Contents
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
xi
1 Allostery: The Rebound of Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
Alessandro Finazzi Agro ` and Giampiero Mei
2 Disclosing Allostery Through Protein Contact Networks . . . . . . . . . . . . . . . . . . . .
7
Luisa Di Paola, Giampiero Mei, Almerinda Di Venere,
and Alessandro Giuliani
3 Identification of Allosteric Effects in Proteins by Elastic
Network Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Guang Hu
4 Locating and Navigating Energy Transport Networks in Proteins . . . . . . . . . . . . . 37
Korey M. Reid and David M. Leitner
5 Probing Allosteric Mechanism with Long-Range Rigidity
Transmission Across Protein Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Adnan Sljoka
6 Protein Assembly: Defining the Strength of Protein-Protein
Interactions Coupling the Theory with Experiments . . . . . . . . . . . . . . . . . . . . . . . . 77
Giampiero Mei, Almerinda Di Venere, Luisa Di Paola,
and Alessandro Finazzi Agro `
7 Network Re-Wiring During Allostery and Protein-Protein
Interactions: A Graph Spectral Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Vasundhara Gadiyaram, Anasuya Dighe, Sambit Ghosh,
and Saraswathi Vishveshwara
8 Topology Results on Adjacent Amino Acid Networks
of Oligomeric Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Claire Lesieur and Laurent Vuillon
9 Community Network Analysis of Allosteric Proteins. . . . . . . . . . . . . . . . . . . . . . . . . 137
Ivan Rivalta and Victor S. Batista
10 The PyInteraph Workflow for the Study of Interaction Networks
From Protein Structural Ensembles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Matteo Lambrughi, Valentina Sora, and Matteo Tiberti
11 The Allosteric Effect in Antibody-Antigen Recognition. . . . . . . . . . . . . . . . . . . . . . 175
Jun Zhao, Ruth Nussinov, and Buyong Ma
12 Distal Regions Regulate Dihydrofolate Reductase-Ligand
Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Melanie Goldstein and Nina M. Goodey
13 Investigating Conformational Dynamics and Allostery in
the p53 DNA-Binding Domain Using Molecular Simulations . . . . . . . . . . . . . . . . 221
Elena Papaleo
ix
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
xi
1 Allostery: The Rebound of Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
Alessandro Finazzi Agro ` and Giampiero Mei
2 Disclosing Allostery Through Protein Contact Networks . . . . . . . . . . . . . . . . . . . .
7
Luisa Di Paola, Giampiero Mei, Almerinda Di Venere,
and Alessandro Giuliani
3 Identification of Allosteric Effects in Proteins by Elastic
Network Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Guang Hu
4 Locating and Navigating Energy Transport Networks in Proteins . . . . . . . . . . . . . 37
Korey M. Reid and David M. Leitner
5 Probing Allosteric Mechanism with Long-Range Rigidity
Transmission Across Protein Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Adnan Sljoka
6 Protein Assembly: Defining the Strength of Protein-Protein
Interactions Coupling the Theory with Experiments . . . . . . . . . . . . . . . . . . . . . . . . 77
Giampiero Mei, Almerinda Di Venere, Luisa Di Paola,
and Alessandro Finazzi Agro `
7 Network Re-Wiring During Allostery and Protein-Protein
Interactions: A Graph Spectral Approach. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Vasundhara Gadiyaram, Anasuya Dighe, Sambit Ghosh,
and Saraswathi Vishveshwara
8 Topology Results on Adjacent Amino Acid Networks
of Oligomeric Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Claire Lesieur and Laurent Vuillon
9 Community Network Analysis of Allosteric Proteins. . . . . . . . . . . . . . . . . . . . . . . . . 137
Ivan Rivalta and Victor S. Batista
10 The PyInteraph Workflow for the Study of Interaction Networks
From Protein Structural Ensembles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Matteo Lambrughi, Valentina Sora, and Matteo Tiberti
11 The Allosteric Effect in Antibody-Antigen Recognition. . . . . . . . . . . . . . . . . . . . . . 175
Jun Zhao, Ruth Nussinov, and Buyong Ma
12 Distal Regions Regulate Dihydrofolate Reductase-Ligand
Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Melanie Goldstein and Nina M. Goodey
13 Investigating Conformational Dynamics and Allostery in
the p53 DNA-Binding Domain Using Molecular Simulations . . . . . . . . . . . . . . . . 221
Elena Papaleo
ix