Molecular modelling of peptide folding, misfolding and aggregation phenomena
نویسندگان
چکیده
....................................................................................................................................1 1. Computational studies of protein folding and aggregation ..........................................3 1.1 Overview ....................................................................................................................3 1.2 Protein structure..........................................................................................................4 1.3 Protein folding ..........................................................................................................11 1.3.1 Studies of protein folding mechanisms ............................................................11 1.3.2 Protein folding kinetics.....................................................................................15 1.3.3 Transition / intermediate states in protein folding............................................16 1.3.4 Unfolded or denatured states ............................................................................18 1.4 Protein self-association and aggregation ..................................................................20 1.4.1 Early history of amyloid diseases.....................................................................20 1.4.2 Protein aggregation related diseases.................................................................21 1.4.3 Structure of amyloid fibrils...............................................................................23 1.4.4 Mechanisms of fibril formation........................................................................24 1.4.5 Sequence and mutation effects on fibril formations.........................................28 1.4.6 Lipid effects on fibril formation .......................................................................29 1.4.7 Oligomer stability.............................................................................................30 2. Computational techniques for protein studies.............................................................32 2.1 Overview ..................................................................................................................32 2.2 Molecular modelling ................................................................................................34
منابع مشابه
Effects of Dimethyl Sulfoxide and Mutations on the Folding of Abeta(25-35) Peptide: Molecular Dynamics Simulations
The 25-35 fragment of the amyloid β (Aβ) peptide is a naturally occurring proteolytic by-product of its larger parent molecule that retains the amyloid characteristics and toxicity of the full length parent molecule. Aggregation of this peptide occurs rapidly in aqueous solutions and thus characterization of its folding process is very difficult. In the present study, early stages of Aβ(25–35) ...
متن کاملProtein Folding and Misfolding on Surfaces
Protein folding, misfolding and aggregation, as well as the way misfolded and aggregated proteins affects cell viability are emerging as key themes in molecular and structural biology and in molecular medicine. Recent advances in the knowledge of the biophysical basis of protein folding have led to propose the energy landscape theory which provides a consistent framework to better understand ho...
متن کاملStabilization of partially folded states in protein folding/misfolding transitions by hydrostatic pressure.
In the last few years, hydrostatic pressure has been extensively used in the study of both protein folding and misfolding/aggregation. Compared to other chemical or physical denaturing agents, a unique feature of pressure is its ability to induce subtle changes in protein conformation, which allow the stabilization of partially folded intermediate states that are usually not significantly popul...
متن کاملNanoscale Studies on Aggregation Phenomena in Nanofluids
Understanding the microscopic dispersion and aggregation of nanoparticles at nanoscale media has become an important challenge during the last decades. Nanoscale modeling techniques are the important tools to tackle many of the complex problems faced by engineers and scientists. Making progress in the investigations at nanoscale whether experimentally or computationally has helped understand th...
متن کاملInactivation of parkin by oxidative stress and C-terminal truncations: a protective role of molecular chaperones.
Loss of parkin function is linked to autosomal recessive juvenile parkinsonism. Here we show that proteotoxic stress and short C-terminal truncations induce misfolding of parkin. As a consequence, wild-type parkin was depleted from a high molecular weight complex and inactivated by aggregation. Similarly, the pathogenic parkin mutant W453Stop, characterized by a C-terminal deletion of 13 amino ...
متن کامل