Advances in Protein Chemistry and Structural Biology - 1st Edition - ISBN: 9780128001684, 9780128003732

Advances in Protein Chemistry and Structural Biology, Volume 94

1st Edition

Serial Editors: Rossen Donev
Hardcover ISBN: 9780128001684
eBook ISBN: 9780128003732
Imprint: Academic Press
Published Date: 27th March 2014
Page Count: 488
Tax/VAT will be calculated at check-out
171.00
104.00
129.00
Unavailable
Compatible Not compatible
VitalSource PC, Mac, iPhone & iPad Amazon Kindle eReader
ePub & PDF Apple & PC desktop. Mobile devices (Apple & Android) Amazon Kindle eReader
Mobi Amazon Kindle eReader Anything else

Institutional Access


Table of Contents

Contributors
Chapter One: Bioinformatics Tools to Identify and Quantify Proteins Using Mass Spectrometry Data
Abstract

1 Introduction

2 MS Data

3 Protein Identification

4 Protein Quantification

5 Conclusion

Acknowledgments

Chapter Two: Unraveling Oxidation-Induced Modifications in Proteins by Proteomics
Abstract

1 A Very Brief Introduction to Oxidative Stress and Redox Homeostasis

2 Proteins as Targets of Oxidative Modification

3 Redox Proteomics: The Comprehensive Study of Oxidation-Induced Protein Damage

4 The Use of Proteomics for Mapping the Redox Homeostasis Network: Lessons from Cancer Research

5 Perspectives and Conclusions

Chapter Three: Role of Proteomics in Biomarker Discovery: Prognosis and Diagnosis of Neuropsychiatric Disorders
Abstract

1 Summary

2 Commonly Used Methods for Proteome Characterization

3 Proteomics and Biomarker

4 Diagnosis of Neuropsychiatric Disorders

5 Proteomics of Neuropsychiatric Disorders

6 Strength, Weakness, and Future Challenges: Biomarker Discovery

7 Concluding Remarks

Chapter Four: On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
Abstract

1 Introduction

2 Knowledge-Based Potentials

3 Modeling of Protein Interactions Using Templates

4 Modeling Interactions of Proteins Using Docking

5 Prediction of Protein-Binding Regions

6 Characterization of Transcription Factor-Binding Sites

7 Adapting Split-Statistical Potentials for Protein–DNA Interactions

8 Conclusions

Acknowledgments

Chapter Five: Algorithms, Applications, and Challenges of Protein Structure Alignment
Abstract

1 Introduction

2 Structural Alphabet

3 Protein Pairwise Structure Alignment

4 Protein MSA

5 Conclusions and Perspectives

Chapter Six: Application of Evolutionary Based in Silico Methods to Predict the Impact of Single Amino Acid Substitutions in Vitelliform Macular Dystrophy
Abstract

1 Introduction

2 Materials and Methods

3 Results

4 Discussion

5 Conclusion

Acknowledgments

Chapter Seven: Current State-of-the-Art Molecular Dynamics Methods and Applications
Abstract

1 Introduction

2 The Role of Computer Experiments in Modern Science

3 Brief History of Computer Molecular Simulations

4 Physics in MD

5 Algorithms for MD Simulations

6 Computational Complexity of MD Simulations and Methods to Increase Efficiency

7 High-Performance Parallel Computing

8 General-Purpose Computing Using Graphics Processing Units

9 Software for MD Simulations

10 Force Fields for MD

11 Current Limitations of MD

12 Conclusions

Acknowledgments

Chapter Eight: Intrinsically Disordered Proteins—Relation to General Model Expressing the Active Role of the Water Environment
Abstract

1 Introduction

2 Definition of the Fuzzy Oil Drop Model

3 Results

4 Discussion

5 Conclusions

Acknowledgments

Chapter Nine: Conformational Elasticity can Facilitate TALE–DNA Recognition
Abstract

1 Introduction

2 Methods

3 Results

4 Discussion

Acknowledgments

Chapter Ten: Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research
Abstract

1 Introduction

2 Computational Methods in SAP Analysis

3 Database Resources for SAPs

4 Molecular Phenotypic Effect Analysis

5 Sequence Information Analysis

6 Computational Methods for Structure Determination

7 Docking

8 Types of Docking

9 Molecular Dynamics

10 Concluding Remarks

Acknowledgments

Author Index
Subject Index


Description

This eclectic volume features two major topics: applications of mass spectrometry in bioscience; and computational methods for analysis of protein structure and interactions with other macromolecules.

Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series has been the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics.

Key Features

  • Describes advances in application of powerful techniques in a wide bioscience area
  • Chapters are written by authorities in their field
  • Targeted to a wide audience of researchers, specialists, and students
  • The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables

Readership

The intended audiences for this volume are researchers and specialists in protein structure and interactions, cancer biology, psychiatry and mass spectrometry. This volume would be also of a great use to students working on projects from the abovementioned areas.


Details

No. of pages:
488
Language:
English
Copyright:
© Academic Press 2014
Published:
Imprint:
Academic Press
eBook ISBN:
9780128003732
Hardcover ISBN:
9780128001684

About the Serial Editors

Rossen Donev Serial Editor

Rossen Donev received his PhD degree in 1999 from the Institute of Molecular Biology, Bulgarian Academy of Sciences. He did postdoctoral training at Imperial Cancer Research Fund, UK (renamed after the merger with Cancer Research Campaign to Cancer Research UK, London Research Institute) and Cardiff University. In 2010 Dr. Donev was appointed Lecturer in Swansea University. Currently he is Director of Biomed Consult Ltd, UK. His major research interests include signalling pathways involved in neuropsychiatric disorders and tumour escape from the immune system, and development of therapeutic strategies for treatment. He has published more than 50 research papers, has chaired scientific meetings in Molecular Medicine and given plenary talks at Attention Deficit/Hyperactivity Disorder meetings. Rossen Donev has consulted on projects related to development of treatments for neurodevelopmental disorders and cancer therapies. He serves as Editor-in-Chief of the Advances in Protein Chemistry and Structural Biology and on editorial board of several other journals.

Affiliations and Expertise

Swansea University, Swansea, Wales, UK