Frontiers in Protein and Peptide Sciences

Volume 1

by

Ben M. Dunn

DOI: 10.2174/97816080586241140101
eISBN: 978-1-60805-862-4, 2014
ISBN: 978-1-60805-863-1
ISSN: 2213-9877 (Print)



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Frontiers in Protein and Peptide Sciences is a book series focused on leading-edge research on the structure, physica...[view complete introduction]

Table of Contents

Foreword

- Pp. i-ii (2)

Vladimir N. Uversky

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Preface

- Pp. iii

Ben M. Dunn

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List of Contributors

- Pp. iv-ix (6)

Ben M. Dunn

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Oxygen Binding Properties and Tetrameric Stability of Hemoglobins From the Snakes Crotalus Durissus Terrificus and Liophis Miliaris

- Pp. 3-30 (28)

Fábio Renato Lombardi, Maristella Conte Anazetti, Giovanni César Santos, Patrícia Peres Polizelli, Johnny Rizzieri Olivieri, Walter Filgueira de Azevedo and Gustavo Orlando Bonilla-Rodriguez

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Major Enzymes of Endocannabinoid Metabolism

- Pp. 31-62 (32)

Balapal S. Basavarajappa

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Molecular Modeling of Two CYP2C19 SNPs and its Implications for Personalized Drug Design

- Pp. 63-74 (12)

Jing-Fang Wang, Li-Na Ma, Dong-Qing Wei, Chao Chen, Yixue Li and Kuo-Chen Chou

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Anti-Apoptotic and Oncogenic Function of HSP27

- Pp. 75-90 (16)

Yusuf Tutar, Aykut Özgür, Esen Tutar, Kübra Açıkalın Coşkun and Lütfi Tutar

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Understanding the Folding Rates and Folding Nuclei of Globular Proteins

- Pp. 91-138 (48)

Alexei V. Finkelstein, Dmitry N. Ivankov, Sergiy O. Garbuzynskiy and Oxana V. Galzitskaya

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Heat Shock Response Agents and the Diseases

- Pp. 139-160 (22)

Lütfi Tutar, Aykut Özgür, Esen Tutar, Kübra Açıkalın Coşkun and Yusuf Tutar

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Prediction of Protein Secondary Structure Content by Using the Concept of Chou’s Pseudo Amino Acid Composition and Support Vector Machine

- Pp. 161-173 (13)

Chao Chen, Lixuan Chen, Xiaoyong Zou and Peixiang Cai

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Prediction of Golgi-Resident Protein Types Using Computational Method

- Pp. 174-193 (20)

Hao Lin, Hui Ding and Wei Chen

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Predicting Membrane Protein Types with Bagging Learner

- Pp. 194-205 (12)

Bing Niu, Yu-Huan Yu-Huan Jin, Kai-Yan Feng, Liang Liu, Wen-Cong Lu, Yu-Dong Cai and Guo-Zheng Li

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Prediction of Human Protein Subcellular Locations with Feature Selection and Analysis

- Pp. 206-225 (20)

Bi-Qing Li, Tao Huang, Lei Chen, Kai-Yan Feng and Yu-Dong Cai

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Analysis of Sequence Divergence in Metabolic Proteins of Plasmodium falciparum: Implications for Remote Homology Detection

- Pp. 226-272 (47)

Smita Mohanty, Gayatri Ramakrishnan, Pratik Dave and Narayanaswamy Srinivasan

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Index

- Pp. 273-296 (24)

Ben M. Dunn

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Foreword

This year, Protein and Peptide Letters is in its 20th anniversary. Over the years, this journal played an important role not only in the illumination of protein and peptide science, but also in the development of several generations of protein and peptide scientists around the globe. As of June 12, 2014, WEB of Science listed 2,265 papers published in Protein and Peptide Letters that were cited 12,405 times. Curiously, although the number of annually published papers reached a plateau in 2005-2006, the number of annual citations of the papers published in Protein and Peptide Letters keeps its steady growth.

The first volume of “Frontiers in Protein and Peptide Science” edited by Prof. Ben Dunn represents an exciting collection of 11 papers which are the revised and updated versions of the manuscripts originally published in Protein and Peptide Letters. Papers for this volume were selected based on the number of citations that the original articles received. Therefore, the resulting volume represents a set of “the best of the best of the best” studies extracted from the Protein and Peptide Protein and Peptide Letters and covers a broad variety of topics ranging from protein function, to protein folding, and to computational methods for prediction of protein structural and functional properties.

Curiously, some authors of the best performing publications are frequent guests in Protein and Peptide Letters, whereas others published just one “hit”. Papers included in this volume talk about structure and functional properties of hemoglobins from snakes, discuss major enzymes of the endocannabinoid metabolism, represent anti-apoptotic and oncogenic functions of Hsp27, show the results of the molecular modeling of CYP2C19 SNPs, represent new updates related to understanding of the folding rates and folding nuclei of globular proteins, discuss the roles of heat shock response agents in diseases, talk about prediction of protein secondary structure content, provide analysis of sequence divergence in metabolic proteins of Plasmodium falciparum, and show how computational tools can be used to predict protein subcellular locations, types of membrane proteins, and types of Golgi-resident protein. The volume will be particularly useful to basic investigators, applied scientists, and clinicians interested in the latest advances in the field of protein and peptide research.

Vladimir N. Uversky
University of South Florida
USA


Preface

The first issue of Protein and Peptide Letters (Vol 1 issue 1) was published in July 1994. Since then, this international journal has grown steadily to become widely recognized for publishing excellent work in the field of proteins and peptide research. The Aims and Scope of the journal include a range of topics, but the journal is firmly rooted in studies of the properties of the title molecules and their interactions. Over the years we have welcomed a truly international group of authors and provided a valuable service to many new scientists publishing their first papers in English.

As we have moved through the years, the popularity of the journal and its content has increased. Recently, an analysis was done of the citation record for the past few years for all published papers. From that listing we selected the the top 100 papers receiving the highest citation numbers. Those authors were invited to submit revised and updated manuscripts; the ones received were subjected to a new round of peer review, revisions were requested, and the final manuscripts were edited by the editor. The resulting top papers were selected to be included in this first volume of “Frontiers in Protein and Peptide Science”. Future volumes will follow based on a continuing analysis of citation history.

I would like to thank all contributors to this volume for their efforts to update their papers with new information and references and for their efforts to prepare the new manuscripts according to the format specified in the invitation to submit. I would also like to thank two managers at Bentham Science publishing, Dur-e- Shahnaz Shafi, who worked with me to initiate this book and Sara Yaser, who took over the book and saw it through to completion.

Ben M. Dunn
Department of Biochemistry and Molecular Biology
University of Florida
College of Medicine
USA

List of Contributors

Editor(s):
Ben M. Dunn
Department of Biochemistry and Molecular Biology
College of Medicine
University of Florida
USA




Contributor(s):
Alexei V. Finkelstein
Institute of Protein Research
Russian Academy of Sciences
Pushchino
Moscow Region, 142290
Russian Federation


Aykut Özgür
Gaziosmanpasa University
Faculty of Natural Sciences and Engineering
Department of Bioengineering
Tokat
Turkey


Balapal S. Basavarajappa
Division of Analytical Psychopharmacology
New York State Psychiatric Institute
New York
USA
/
Department of Psychiatry
College of Physicians & Surgeons
Columbia University
New York
USA
/
Nathan Kline Institute for Psychiatric Research
College of Physicians & Surgeons
Columbia University
New York
USA


Bing Niu
College of Life Science
Shanghai University
99 Shang-Da Road
Shanghai, 200444
PRChina


Bi-Qing Li
Institute of Systems Biology
Shanghai University
Shanghai
People’s Republic of China


Dmitry N. Ivankov
Institute of Protein Research
Russian Academy of Sciences
Pushchino, Moscow Region, 142290, Russian Federation



Dong-Qing Wei
National Micro-measurement Center
Xibei University
Xian 710069
China


Esen Tutar
Kahramanmaraş, Sütçü İmam University
ÜSKİM Research Center, Central Laboratory
Kahramanmaraş
Turkey


Fábio Renato Lombardi
Centro Universitário de Jales (UNIJales)
Guangdong Pharmaceutical University
Jales – S.P.
Brazil


Gayatri Ramakrishnan
Indian Institute of Science Mathematics Initiative and Department of Microbiology and Cell Biology
Indian Institute of Science
Bangalore-560012
India


Giovanni César Santos
Depto. de Bioquímica
UNICAMP
Campinas
S.P.
Brazil


Guo-Zheng Li
School of Computer Science & Engineering
Shanghai University
Shanghai, 200072
China


Gustavo Orlando Bonilla-Rodriguez
Depto. de Química e Ciências Ambientais
IBILCE-UNESP
São José do Rio Preto
S.P., CEP: 15054
Brazil


Hao Lin
Key Laboratory for NeuroInformation of Ministry of Education
Center of Bioinformatics
School of Life Science and Technology
University of Electronic Science and Technology of China
Chengdu, 610054
China


Hui Ding
Department of Physics
School of Sciences
Center for Genomics and Computational Biology
Hebei United University
Tangshan
China


Jing-Fang Wang
College of Life Science and Biotechnology
Shanghai Jiaotong University
Shanghai 200240
China


Johnny Rizzieri Olivieri
Depto. de Física
IBILCE-UNESP
São José do Rio Preto
S.P., CEP: 15054-
Brazil


Kai-Yan Feng
Division of Imaging Science & Biomedical Engineering
The University of Manchester
Room G424 Stopford Building
M13 9PT
UK


Kübra Açıkalın Coşkun
Kahramanmaraş, Sütçü İmam University
Faculty of Science and Letters
Department of Biology
Kahramanmaraş
Turkey


Kuo-Chen Chou
Bioinformatics Center, Key Lab of Systems Biology
Shanghai Institutes for Biological Sciences
Graduate School of the Chinese Academy of Sciences
Chinese Academy of Sciences
Shanghai, 200031
China


Lei Chen
Department of Genetics and Genomic Sciences
Mount Sinai School of Medicine
New York
United States of America


Liang Liu
Department of Chemistry
College of Sciences
Shanghai University
99 Shang-Da Road
Shanghai, 200444
People’s Republic of China


Li-Na Ma
Bioinformatics Center, Key Lab of Systems Biology
Shanghai Institutes for Biological Sciences
Graduate School of the Chinese Academy of Sciences
Chinese Academy of Sciences
Shanghai, 200031
China


Li-Na Ma
Bioinformatics Center, Key Lab of Systems Biology
Shanghai Institutes for Biological Sciences
Graduate School of the Chinese Academy of Sciences
Chinese Academy of Sciences
Shanghai, 200031
China


Lixuan Chen
School of Traditional Chinese Medicine
Guangdong Pharmaceutical University
Guangzhou 510006
PR China


Lütfi Tutar
Kahramanmaraş, Sütçü İmam University
Faculty of Science and Letters
Department of Biology
Kahramanmaraş
Turkey


Maristella Conte Anazetti
Centro Universitário de Jales (UNIJales)
Jales – S.P.
Brazil


Narayanaswamy Srinivasan
Department of Microbiology and Cell Biology
Indian Institute of Science
Bangalore-560012
India


Oxana V. Galzitskaya
Department of Genome Oriented Bioinformatics
Technische Universitaet Muenchen
Wissenschaftszentrum Weihenstephan
85354 Freising
Germany


Oxana V. Galzitskaya
Department of Genome Oriented Bioinformatics
Technische Universitaet Muenchen
Wissenschaftszentrum Weihenstephan
85354 Freising
Germany


Patrícia P. Polizelli
Depto. de Física
IBILCE-UNESP
São José do Rio Preto
S.P., CEP: 15054-
Brazil


Peixiang Cai
Guangzhou Institute of Standardization
PR China
/
Sun Yat-Sen University
PR China


Pratik Dave
Department of Microbiology and Cell Biology
Indian Institute of Science
India


Sergiy O. Garbuzynskiy
Pushchino Branch of the Moscow State Lomonosov University
Moscow Region, 142290 Pushchino
Russian Federation


Smita Mohanty
Molecular Biophysics Unit
Indian Institute of Science
Banglore
India


Tao Huang
Key Laboratory of Systems biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
Shanghai
People’s Republic of China


Walter Filgueira de Azevedo Jr.
Depto. de Química e Ciências Ambientais
IBILCE-UNESP
São José do Rio Preto
S.P., CEP: 15054
Brazil


Wei Chen
Department of Physics
School of Sciences
Center for Genomics and Computational Biology
Hebei United University
Tangshan
China


Wen-Cong Lu
Department of Mathematics
University of Manchester
Manchester M60
1QD
UK


Xiaoyong Zou
Guangzhou Institute of Standardization
Guangzhou 510170
PR China
/
School of Chemistry and Chemical Engineering
Sun Yat-Sen University
Guangzhou 510170
PR China


Yix Li
Bioinformatics Center
Key Lab of Systems Biology
Shanghai Institutes for Biological Sciences
Graduate School of the Chinese Academy of Sciences
Chinese Academy of Sciences
Shanghai, 200031
China


Yu-Dong Cai
Department of Combinatorics and Geometry
CAS-MPG Partner Institute for Computational Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences
Shanghai, 200031
People’s Republic of China
/
Department of Mathematics
University of Manchester
Manchester M60
1QD
UK


Yu-Huan Jin
School of Materials Science and Engineering
Shanghai University
149 Yan-Chang Road
People’s Republic of China


Yusuf Tutar
Kahramanmaraş, Sütçü İmam University
ÜSKİM Research Center
Central Laboratory
Kahramanmaraş
Turkey




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