Effects Of Confinement And Macromolecular Crowding On Protein Stability And Protein Folding Dynamics

This book describes recent important advancements in protein folding dynamics and stability research, as well as explaining fundamentals and examining potential methodological approaches in protein science. In vitro, in silico, and in vivo method based research of how the stability and folding of proteins help regulate the cellular dynamics and impact cell function that are crucial in explaining various physiological and pathological processes. This book offers a comprehensive coverage on various techniques and related recent developments in the experimental and computational methods of protein folding, dynamics, and stability studies. The book is also structured in such a way as to summarize the latest developments in the fiddle and key concepts to ensure that readers can understand advanced concepts as well as the fundamental big picture. And most of all, fresh insights are provided into the convergence of protein science and technology. Protein Folding Dynamics and Stability is an ideal guide to the field that will be of value for all levels of researchers and advanced graduate students with training in biochemical laboratory research.

Although the information necessary for a protein to fold is encoded in its amino acid sequence, the environment in which it folds can have a significant impact on the folding process. To date, the majority of protein folding studies (theoretical, computational and experimental) have been carried out in an idealized, dilute environment. In this work, we use molecular dynamics simulations of minimalist model proteins and peptides to examine the impact of two types of confinement on protein folding and peptide assembly. First, we utilize a spherical potential to emulate the cellular confinement and crowding that proteins experience when folding in vivo. Using this potential, we examine the impact on the thermodynamics and kinetics of both protein folding and peptide assembly. Then, we examine how tethering a protein to a surface impacts its stability and folding mechanism. Both types of confinement can have a significant impact on the thermodynamic stability, unfolded state, and mechanisms of folding and assembly, but they do so in unique ways. In addition to examining in detail the specific ways confinement impacts protein folding, we will also discuss the implications of our results for various biological problems and technological applications.

This snapshot volume is designed to provide a smooth entry into the field of protein folding. Presented in a concise manner, each section introduces key concepts while providing a brief overview of the relevant literature. Outlook subsections will pinpoint specific aspects related to emerging methodologies, concepts and trends.

To further broaden our research in understanding biophysical properties of proteins in living cells, we have investigated the effects of macromolecular crowding on the folding stability of one of the less stable mutant of FKBP. We show that there is an optimal size of crowder at which stability increase is maximum and also, the stabilization effect of mixture (different crowders) is greater than the sum of constituent crowding agents. These findings may have profound implications for understanding crowding effects inside cells. The main aim of my dissertation is to understand protein folding and stability, which are the fundamental problems in biophysics. Experiments are underway to understand effects of crowding on protein binding and their quantitative information will provide key insights to the biological relevance of experimental results obtained in vitro. Overall my research aims for understanding fundamental study on protein folding stability and binding which will serve as a valuable tool for designing therapies for human diseases.

Abstract: Conformational dynamics is of fundamental importance for the folding and the function of proteins. Structural changes occur over a wide range of time scales, and folding itself is the slowest, long-time process, Rates vary with the extent of folding, as measured by an order parameter, Q. The dynamics of the order parameter is studied in detail using a coarse-grained model of the protein and classical molecular dynamics simulations. A description of folding is attempted in terms of the Smoluchowski equation (SE), based on a picture of diffusion of the order parameter under the influence of a thermodynamic force. A new method is developed to obtain the order parameter dependent diffusion coefficient, D ( Q ), from short-time simulations. D ( Q ) is shown to change significantly as the protein folds. It is found that folding obeys neither the one-dimensional SE nor a normal-diffusion continuous time random walk (CTRW), because the order parameter follows sub-diffusion. The anomalous nature of the order parameter dynamics is incorporated into the ordinary SE based on the idea that the folding pathways have fractal character. Obtaining the free energy from the statistical temperature molecular dynamics (STMD) enhanced sampling algorithm and D ( Q ) from short-time simulations, mean first passage times of folding (MFPT) calculated from our fractal SE theory are in quantitative agreement with simulated long-time folding dynamics. Protein folding occurs in a crowded and heterogeneous environment inside the cell. Interactions of the protein with other cellular biomolecules may hamper the folding process. Chaperones are known to help a large fraction of newly synthesized proteins in their proper folding. To understand the mechanism of chaperonin-mediated protein folding, the thermodynamics and kinetics of a frustrated model protein are studied inside a chaperonin cavity modeled as a sphere of tunable hydrophobicity. Using the inherent structure (IS) approach, we found that folding is preferred over misfolding inside a slightly hydrophobic chaperonin cavity. The occupation probabilities of the misfolded states are entropically suppressed due to smaller associated configurational volumes.

This book reviews current research on the important processes involved in neurodegenerative diseases (e.g. Alzheimer's disease) and the peptides and proteins involved in the amyloidogenic processes. It covers the design and developments of anti-amyloid inhibitors, and gives readers a fundamental understanding of the underlying oligomerization and aggregation processes of these diseases from both computational and experimental points of view.

Here, leading contributors from the forefront of this exciting technology present authoritative and timely reviews on the state of the art of biocatalysis. They cover the whole spectrum from the discovery of novel enzymes - by modern screening, evolutionary or immunological approaches - through immobilization techniques for technical processes, to their use in the asymmetric synthesis of important target compounds.