The method given earlier for predicting the thermodynamics of protein unfolding from the x-ray structure of a protein is applied here to the poly(L-alanine) helix. First, the fitting parameters derived earlier from a data base of 10 proteins were used to predict the unfolding thermodynamics of 4 other proteins. The agreement between the observed and predicted values is comparable to that found ...

Traditional research means, such as in vitro and vivo models, have consistently been used by scientists to test hypotheses biochemistry. Computational (in silico) methods increasingly devised applied testing hypothesis development biochemistry over the last decade. The aim of silico is analyze quantitative aspects scientific (big) data, whether these are stored databases for large data or gener...

Understanding the process of protein folding has been recognized as an important challenge for >70 years. It is, quintessentially, a thermodynamic problem and, arguably, thermodynamics is our most powerful discipline for understanding biological systems. Yet, despite all this, we still lack predictive understanding of protein folding. Is something missing from this picture?

Inherent structure theory is used to discover strong connections between simple characteristics of protein structure and the energy landscape of a Gō model. The potential energies and vibrational free energies of inherent structures are highly correlated, and both reflect simple measures of networks of native contacts. These connections have important consequences for models of protein dynamics...

For many years the emphasis in protein-folding simulations has been laid as to how to predict the three dimensional structure of proteins. Only recently has there be a shift in interest towards the the thermodynamics of folding. We show that generalized-ensemble techniques are well suited to study both questions for realistic protein models.

.......................................................................................................................................... 3 Introduction ..................................................................................................................................... 4 Protein Structure ............................................................................................

Experiments in which two specifically interacting protein molecules are dissociated by external force have yielded new insights into mechanisms involved in cell adhesion, leukocyte rolling, regulation of integrin activity, antigen-antibody interactions and other protein-mediated reactions contingent upon molecular recognition. Another important aspect of force-induced protein-protein unbinding ...

High-resolution nuclear magnetic resonance (NMR) has emerged as one of the most versatile tools for the quantitative study of structure, kinetics, and thermodynamics of biomolecules and their interactions at atomic resolution. Traditionally, nuclear Overhauser enhancements (NOEs) and chemical shift perturbation methods are used to determine molecular geometries and to identify contact surfaces,...