Proteins in Solution and at Interfaces

JUAN M. RUSO is currently Associate Professor in the Department of Applied Physics at the University of Santiago de Compostela, Spain. He has contributed to more than 100 publications on a broad range of physical, chemical, and biophysics studies. His research interests include protein ligand interactions, thermal stabilization of protein, Phase behavior, and self-assembly processes in soft matter systems, biocompatible materials design, and nanocarrier design for targeted drug delivery. ÁNGEL PIÑEIRO is an IPP Research Fellow at the Department of Applied Physics of the University of Santiago de Compostela, Spain. His current research interests include the design and characterization of self-assembled systems as well as the study of macromolecules in solution, embedded in membranes or at interfaces. His work is mainly based on computational methods including multiscale molecular dynamics simulations and the development of software for the analysis of different experimental properties.

PREFACE ix

CONTRIBUTORS xiii

PART I

1 X-Ray Crystallography of Biological Macromolecules: Fundamentals and Applications 3
Antonio L. Llamas-Saiz and Mark J. van Raaij

2 Nuclear Magnetic Resonance Methods for Studying Soluble, Fibrous, and Membrane-Embedded Proteins 23
Victoria A. Higman

3 Small-Angle X-Ray Scattering Applied to Proteins in Solution 49
Leandro Ramos Souza Barbosa, Francesco Spinozzi, Paolo Mariani, and Rosangela Itri

4 Analyzing the Solution State of Protein Structure, Interactions, and Ligands by Spectroscopic Methods 73
Veronica I. Dodero and Paula V. Messina

5 Resolving Membrane-Bound Protein Orientation and Conformation by Neutron Reflectivity 99
Hirsh Nanda

6 Investigating Protein Interactions at Solid Surfaces—In Situ, Nonlabeling Techniques 113
Olof Svensson, Javier Sotres, and Alejandro Barrantes

7 Calorimetric Methods to Characterize the Forces Driving Macromolecular Association and Folding Processes 139
Conceic¸ ˜ao A.S.A. Minetti, Peter L. Privalov, and David P. Remeta

8 Virtual Ligand Screening Against Comparative Models of Proteins 179
Hao Fan

9 Atomistic and Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins 193
Thomas J. Piggot, Peter J. Bond, and Syma Khalid

PART II

10 Preparation of Nanomaterials Based on Peptides and Proteins 209
Yujing Sun and Zhuang Li

11 Natural Fibrous Proteins: Structural Analysis, Assembly, and Applications 219
Mark J. van Raaij and Anna Mitraki

12 Amyloid-Like Fibrils: Origin, Structure, Properties, and Potential Technological Applications 233
Pablo Taboada, Silvia Barbosa, Josue Juarez, Manuel-Alatorre Meda, and Výctor Mosquera

13 Proteins and Peptides in Biomimetic Polymeric Membranes 283
Alfredo Gonzalez-Perez

14 Study of Proteins and Peptides at Interfaces By Molecular Dynamics Simulation Techniques 291
David Poger and Alan E. Mark

15 A Single-Molecule Approach to Explore the Role of the Solvent Environment in Protein Folding 315
Katarzyna Tych and Lorna Dougan

16 Enhanced Functionality of Peroxidases By Its Immobilization at The Solid–Liquid Interface of Mesoporous Materials and Nanoparticles 335
Jose Campos-Teran, Iker Inarritu, Jorge Aburto, and Eduardo Torres

17 Superactivity of Enzymes in Supramolecular Hydrogels 353
Ye Zhang and Bing Xu

18 Surfactant Proteins and Natural Biofoams 365
Malcolm W. Kennedy and Alan Cooper

19 Promiscuous Enzymes 379
Luis F. Olguin

20 Thermodynamics and Kinetics of Mixed Protein/Surfactant Adsorption Layers at Liquid Interfaces 389
Reinhard Miller, E.V. Aksenenko, V.S. Alahverdjieva, V.B. Fainerman, C.S. Kotsmar, J. Kragel, M.E. Leser, J. Maldonado-Valderrama, V. Pradines, C. Stefaniu, A. Stocco, and R. Wustneck

21 Application of Force Spectroscopy Methods to the Study of Biomaterials 429
Chuan Xu and Erika F. Merschrod S.

22 Protein Gel Rheology 437
Katie Weigandt and Danilo Pozzo

23 Exploring Biomolecular Thermodynamics in Aqueous and Nonaqueous Environments using Time-Resolved Photothermal Methods 449
Randy W. Larsen, Carissa M. Vetromile, William A. Maza, Khoa Pham, Jaroslava Miksovska

INDEX 473