This item is in: Biomedicine > Bioinformatics, computing and life sciences

Protein folding in silico: Protein folding versus protein structure prediction

Edited by I Roterman-Konieczna, Jagiellonian University Medical College

Woodhead Publishing Series in Biomedicine No. 22

 - discusses a range of ab initio models for protein structure prediction
 - introduces a unique model based on experimental observations
 - describes various methods for the quantitative assessment of the presented models from the viewpoint of information theory
 - offers an answer to the question of - Why do proteins fold the way they do?

Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks.

ISBN 1 907568 17 4
ISBN-13: 978 1 907568 17 6
October 2012
240 pages  234 x 156mm  hardback  
£120.00 / US$205.00 / €145.00

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About the editor

Dr Irena Roterman-Konieczna heads the bioinformatics group at the Jagiellonian University Medical College and the Faculty of Physics, Astronomy and Applied Computer Science. Her background is in theoretical chemistry, and her research focuses on bioinformatics, with specific focus on protein structure prediction.

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Contents

The early-stage intermediate
W. Jurkowski, Z. Baster, D. Dułak, and I. Roterman-Konieczna
 - Geometric model
 - Structural alphabet
 - Contingency table
 - In search of structural similarities
 - References
 - Suggested reading

The late-stage intermediate
M. Banach, L. Konieczny, and I. Roterman-Konieczna
 - The “fuzzy oil drop” model
 - Quantitative description of the hydrophobic core
 - Protein characteristics with respect to the hydrophobic core
 - Simulation of late-stage folding
 - References
 - Suggested reading

Structural information involved in the interpretation of the stepwise protein folding process
P. Alejster, W. Jurkowski, and I. Roterman-Konieczna
 - Balancing the quantity of information in the amino acid sequence and the early-stage intermediate
 - Zones on the Ramachandran map
 - References
 - Suggested reading

The divergence entropy characterizing the internal force fi eld in proteins
M. Banach, D. Marchewka, M. Piwowar, and I. Roterman-Konieczna
 - Internal force field for nonbonding interactions
 - The impact of ligands
 - Structures of homodimers – protein–protein interaction
 - Protein containing a catalytic center
 - The role of exons
 - Conclusions
 - References

Ligand-binding-site recognition
M. Banach, L. Konieczny, and I. Roterman-Konieczna
 - General model
 - ROC curves
 - Summary
 - References
 - Suggested reading

Use of the “fuzzy oil drop” model to identify the complexation area in protein homodimers
M. Banach, L. Konieczny, and I. Roterman-Konieczna
 - General description
 - ROC curves
 - Conclusions
 - References
 - Suggested reading

Simulation of the polypeptide chain folding process using the “fuzzy oil drop” model
L. Konieczny and I. Roterman-Konieczna
 - Simulation of the folding process in the presence of an external hydrophobic force field
 - Folding in the presence of a ligand
 - Influence of external factors on polypeptide
 - chain folding
 - References
 - Suggested reading

Misfolded proteins
M. Król, L. Konieczny, K. Stapor, Z. Wis´ niowski, W. Ziajka, G. Szoniec, and I. Roterman-Konieczna
 - Introduction
 - In silico experiment
 - Conclusions
 - Appendix 1: details of the molecular dynamics simulation
 - Appendix 2: details of the cluster analysis
 - References
 - Suggested reading

A short description of other selected ab initio methods for protein structure prediction
I. Roterman-Konieczna
 - Introduction
 - Simplifying the geometric model and the field function
 - Lattice mode
 - ROSETTA
 - In search of a global minimum – force field deformation
 - References
 - Suggested reading
 - Selected servers oriented toward protein
 - structure prediction available on the Internet

Conclusion
L. Konieczny and I. Roterman-Konieczna
 - Acknowledgements
 - References
 - Suggested reading