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Molecular dynamics simulations phd thesis


molecular dynamics simulations phd thesis

or unmodified histone H3 tails. Calculation of the rmsip can also be used to compare eigenvectors describing different time windows of the same simulations in order to verify simulation convergence. Brown SP, Muchmore SW (2006) High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-pbsa protocol to enterprise grid computing. Conformational analysis of free and bound aire-PHD1. For NMR determined complexes five starting structures were extracted from the deposited structure ensembles (2l75, 2l43 whereas for the crystallographic structures (2puy, 3o37) different seed numbers were used for five independent dynamics runs. (2009) The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation. Moreira IS, Fernandes PA, Ramos MJ (2008) Protein-protein recognition: A computational mutagenesis study of the MDM2-P53 complex. The observation that H3R8 alanine mutation reduces H3 affinity for aire-PHD1, as assessed both computationally and experimentally, supports this hypothesis. (H) Distribution of the distances between the C atoms of Glu307 and Gly333 along the dynamics of free (cyan) and bound (blue) aire-PHD1.

Koh AS, Kingston RE, Benoist C, Mathis D (2010) Global relevance of aire binding to hypomethylated lysine-4 of histone-3. Massova I, Kollman PA (1999) Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies. Overall peptide binding restricted the conformational space explored by aire-PHD1 as assessed by a general reduction of the C root mean square fluctuations (rmsf) ( Figure 1C, Figure S2 ). This assumption is reasonable for PHD fingers, as they do not undergo structural rearrangements upon binding. Lafont V, Schaefer M, Stote RH, Altschuh D, Dejaegere A (2007) Protein-protein recognition and interaction hot spots in an antigen-antibody complex: Free energy decomposition identifies efficient amino acids. In this analysis, a contact defines an interactomic distance ( 3 Å) between any pair of atoms occurring in more than 30 of the total simulation frames. Chem Biol Drug Des 78 (2 252259. Nature 442 (7098 9699. Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. On the other hand, the polar energy term considerably antagonized peptide binding to both native and mutant aire-PHD1. Importantly MM/pbsa calculations extended to other PHD/H3K4me0 complexes display a similar distribution in the energy contributions. Interestingly, science essay marking rubric domain regions not in direct contact with the peptide, like for example the loop connecting the two -strands (Gly313Arg316 also reduced their fluctuation in the complex.


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