Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution
نویسندگان
چکیده
منابع مشابه
Conformational Search for the Protein Native State
This chapter presents a survey of computational methods that obtain a structural description of the protein native state. This description is important to understand a protein's biological function. The chapter presents the problem of characterizing the native state in conformational detail in terms of the challenges that it raises in computation. Computing the conformations populated by a prot...
متن کاملEnhancing Sampling of the Conformational Space Near the Protein Native State
A protein molecule assumes specific conformations under native conditions to fit and interact with other molecules. Due to the role that three-dimensional structure plays in protein function, significant efforts are devoted to elucidating native conformations. Many search algorithms are proposed to navigate the high-dimensional protein conformational space and its underlying energy surface in s...
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Hydrogen/deuterium exchange detected by mass spectrometry (HDXMS) provides valuable information on protein structure and dynamics. Although HDX-MS data is often interpreted using crystal structures, it was suggested that conformational ensembles produced by molecular dynamics simulations yield more accurate interpretations. In this paper, we analyse the complement protein C3d by performing an H...
متن کاملNative State of Complement Protein C3d Analyzed via Hydrogen Exchange and Conformational Sampling
Background: Hydrogen/deuterium exchange detected by mass spectrometry (HDX-MS) is an experimental technique that provides valuable information about a protein’s structure and dynamics. Data produced by HDX-MS experiments is often interpreted using a crystal structure of the protein. However, it has been suggested that more accurate interpretations can be derived from conformational ensembles pr...
متن کاملMonte Carlo vs Molecular Dynamics for Conformational Sampling
A comparison study has been carried out to test the relative efficiency of Metropolis Monte Carlo and molecular dynamics simulations for conformational sampling. The test case that has been examined is liquid hexane. OPLS potential functions have been used with sampling of external motions and internal angle bending and torsions. The BOSS 3.6 and AMBER 4.0 programs were used to perform the inte...
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ژورنال
عنوان ژورنال: Biophysical Chemistry
سال: 2012
ISSN: 0301-4622
DOI: 10.1016/j.bpc.2012.02.002