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divide and conquer: cleavable cross-linkers to study protein conformation and protein-protein interactions

ANALYTICAL ANd BIOANALYTICAL CHEMISTRY 2017年第1期409卷 33-44页

作者： Sinz, Andrea Martin Luther Univ Halle Wittenberg Inst Pharm Dept Pharmaceut Chem & Bioanalyt Wolfgang Langenbeck Str 4 D-06120 Halle Saale Germany

Chemical cross-linking combined with mass spectrometry (MS) and computational modeling has evolved as an alternative method to address fundamental questions in structural biology. The constraints revealed by the cross-links yield valuable distance information and allow one to deduce three-dimensional structural information on very large and transient protein complexes. during the past few years, technical advances in the cross-linking/MS approach have been enormous, mainly owing to the fantastic advances in MS technology, and it is easily overlooked that significant progress has been made in the design of novel cross-linking reagents. In this review, the advent of cleavable cross-linking reagents will be highlighted. In particular, gas-phase (MS-) cleavable cross-linkers offer unique properties for an automated, data-dependent assignment of cross-linked products based on the generation of characteristic fragment ion signatures in MS/MS and MS3 spectra. Therefore, MS-cleavable cross-linkers are envisioned to hold the key for proteome-wide applications of the chemical cross-linking/MS approach, not only to delineate the conformation of single proteins but also to decipher protein interaction networks.

关键词： Chemical cross-linking Cleavable cross-linkers Mass spectrometry protein 3d structure protein interaction networks

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The ProFunc Function Prediction Server

The ProFunc Function Prediction Server

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作者： Roman A. Laskowski

The ProFunc web server is a tool for helping identify the function of a given protein whose 3d coordinates have been experimentally determined or homology modeled. It uses a cocktail of both sequence- and structure-based methods to identify matches to other proteins that may, in turn, suggest the query protein’s most likely function. The server was originally developed to aid the worldwide structural genomics effort at the start of the millennium. It accepts a file containing the protein’s 3d coordinates in PdB format, and, when processing is complete, sends an email containing a link to the password-protected result pages. The results include an at-a-glance summary, as well as separate pages containing more detailed analyses. The server can be found at: http://***/thornton-srv/databases/profunc . less

关键词： Genomics protein structure Analysis X-ray Crystallography Jmol Statistical Calculation Sequence Alignment Analysis (conservation) PROSITE Function prediction Motifs ProFunc protein 3d structure Structural templates Fold matching

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VaProS: a database-integration approach for protein/genome information retrieval

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Journal of Structural and Functional Genomics 2016年第4期17卷 69-81页

作者： Gojobori, Takashi Ikeo, Kazuho Katayama, Yukie Kawabata, Takeshi Kinjo, Akira R. Kinoshita, Kengo Kwon, Yeondae Migita, Ohsuke Mizutani, Hisashi Muraoka, Masafumi Nagata, Koji Omori, Satoshi Sugawara, Hideaki Yamada, daichi Yura, Kei Computational Bioscience Research Center Biological and Environmental Sciences and Engineering King Abdullah University of Science and Technology Thuwal 23955-6900 Saudi Arabia National Institute of Genetics Shizuoka Mishima 411-8540 Japan Graduate School of Agricultural and Life Sciences University of Tokyo Bunkyo Tokyo 113-8657 Japan Institute for Protein Research Osaka University Suita Osaka 565-0871 Japan Graduate School of Information Sciences Tohoku University Miyagi Sendai 980-8597 Japan Tohoku Medical Megabank Organization Tohoku University Miyagi Sendai 980-8573 Japan Department of Maternal-Fetal Biology National Research Institute for Child Health and Development Setagaya Tokyo 157-8535 Japan Department of Pediatrics St. Marianna University School of Medicine Miyamae Kawasaki 216-8511 Japan Center for Informational Biology Ochanomizu University 2-1-1 Otsuka Bunkyo Tokyo 112-8610 Japan

Life science research now heavily relies on all sorts of databases for genome sequences, transcription, protein three-dimensional (3d) structures, protein–protein interactions, phenotypes and so forth. The knowledge accumulated by all the omics research is so vast that a computer-aided search of data is now a prerequisite for starting a new study. In addition, a combinatory search throughout these databases has a chance to extract new ideas and new hypotheses that can be examined by wet-lab experiments. By virtually integrating the related databases on the Internet, we have built a new web application that facilitates life science researchers for retrieving experts’ knowledge stored in the databases and for building a new hypothesis of the research target. This web application, named VaProS, puts stress on the interconnection between the functional information of genome sequences and protein 3d structures, such as structural effect of the gene mutation. In this manuscript, we present the notion of VaProS, the databases and tools that can be accessed without any knowledge of database locations and data formats, and the power of search exemplified in quest of the molecular mechanisms of lysosomal storage disease. VaProS can be freely accessed at http://***/vapros/. © 2016, The Author(s).

关键词： Big data analysis database integration Lysosomal storage disease protein 3d structure

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Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

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protein SCIENCE 2015年第8期24卷 1193-1209页

作者： Sinz, Andrea Arlt, Christian Chorev, dror Sharon, Michal Univ Halle Wittenberg Inst Pharm Dept Pharmaceut Chem & Bioanalyt D-06120 Halle Germany Weizmann Inst Sci Dept Biol Chem IL-76100 Rehovot Israel

Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.

关键词： chemical cross-linking native mass spectrometry protein 3d structure protein-protein interactions

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An ice nucleation protein from Fusarium acuminatum: cloning, expression, biochemical characterization and computational modeling

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BIOTECHNOLOGY LETTERS 2014年第10期36卷 2043-2051页

作者： Lagzian, Milad Latifi, Ali Mohammad Bassami, Mohammad Reza Mirzaei, Morteza Ferdowsi Univ Mashhad Fac Vet Med Div Biotechnol Mashhad Iran Ferdowsi Univ Mashhad Inst Biotechnol Mashhad Iran Baqiyatallah Univ Med Sci Appl Biotechnol Res Ctr Tehran Iran

Ice nucleation proteins (INP) are a major cause of frost damage in plants and crops. Here, an INP gene from Fusarium acuminatum was optimized, synthesized, expressed in *** and subsequently purified and characterized. The protein belongs to the second class of ice nucleation proteins with an optimum pH 5.5, relative activity and stability between pH 5 and 9.5 and up to 45 A degrees C. The protein was fully active and stable in the presence of dimethyl sulfoxide (dMSO), dioxane, acetone and ethyl acetate. Moreover, it retained over 50 % of its original activity in the presence of polyvinyl alcohol. The 3d structure model of the INP-F indicated the protein had three distinct domains as exist in other ice nucleation proteins with some variations. Considering these promising results, INP-F could be a novel candidate for industrial applications.

关键词： Cloning and expression Fusarium acuminatum Ice nucleation protein protein 3d structure

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On the functional and structural characterization of hubs in protein-protein interaction networks

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BIOTECHNOLOGY AdVANCES 2013年第2期31卷 274-286页

作者： Bertolazzi, Paola Bock, Mary Ellen Guerra, Concettina IASI CNR Rome Italy Purdue Univ Dept Stat W Lafayette IN 47907 USA Georgia Inst Technol Coll Comp Atlanta GA 30332 USA

A number of interesting issues have been addressed on biological networks about their global and local properties. The connection between the topological properties of proteins in protein-protein Interaction (PPI) networks and their biological relevance has been investigated focusing on hubs, i.e. proteins with a large number of interacting partners. We will survey the literature trying to answer the following questions: do hub proteins have special biological properties? do they tend to be more essential than non-hub proteins? Are they more evolutionarily conserved? do they play a central role in modular organization of the protein interaction network? Are there structural properties that characterize hub proteins? (C) 2012 Elsevier Inc. All rights reserved.

关键词： protein-protein interaction networks Network topology Hubs protein 3d structure Evolution Lethality Structural disorder

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Predict Interactions between protein Residues for developing Antibody Therapeutics

Predict Interactions between Protein Residues for Developing...

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International Conference on Manufacturing Science and Technology (ICMST 2011)

作者： Shu, Wenlung Lee, Chia-Hsuan Chung Hua Univ Bioinformat Dept Hsinchu 300 Taiwan

ISBN: (纸本)9783037852958

Recently, protein-antibody therapeutics becomes a hot search topic. In this paper, all protein interaction data files are collected from INTERPARE. protein sequence and its secondary structure both are used to build HMM mathematical model. We randomly take 80% data to train positive and negative HMM models and 20% data to test. The accuracy of this approach can reach to 79.80%. This model can further be used to predict protein function sites and predict if a protein interacts with other proteins.

关键词： Antibody Therapeutics protein 1d and 2d sequence protein 3d structure Predict protein Interactions HMM

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protein allergenicity prediction on the basis of conformational peptides

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Russian Journal of Genetics: Applied Research 2012年第1期2卷 18-22页

作者： Bragin, A.O. demenkov, P.S. Ivanisenko, V.A. Institute of Cytology and Genetics Siberian Branch Russian Academy of Sciences Novosibirsk Russian Federation

Allergies are one of the most common health problems for developed countries. The accuracy of the prediction of protein allergenicity from their amino-acid sequences is limited due to the spatial organization of protein patches that contain allergenic epitopes. A new method for the prediction of allergenic proteins based on an analysis of conformational peptides on their surfaces was proposed. It was shown that the use of information on the conformational peptides of a protein improves the accuracy of the method for allergenicity prediction. © 2012 Pleiades Publishing, Ltd.

关键词： allergen conformational peptide protein 3d structure protein allergenicity prediction

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Homology modeling of 3d structure of human chitinase-like protein CHI3L2

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CENTRAL EUROPEAN JOURNAL OF BIOLOGY 2010年第4期5卷 407-420页

作者： Iershov, Anton Odynets, Konstantin Kornelyuk, Alexander Kavsan, Vadim Natl Acad Sci Ukraine Dept Biosynth Nucle Acids Inst Mol Biol & Genet UA-03680 Kiev Ukraine Natl Acad Sci Ukraine Dept Prot Engn & Bioinformat Inst Mol Biol & Genet UA-03680 Kiev Ukraine

The human genome encodes six proteins of family 18 glycosyl hydrolases, two active chitinases and four chitinase-like lectins (chi-lectins) lacking catalytic activity. The present article is dedicated to homology modeling of 3d structure of human chitinase 3-like 2 protein (CHI3L2), which is overexpressed in glial brain tumors, and its structural comparison with homologous chi-lectin CHI3L1. Two crystal structures of CHI3L1 in free state (protein data Bank codes 1HJX and 1NWR) were used as structural templates for the homology modeling by Modeller 9.7 program, and the best quality model structure was selected from the obtained model ensemble. Analysis of potential oligosaccharide-binding groove structures of CHI3L1 and CHI3L2 revealed significant differences between these two homologous proteins. 8 of 19 amino acid residues important for ligand binding are substituted in CHI3L2: Tyr(34)/Asp(39), Trp(69)/Lys(74), Trp(71)/Lys(76), Trp(99)/Tyr(104), Asn(100)/Leu(105), Met(204)/Leu(210), Tyr(206)/Phe(212) and Arg(263)/His(271). The differences between these residues could influence the structure of the ligand-binding groove and substantially change the ability of CHI3L2 to bind oligosaccharide ligands.

关键词： Chitinase 3-like 2 protein (CHI3L2, YKL-39) Chitinase 3-like 1 protein (CHI3L1, YKL-40) Chi-lectins Homology modeling protein 3d structure Oligosaccharide binding

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RESOPS: A database for Analyzing the Correspondence of RNA Editing Sites to protein Three-dimensional structures

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PLANT ANd CELL PHYSIOLOGY 2009年第11期50卷 1865-1873页

作者： Yura, Kei Sulaiman, Sintawee Hatta, Yosuke Shionyu, Masafumi Go, Mitiko Ochanomizu Univ Grad Sch Humanities & Sci Bunkyo Ku Tokyo 1128610 Japan Ochanomizu Univ Ctr Informat Biol Bunkyo Ku Tokyo 1128610 Japan King Mongkuts Univ Technol Thonburi Bioinformat Program Bangmod Toongkru Thailand Nagahama Inst Biosci & Technol Fac Biosci Dept Biosci Shiga 5260829 Japan Tokyo Med & Dent Univ Bunkyo Ku Tokyo 1138510 Japan Res Org Informat & Syst Minato Ku Tokyo 1050001 Japan

Transcripts from mitochondrial and chloroplast dNA of land plants often undergo cytidine to uridine conversion-type RNA editing events. RESOPS is a newly built database that specializes in displaying RNA editing sites of land plant organelles on protein three-dimensional (3d) structures to help elucidate the mechanisms of RNA editing for gene expression regulation. RESOPS contains the following information: unedited and edited cdNA sequences with notes for the target nucleotides of RNA editing, conceptual translation from the edited cdNA sequence in pseudo-UniProt format, a list of proteins under the influence of RNA editing, multiple amino acid sequence alignments of edited proteins, the location of amino acid residues coded by codons under the influence of RNA editing in protein 3d structures and the statistics of biased distributions of the edited residues with respect to protein structures. Most of the data processing procedures are automated;hence, it is easy to keep abreast of updated genome and protein 3d structural data. In the RESOPS database, we clarified that the locations of residues switched by RNA editing are significantly biased to protein structural cores. The integration of different types of data in the database also help advance the understanding of RNA editing mechanisms. RESOPS is accessible at http://***/RNAEdITING/.

关键词： Chloroplast Mitochondrion Molecular evolution Organelle genome protein 3d structure RNA editing

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