Proteins in Solution and at Interfaces – Methods and Applications in Biotechnology and Materials Science

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. ANGEL PINEIRO 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 Vyctor 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