Professor Irena Roterman-Konieczna completed her PhD at the Nicolaus Copernicus Medical Academy Krakow, Poland and undertook her postdoctoral studies at Cornell University, USA. She is the director of the Department of Bioinformatics and Telemedicine at Jagiellonian University - Medical College, Poland. Her fields of interest are protein structure, folding simulation as well as systems biology. She is the author of "Protein Folding in Silico", published by Woodhead Publishing in 2012., and "From Globular Proteins to Amyloids" published by Elsevier in 2020. She is the Chief Editor of the journal Bio-Algorithms and Med-Systems (de Gruyter).

Dedication

List of figures

List of tables

About the editor

List of contributors

Introduction

Chapter 1: The early-stage intermediate

Abstract

1.1 Geometric model

1.2 Structural alphabet

1.3 Contingency table

1.4 In search of structural similarities

Chapter 2: The late-stage intermediate

Abstract:

2.1 The " fuzzy oil drop ” model

2.2 Quantitative description of the hydrophobic core

2.3 Protein characteristics with respect to the hydrophobic core

2.4 Simulation of late-stage folding

Chapter 3: Structural information involved in the interpretation of the stepwise protein folding process

Abstract:

3.1 Balancing the quantity of information in the amino acid sequence and the early-stage intermediate

3.2 Zones on the Ramachandran map

Chapter 4: The divergence entropy characterizing the internal force field in proteins

Abstract:

4.1 Internal force field for nonbonding interactions

4.2 The impact of ligands

4.3 Structures of homodimers - protein-protein interaction

4.4 Protein containing a catalytic center

4.5 The role of exons

4.6 Conclusions

Chapter 5: Ligand-binding-site recognition

Abstract:

5.1 General model

5.2 ROC curves

5.3 Summary

Chapter 6: Use of the â?ofuzzy oil dropâ? model to identify the complexation area in protein homodimers

Abstract:

6.1 General description

6.2 ROC curves

6.3 Conclusions

Chapter 7: Simulation of the polypeptide chain folding process using the "fuzzy oil drop" model

Abstract:

7.1 Simulation of the folding process in the presence of an external hydrophobic force field

7.2 Folding in the presence of a ligand

7.3 Influence of external factors on polypeptide chain folding

Chapter 8: Misfolded proteins

Abstract:

8.1 Introduction

8.2 In silico experiment

8.3 Conclusions

8.4 Appendix 1: details of the molecular dynamics simulation

8.5 Appendix 2: details of the cluster analysis

Chapter 9: A Short description of other selected ab initio methods for protein structure prediction

Abstract:

9.1 Introduction

9.2 Simplifying the geometric model and the field function

9.3 Lattice model

9.4 ROSETTA

9.5 In search of a global minimum - force field deformation

Chapter 10: Conclusion

Abstract:

10.1 Acknowledgements

Index

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.