid preferences, hydrogen bond/side-chain interaction preferences in the multiple turns and secondary structure preferences for residues immediately flanking these turns. The results of our analysis would be useful in the modeling, prediction or design of multiple turns in proteins. The amino acid sequence corresponding to the multiple turn, position in the protein chain, PDB Code/chain in which multiple turn is present and the individual turn types constituting the multiple turns are available from our website and this information would also be integrated in our Database of Structural Motifs in Proteins (http://www.cdfd.org.in/dsmp.html).
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Affiliation(s)
- K Guruprasad
- Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India.
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23
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The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in two crystal forms at 2.2 and 2.9 Å resolution. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02758622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Narita M, Sode K, Ohuchi S. Single Amino Acid Preferences for Specific Locations at Type-Iα-Turns in Globular Proteins. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1999. [DOI: 10.1246/bcsj.72.1807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Sarma AV, Raju TV, Kunwar AC. NMR study of the peptide present in the principal neutralizing determinant (PND) of HIV-1 envelope glycoprotein gp120. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1997; 34:83-98. [PMID: 9178085 DOI: 10.1016/s0165-022x(97)01205-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The peptide sequence Gly-Pro-Gly-Arg-Ala-Phe (GPGRAF) is present in many principal neutralizing determinants (PND) of the human immunodeficiency virus type-1 (HIV-1). It has been shown that peptides from the PND sequence contain a significant beta turn in the conserved Gly-Pro-Gly-Arg sequence. In order to find out whether or not the smaller subunits also contain this turn, we have studied the NMR of a hexapeptide [GPGPRAF, peptide (I)], a heptapeptide Gly-Pro-Gly-Arg-Ala-Phe-Cys [GPGRAFC, peptide (II)] and a dodecapeptide [GPGRAFGPGRAF, peptide (III)], retaining the side chain protecting groups. Although the majority of conformations for these peptides are disordered, there is a considerable propensity of structures with beta turn in the GPGR sequence. While peptide (I) and peptide (III) seem to have both type I and type II beta turn conformations, peptide (II) shows a propensity of only type II beta turn. The nascent structures obtained in these peptides may get stabilized as the receptor binding conformation in the presence of the receptors, thus playing a significant role in vaccine development against HIV.
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Affiliation(s)
- A V Sarma
- Indian Institute of Chemical Technology, Hyderabad, India
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26
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Van Dijk AA, Van Wijk LL, Van Vliet A, Haris P, Van Swieten E, Tesser GI, Robillard GT. Structure characterization of the central repetitive domain of high molecular weight gluten proteins. I. Model studies using cyclic and linear peptides. Protein Sci 1997; 6:637-48. [PMID: 9070446 PMCID: PMC2143669 DOI: 10.1002/pro.5560060313] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The high molecular weight (HMW) proteins from wheat contain a repetitive domain that forms 60-80% of their sequence. The consensus peptides PGQGQQ and GYYPTSPQQ form more than 90% of the domain; both are predicted to adopt beta-turn structure. This paper describes the structural characterization of these consensus peptides and forms the basis for the structural characterization of the repetitive HMW domain, described in the companion paper. The cyclic peptides cyclo-[PGQGQQPGQGQQ] (peptide 1), cyclo-[GYYPTSPQQGA] (peptide 2), and cyclo-[PGQGQQGYYPTSPQQ] (peptide 3) were prepared using a novel synthesis route. In addition, the linear peptides (PGQGQQ)n (n = 1, 3, 5) were prepared. CD, FTIR, and NMR data demonstrated a type II beta-turn structure at QPGQ in the cyclic peptide 1 that was also observed in the linear peptides 9PGQGQQ)n. A type I beta-turn was observed at YPTS and SPQQ in peptides 2 and 3, with additional beta-turns of either type I or II at GAGY (peptide 2) and QQGY (peptide 3). The proline in YPTS showed considerable cis/trans isomerization, with up to 50% of the population in the cis-conformation; the other prolines were more than 90% in the trans conformation. The conversion from trans to cis destroys the type I beta-turn at YPTS, but leads to an increase in turn character at SPQQ and GAGY (peptide 2) or QQGY (peptide 3).
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Affiliation(s)
- A A Van Dijk
- Department of Biochemistry and Biophysical Chemistry, University of Groningen, The Netherlands
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27
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Awasthi SK, Raghothama SR, Balaram P. Conformational variability in short acyclic peptides. Stabilization of multiple β-turn structures in organic solvents. ACTA ACUST UNITED AC 1996. [DOI: 10.1039/p29960002701] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Gurunath R, Balaram P. A nonhelical, multiple beta-turn conformation in a glycine-rich heptapeptide fragment of trichogin A IV containing a single central alpha-aminoisobutyric acid residue. Biopolymers 1995; 35:21-9. [PMID: 7696554 DOI: 10.1002/bip.360350104] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The conformational properties of the protected seven-residue C-terminal fragment of the lipopeptaibol antibiotic Trichogin A IV (Boc-Gly-Gly-Leu-Aib-Gly-Ile-Leu-OMe) has been examined in CDCl3 and (CD3)2SO by 1H-nmr. Evidence for a multiple beta-turn conformation [type I' at Gly(1)-Gly(2), type II at Leu(3)-Aib(4), and a type I' at Aib(4)-Gly(5)] suggests that Leu(3) has preferred an extended or semiextended conformation over a helical conformation in CDCl3. This structure is thus in contrast to earlier observations of seven-residue peptides containing a single central Aib preferring helical conformations in both solution and crystalline states. A structural transition to a frayed right-handed helix is observed in (CD3)2SO. These results suggest that nonhelical conformations may be important in Gly-rich peptides containing Aib. Further, the presence of amino acids with contradictory influences on backbone conformational freedom can lead to well-defined conformational transitions even in small peptides.
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Affiliation(s)
- R Gurunath
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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29
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Abstract
Three thousand eight hundred ninety-nine beta-turns have been identified and classified using a nonhomologous data set of 205 protein chains. These were used to derive beta-turn positional potentials for turn types I' and II' for the first time and to provide updated potentials for formation of the more common types I, II, and VIII. Many of the sequence preferences for each of the 4 positions in turns can be rationalized in terms of the formation of stabilizing hydrogen bonds, preferences for amino acids to adopt a particular conformation in phi, psi space, and the involvement of turn types I' and II' in beta-hairpins. Only 1,632 (42%) of the turns occur in isolation; the remainder have at least 1 residue in common with another turn and have hence been classified as multiple turns. Several types of multiple turn have been identified and analyzed.
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Affiliation(s)
- E G Hutchinson
- Department of Biochemistry and Molecular Biology, University College, London, United Kingdom
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30
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31
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Srinivasan N, Anuradha VS, Ramakrishnan C, Sowdhamini R, Balaram P. Conformational characteristics of asparaginyl residues in proteins. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 44:112-22. [PMID: 7982754 DOI: 10.1111/j.1399-3011.1994.tb00565.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Backbone conformations at 1064 asparaginyl residues in 123 non-homologous, high-resolution X-ray structures of proteins were analysed. Asn adopts conformations in left-handed alpha-helical region and other partially allowed regions in the Ramachandran map more readily than any other non-glycyl residue. Asn conformational clusters in the (phi, psi) regions of left-handed alpha-helix right-handed alpha-helix and extended (beta) strands were investigated in detail for their occurrence in various secondary structures, especially in beta-turn regions. Preferences were observed for Asn conformations in different positions in various beta-turn types, including the first and fourth positions of the turn. Asparaginyl residues with extended conformations are found to occur frequently in irregular regions, although they are expected to occur predominantly in extended strands or in the third position of type II beta-turns. Asn conformations at the N-cap positions of helices strongly prefer extended conformation than alpha L, which seems to be characteristic of non-glycyl residues at that position. In the liners connecting two extended strands and those connecting an alpha-helix and an extended strand, Asn with alpha L or alpha R conformation is more favoured than Asn with the beta-conformation. Analysis of Asn-Asn doublets and Asn-X-Asn triplets permitted identification of conformational families in such sequences. Results of this investigation provide useful hints in modelling Asn-rich regions in proteins such as malaria parasite coat protein.
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Affiliation(s)
- N Srinivasan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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32
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Ghiara JB, Stura EA, Stanfield RL, Profy AT, Wilson IA. Crystal structure of the principal neutralization site of HIV-1. Science 1994; 264:82-5. [PMID: 7511253 DOI: 10.1126/science.7511253] [Citation(s) in RCA: 214] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The crystal structure of a complex between a 24-amino acid peptide from the third variable (V3) loop of human immunodeficiency virus-type 1 (HIV-1) gp 120 and the Fab fragment of a broadly neutralizing antibody (59.1) was determined to 3 angstrom resolution. The tip of the V3 loop containing the Gly-Pro-Gly-Arg-Ala-Phe sequence adopts a double-turn conformation, which may be the basis of its conservation in many HIV-1 isolates. A complete map of the HIV-1 principal neutralizing determinant was constructed by stitching together structures of V3 loop peptides bound to 59.1 and to an isolate-specific (MN) neutralizing antibody (50.1). Structural conservation of the overlapping epitopes suggests that this biologically relevant conformation could be of use in the design of synthetic vaccines and drugs to inhibit HIV-1 entry and virus-related cellular fusion.
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Affiliation(s)
- J B Ghiara
- Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037
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33
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Arteca GA. Scaling behavior of some molecular shape descriptors of polymer chains and protein backbones. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1994; 49:2417-2428. [PMID: 9961485 DOI: 10.1103/physreve.49.2417] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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34
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Arteca GA. Overcrossing spectra of protein backbones: characterization of three-dimensional molecular shape and global structural homologies. Biopolymers 1993; 33:1829-41. [PMID: 8268409 DOI: 10.1002/bip.360331209] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A procedure is developed and applied to characterize the global shape and folding features of the backbone of a chain molecule. The methodology is based on the following concept: the probability of observing a rigid placement of a backbone in 3-space as a projected curve with N overcrossings. The numerical computation of these probabilities allows one to construct the overcrossing spectrum of a macromolecule at a given configuration. Although the spectrum is built from the knowledge of the nuclear geometry of the main-chain atoms, the shape descriptor overlooks local geometrical features (such as distances and contacts) and provides a characterization of essential (topological) features of the overall fold, such as its compactness and degree of entanglement. In contrast with other shape descriptors, the present approach gives an absolute characterization of the configuration considered, and not one that is relative to an arbitrarily chosen reference structure. Moreover, it is possible to discriminate between folding features that otherwise may not be distinguished when using other geometrical or topological global descriptors. The overcrossing spectrum is proposed as a tool that complements current structural analyses of macromolecules, especially when monitoring structural homologies within a group of related or unrelated polymers. In this work, we apply the methodology to the analysis of proteins having the globin fold. The results are compared with those of other proteins exhibiting similar size and number of residues. Some basic properties of the spectra as a function of the chain length are also discussed.
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Affiliation(s)
- G A Arteca
- Département de Chimie et Biochimie, Laurentian University, Sudbury, Ontario, Canada
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35
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Perczel A, Foxman BM, Fasman GD. How reverse turns may mediate the formation of helical segments in proteins: an x-ray model. Proc Natl Acad Sci U S A 1992; 89:8210-4. [PMID: 1518848 PMCID: PMC49887 DOI: 10.1073/pnas.89.17.8210] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The three-dimensional structure of a protein is the assembly of different secondary structural elements, such as alpha-helices, beta-pleated sheets, and beta-turns. Although the conformation of hundreds of proteins has been elaborated in the solid state, only a vague understanding of the mechanism of their conformational folding is known. One facet of this topic is the conformational interconversion of one or more beta-turns to a helical structure (and vice versa), which may also be related to the formation of helix-turn-helix motifs often observed in globular proteins. Based on a comprehensive structural analysis of proteins, Sundaralingam and Sekharudu [Sundaralingam, M. & Sekharudu, Y. C. (1989) Science 244, 1333-1337] previously suggested that "structure-water" molecules in proteins may mediate such a conformational change. An x-ray crystal structure determination of t-butoxycarbonyl (Boc)-Val-Ser-NHCH3 reveals (i) an ideal type I beta-turn backbone conformation and (ii) a hydrogen-bond network more typical of an alpha-helix than a beta-turn conformation. The molecular packing of this simple beta-turn model reported here provides a plausible and simple alternative of how a beta-turn-like conformation may serve as a conformational template for helical-structure formation (and vice versa) during the folding procedure.
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Affiliation(s)
- A Perczel
- Graduate Department of Biochemistry, Brandeis University, Waltham, MA 02254-9110
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36
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Halford NG, Tatham AS, Sui E, Daroda L, Dreyer T, Shewry PR. Identification of a novel beta-turn-rich repeat motif in the D hordeins of barley. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1122:118-22. [PMID: 1643086 DOI: 10.1016/0167-4838(92)90313-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The amino acid sequence of the C-terminal part of a barley D hordein seed protein was deduced from the nucleotide sequence of a partial cDNA. It showed high homology with the HMW glutenin subunits of wheat, both proteins consisting predominately of repeated sequences. Whereas the wheat repeats are based on tri-, hexa- and nonapeptides that are rich in glycine, proline and glutamine, the D hordein also contains eleven copies of a novel unrelated motif: Thr-Thr-Val-Ser. The repeated sequences in the wheat glutenin subunits have been demonstrated to form an unusual spiral supersecondary structure based on beta-turns. Conformational analysis of the Thr-Thr-Val-Ser motif by secondary structure prediction and by circular dichroism spectroscopy of an 18 residue synthetic peptide demonstrates that it also forms beta-turns. Thus, D hordein may also have a spiral structure like that of HMW glutenin, despite the presence of a different repeat motif. This conservation of protein conformation in D hordein and the wheat glutenin subunits may indicate a structural role, perhaps in packing of the proteins within the protein bodies of the developing grain.
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Affiliation(s)
- N G Halford
- Department of Agricultural Sciences, University of Bristol, UK
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Wilmanns M, Priestle JP, Niermann T, Jansonius JN. Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution. J Mol Biol 1992; 223:477-507. [PMID: 1738159 DOI: 10.1016/0022-2836(92)90665-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The three-dimensional structure of the monomeric bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from Escherichia coli has been refined at 2.0 A resolution, using oscillation film data obtained from synchrotron radiation. The model includes the complete protein (452 residues), two phosphate ions and 628 water molecules. The final R-factor is 17.3% for all observed data between 15 and 2 A resolution. The root-mean-square deviations from ideal bond lengths and bond angles are 0.010 A and 3.2 degrees, respectively. The structure of N-(5'-phosphoribosyl)anthranilate isomerase: indole-3-glycerol-phosphate synthase from E. coli comprises two beta/alpha-barrel domains that superimpose with a root-mean-square deviation of 2.03 A for 138 C alpha-pairs. The C-terminal domain (residues 256 to 452) catalyses the PRAI reaction and the N-terminal domain (residues 1 to 255) catalyses the IGPS reaction, two sequential steps in tryptophan biosynthesis. The enzyme has the overall shape of a dumb-bell, resulting in a surface area that is considerably larger than normally observed for monomeric proteins of this size. The active sites of the PRAI and the IGPS domains, both located at the C-terminal side of the central beta-barrel, contain equivalent binding sites for the phosphate moieties of the substrates N-(5'-phosphoribosyl) anthranilate and 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate. These two phosphate binding sites are identical with respect to their positions within the tertiary structure of the beta/alpha-barrel, the conformation of the residues involved in phosphate binding and the hydrogen-bonding network between the phosphate ions and the protein. The active site cavities of both domains contain similar hydrophobic pockets that presumably bind the anthranilic acid moieties of the substrates. These similarities of the tertiary structures and the active sites of the two domains provide evidence that N-(5'-phosphoribosyl)anthranilate isomerase:indole-3-glycerol-phosphate synthase from E. coli results from a gene duplication event of a monomeric beta/alpha-barrel ancestor.
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Affiliation(s)
- M Wilmanns
- Department of Structural Biology, University of Basel, Switzerland
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39
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Onesti S, Brick P, Blow DM. Crystal structure of a Kunitz-type trypsin inhibitor from Erythrina caffra seeds. J Mol Biol 1991; 217:153-76. [PMID: 1988676 DOI: 10.1016/0022-2836(91)90618-g] [Citation(s) in RCA: 114] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The trypsin inhibitor DE-3 from Erythrina caffra (ETI) belongs to the Kunitz-type soybean trypsin inhibitor (STI) family and consists of 172 amino acid residues with two disulphide bridges. The amino acid sequence of ETI shows high homology to other trypsin inhibitors from the same family but ETI has the unique ability to bind and inhibit tissue plasminogen activator. The crystal structure of ETI has been determined using the method of isomorphous replacement and refined using a combination of simulated annealing and conventional restrained least-squares crystallographic refinement. The refined model includes 60 water molecules and 166 amino acid residues, with a root-mean-square deviation in bond lengths from ideal values of 0.016 A. The crystallographic R-factor is 20.8% for 7770 independent reflections between 10.0 and 2.5 A. The three-dimensional structure of ETI consists of 12 antiparallel beta-strands joined by long loops. Six of the strands form a short antiparallel beta-barrel that is closed at one end by a "lid" consisting of the other six strands coupled in pairs. The molecule shows approximate 3-fold symmetry about the axis of the barrel, with the repeating unit consisting of four sequential beta-strands and the connecting loops. Although there is no sequence homology, this same fold is present in the structure of interleukin-1 alpha and interleukin-1 beta. When the structure of ETI and interleukin-1 beta are superposed, the close agreement between the alpha-carbon positions for the beta-strands is striking. The scissile bond (Arg63-Ser64) is located on an external loop that protrudes from the surface of the molecule and whose architecture is not constrained by secondary structure elements, disulphide bridges or strong electrostatic interactions. The hydrogen bonds made by the side-chain amide group of Asn12 play a key role in maintaining the three-dimensional structure of the loop. This residue is in a position corresponding to that of a conserved asparagine in the Kazal inhibitor family. Although the overall structure of ETI is similar to the partial structure of STI, the scissile bond loop is displaced by about 4 A. This displacement probably arises from the fact that the structure of STI has been determined in a complex with trypsin but could possibly be a consequence of the close molecular contact between Arg63 and an adjacent molecule in the crystal lattice.
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Affiliation(s)
- S Onesti
- Blackett Laboratory, Imperial College, London, England, U.K
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40
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Conformational studies of peptides corresponding to the coeliac-activating regions of wheat alpha-gliadin. Biochem J 1990; 270:313-8. [PMID: 2400392 PMCID: PMC1131722 DOI: 10.1042/bj2700313] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The structures of four peptides corresponding to parts of the coeliac-activating protein A-gliadin were studied by structure prediction and c.d. spectroscopy. Three of the peptides corresponded to parts of the coeliac-activating N-terminal region (residues 3-55, 3-19 and 39-45) and contained two tetrapeptide motifs common to all coeliac-active regions (Pro-Ser-Gln-Gln and Gln-Gln-Gln-Pro). The Pro-Ser-Gln-Gln sequence was also present in the fourth peptide, on the basis of the C-terminal part of the molecule (211-217). These studies showed that beta-reverse turns were the predominant structural feature in all peptides and were predominantly of type I/III in two of the N-terminal peptides and type II in the C-terminal peptide. These turns form when the peptide is dissolved in solvents of low dielectric constant (trifluoroethanol) and high dielectric constant (water and iso-osmotic saline), although their presence in the N-terminal peptides may be masked in the latter solvents due to equilibrium with a poly-L-proline II structure favoured at lower temperatures.
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41
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Bhandary KK, Senadhi SE, Prasad KU, Urry DW, Vijay-Kumar S. Conformation of a cyclic decapeptide analog of a repeat pentapeptide sequence of elastin: cyclo-bis(valyl-prolyl-alanyl-valyl-glycyl). INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1990; 36:122-7. [PMID: 2272748 DOI: 10.1111/j.1399-3011.1990.tb00954.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The conformation of a cyclic decapeptide analog of a repeat sequence of elastin has been determined in the crystalline state using X-ray crystallographic techniques. Tetragonal crystals were grown from a solution of the decapeptide in water; space group P4(2)2(1)2, a = 19.439(2) & c = 13.602(1) A, with four formula units (C40H66N10O10.4H2O) per unit cell. The cyclic decapeptide in the crystal exhibits exact twofold symmetry. The asymmetric unit contains one pentapeptide and two water molecules for a total of 32 nonhydrogen atoms. The structure has been determined by the application of direct methods and refined by full-matrix least squares to an R index of 0.053 for 2272 reflections with intensities greater than 2 sigma(I). The backbone conformation of the asymmetric pentapeptide can be described as consisting of a double beta bend of Type III-I. The Type III turn has Pro (phi = -59.3 degrees, psi = -26.8 degrees) and Ala (phi = -65.9 degrees, psi = -23.1 degrees) at the corners while Type I turn has Ala (phi = -65.9 degrees, psi = -23.1 degrees) and Val (phi = -98.9 degrees, psi = 8.3 degrees) as the corner residues. The cyclic decapeptide has two such double bends linked together by Gly-Val bridges.
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Affiliation(s)
- K K Bhandary
- Oral Biology Department & Dental Research Institute, School of Dental Medicine, State University of New York, Buffalo
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42
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Tatham AS, Drake AF, Shewry PR. Conformational studies of synthetic peptides corresponding to the repetitive regions of the high molecular weight (HMW) glutenin subunits of wheat. J Cereal Sci 1990. [DOI: 10.1016/s0733-5210(09)80163-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Tamburro AM, Guantieri V, Pandolfo L, Scopa A. Synthetic fragments and analogues of elastin. II. Conformational studies. Biopolymers 1990; 29:855-70. [PMID: 2383648 DOI: 10.1002/bip.360290419] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Conformational studies on synthetic repetitive sequences and analogues of elastin are described. CD and nmr measurements gave evidence of flexible beta-turns as the dominant structural feature whose stability was found to decrease by increasing the number of repetitive units. The sequences comprised the structural unit Gly-X-Gly (X = Val, Leu, Ala), with X-Gly or Gly-Gly located at the corners of the bend. Based on that, it is proposed that these regions of elastin, unlike the proline-containing sequences, contribute to the elasticity of the protein through a classical mechanism in terms of the rotational isomeric state theory.
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Affiliation(s)
- A M Tamburro
- Department of Chemistry, University of Basilicata, Potenza, Italy
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Ishii H, Nadaoka O, Mimura Y, Inoue Y, Chûjô R. Synthesis and conformational analysis of Aib-containing peptide modelling for N-glycosylation site in N-glycoprotein. Int J Biol Macromol 1989; 11:329-34. [PMID: 2489100 DOI: 10.1016/0141-8130(89)90003-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A tetrapetide containing an Aib residue, Boc-Asn-Aib-Thr-Aib-OMe, was synthesized as a peptide model for the N-glycosylation site in N-glycoproteins. Backbone conformation of the peptide and possible intramolecular interaction between the Asn and Thr side chains were elucidated by means of n.m.r. spectroscopy. Temperature dependence of NH proton chemical shift and NOE experiments showed that Boc-Asn-Aib-Thr-Aib-OMe has a tendency to form a beta-turn structure with a hydrogen bond involving Thr and Aib4 NH groups. Incorporation of Aib residues in the peptide model promotes folding of the peptide backbone. With folded backbone conformation, carboxyamide protons of the Asn residue are not involved in hydrogen bond network, while the OH group of the Thr residue is a candidate for a hydrogen bond in DMSO-d6 solution.
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Affiliation(s)
- H Ishii
- Department of Industrial Chemistry, Tokyo National College of Technology
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45
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Henrick K, Collyer CA, Blow DM. Structures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively. J Mol Biol 1989; 208:129-57. [PMID: 2769749 DOI: 10.1016/0022-2836(89)90092-2] [Citation(s) in RCA: 89] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The structures of D-xylose isomerase from Arthrobacter strain B3728 containing the polyol inhibitors xylitol and D-sorbitol have been solved at 2.5 A and 2.3 A, respectively. The structures have been refined using restrained least-squares refinement methods. The final crystallographic R-factors for the D-sorbitol (xylitol) bound molecules, for 43,615 (32,989) reflections are 15.6 (14.7). The molecule is a tetramer and the asymmetric unit of the crystal contains a dimer, the final model of which, incorporates a total of 6086 unique protein, inhibitor and magnesium atoms together with 535 bound solvent molecules. Each subunit of the enzyme contains two domains: the main domain is a parallel-stranded alpha-beta barrel, which has been reported in 14 other enzymes. The C-terminal domain is a loop structure consisting of five helical segments and is involved in intermolecular contacts between subunits that make up the tetramer. The structures have been analysed with respect to molecular symmetry, intersubunit contacts, inhibitor binding and active site geometry. The refined model shows the two independent subunits to be similar apart from local deviations due to solvent contacts in the solvent-exposed helices. The enzyme is dependent on a divalent cation for catalytic activity. Two metal ions are required per monomer, and the high-affinity magnesium(II) site has been identified from the structural results presented here. The metal ion is complexed, at the high-affinity site, by four carboxylate side-chains of the conserved residues, Glu180, Glu216, Asp244 and Asp292. The inhibitor polyols are bound in the active site in an extended open chain conformation and complete an octahedral co-ordination shell for the magnesium cation via their oxygen atoms O-2 and O-4. The active site lies in a deep pocket near the C-terminal ends of the beta-strands of the barrel domain and includes residues from a second subunit. The tetrameric molecule can be considered to be a dimer of "active" dimers, the active sites being composed of residues from both subunits. The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. One of these, between Asp23 and Arg139, appears to play a key role in stabilizing the active dimer and is conserved in the known sequences of this enzyme.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- K Henrick
- Blackett Laboratory, Imperial College, London, England
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Tatham AS, Drake AF, Shewry PR. Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein. Biochem J 1989; 259:471-6. [PMID: 2719660 PMCID: PMC1138532 DOI: 10.1042/bj2590471] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
C hordein, a storage protein from barley grains, has an Mr of about 53,000, and consists predominantly of repeated octapeptides with a consensus sequence of Pro-Gln-Gln-Pro-Phe-Pro-Gln-Gln. Previously reported hydrodynamic and c.d. studies indicate the presence of beta-turns, the repetitive nature of which may lead to the formation of a loose spiral. In order to study these turns we have compared the structures of a synthetic peptide corresponding to the consensus repeat motif and total C hordein by using c.d. and Fourier-transform i.r. spectroscopy. The synthetic peptide exhibited spectra typical of beta I/III reverse turns when dissolved in trifluoroethanol at 22 degrees C and in water at 70 degrees C, but 'random-coil'-like spectra in water at 22 degrees C. The whole protein also showed increases in beta I/III reverse turns when dissolved in increasing concentrations of trifluoroethanol (50-100%, v/v) or heated in ethanol/water (7:3, v/v). Two cryogenic solvent systems were used to determine the c.d. spectra of the peptide and protein at temperatures down to -100 degrees C. Methanol/glycerol (9:1, v/v) and ethanediol/water (2:1, v/v) were selected as analogues of trifluoroethanol/water and water respectively. The peptide exhibited beta I/III-reverse-turn and 'random-coil'-like spectra in methanol/glycerol and ethanediol/water respectively at 22 degrees C, but a spectrum similar to that of a poly-L-proline II helix in both solvents at -100 degrees C. Similarly the proportion of this spectral type also increased when the whole protein was cooled in both solvents. These results indicate that a poly-L-proline II conformation at low temperatures is in equilibrium with a beta I/III-turn-rich conformation at higher temperatures. The latter conformation is also favoured in solvents of low dielectric constant such as trifluoroethanol. The 'random-coil'-like spectra exhibited by the protein and peptide in high-dielectric-constant solvents at room temperature may result from a mixture of the two conformations rather than from the random-coil state.
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Affiliation(s)
- A S Tatham
- Department of Biochemistry, A.F.R.C. Institute of Arable Crops Research, Rothamsted Experimental Station, Harpenden, Herts, U.K
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47
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Mizuno H. Prediction of the conformation of ice-nucleation protein by conformational energy calculation. Proteins 1989; 5:47-65. [PMID: 2748572 DOI: 10.1002/prot.340050107] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The active conformation of an ice-nucleation protein, whose major portion consists of a long polypeptide segment of nearly repetitive octapeptides, is predicted by the analyses of conformational energy and the mechanism of crystal growth. The protein ideally has an exact octapeptide repetition and is assumed to have a helical conformation. The present study searched for low-energy helical conformations and each of the obtained low-energy conformations examined as to whether it has a surface structure that can promote crystal formation. Two conformations obtained were good candidates for an ice nucleus. Both were found to have on their surfaces an arrangement of hydrogen-bonding sites, which fits well with those of hydrogen bonds in hexagonal ice crystal. Further, one of the two conformations had a hexagonal conformational symmetry consistent with the hexagonal ice crystal structure. The other conformation had a pentagonal conformational symmetry that could enable the growth of an ice crystal--dendritic polycrystalline snow crystal--which grows on metastable cubic ice.
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Affiliation(s)
- H Mizuno
- Computer Center for Medical Research, School of Medicine, Kurume University, Japan
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48
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Betzel C, Pal GP, Saenger W. Three-dimensional structure of proteinase K at 0.15-nm resolution. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:155-71. [PMID: 3203685 DOI: 10.1111/j.1432-1033.1988.tb14440.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The crystal and molecular structure of proteinase K was determined by X-ray diffraction data to 0.15-nm resolution. The enzyme belongs to the subtilisin family with an active-site catalytic triad Asp39--His69--Ser224 but is a representative of a subgroup with a free Cys73 close to and 'below' the active His69. Besides this Cys72, proteinase K has two disulfide bonds, Cys34--Cys123 and Cys178--Cys249, which contribute to the stability of the tertiary structure consisting of an extended central parallel beta-sheet decorated by six alpha-helices, three short antiparallel beta-sheets, 18 beta-turns and involving several internal, structurally important water molecules. Proteinase K exhibits two Ca2+-binding sites, one very strong and the other weak, which were the sites of the heavy atoms (Pb2+, Sm3+) used to solve the crystal structure. The weak binding site is liganded to the N and C termini, Thr16 and Asp260, and is only incompletely coordinated by oxygen ligands. The strong binding site is coordinated in the form of a pentagonal bipyramid with the side chain carboxylate of Asp200 and the C = O of Pro175 as apex, and C = O of Val177 and four water molecules in the equatorial plane. Upon removal of this Ca2+, proteinase K loses activity which is interpreted in terms of a local structural deformation involving the substrate-recognition site (Ser132--Gly136), probably associated with a cis----trans isomerization of cis Pro171. Several water molecules are located in the active site. One, W335, is positioned in the 'oxyanion hole' and is displaced by the C = O of the scissile peptide bond of the substrate, as indicated by crystallographic studies with peptide chloromethane inhibitors. Based on these experiments, a reaction mechanism is proposed where the peptide substrate forms a three-stranded antiparallel pleated sheet with the recognition site of proteinase K consisting of Ser132--Leu133--Gly134 on one side and Gly100--Ser101 on the other, followed by expulsion of the oxyanion hole water W335 and hydrolytic cleavage by the Asp39--His69--Serr224 triad. These latter residues display low thermal motion corresponding to well-defined geometry and are hardly accessible to solvent molecules, whereas the recognition-site amino acids are more flexible and partially exposed to solvent.
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Affiliation(s)
- C Betzel
- Institut für Kristallographie, Freie Universität Berlin
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49
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Abstract
beta-Turns have been extracted from 59 non-identical proteins (resolution 2 A) using the standard criterion that the distance between C alpha (i) and C alpha (i + 3) is less than 7 A (1 A = 0.1 nm). The beta-turns have been classified, using phi, psi angles, into seven conventional turn types (I, I', II, II', IV, VIa, VIb) and a new class of beta-turn, designated type VIII, in which the central residues (i + 1, i + 2) adopt an alpha R beta conformation. Most beta-turn types are found in various topological environments, with the exception of I' and II' beta-turns, where 83% and 50%, respectively, are found in beta-hairpins. Sufficient data have been gathered to enable, for the first time, the separate statistical analysis of type I and II beta-turns. The two turn types have been shown to be strikingly different in their sequence preferences. Type I turns favour Asp, Asn, Ser and Cys at i; Asp, Ser, Thr and Pro at i + 1; Asp, Ser, Asn and Arg at i + 2; Gly, Trp and Met at i + 3, whilst type II turns prefer Pro at i + 1; Gly and Asn at i + 2; Gln and Arg at i + 3. These preferences have been explained by the specific side-chain interactions observed within the X-ray structures. The positional trends for type I and II beta-turns have been incorporated into the simple empirical predictive algorithm originally developed by P.N. Lewis et al. The program has improved the positional prediction of beta-turns, and has enhanced and extended the method by predicting the type of beta-turn. Since the observed preferences reflect local interactions these predictions are applicable not only to proteins, but also to peptides, many of which are thought to contain beta-turns.
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Affiliation(s)
- C M Wilmot
- Department of Crystallography, Birkbeck College, London, U.K
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50
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Wetzel R, Buder E, Hermel H, H�ttner A. Conformations of different gelatins in solutions and in films an analysis of circular dichroism (CD) measurements. Colloid Polym Sci 1987. [DOI: 10.1007/bf01417460] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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