Protein folding theory: from lattice to all-atom models
L Mirny, E Shakhnovich - Annual review of biophysics and …, 2001 - annualreviews.org
▪ Abstract This review focuses on recent advances in understanding protein folding kinetics
in the context of nucleation theory. We present basic concepts such as nucleation, folding …
in the context of nucleation theory. We present basic concepts such as nucleation, folding …
Creative elements: network-based predictions of active centres in proteins and cellular and social networks
P Csermely - Trends in biochemical sciences, 2008 - cell.com
Active centres and hot spots of proteins have a paramount importance in enzyme action,
protein-complex formation and drug design. Recently, several publications successfully …
protein-complex formation and drug design. Recently, several publications successfully …
Anisotropy of fluctuation dynamics of proteins with an elastic network model
Fluctuations about the native conformation of proteins have proven to be suitably
reproduced with a simple elastic network model, which has shown excellent agreement with …
reproduced with a simple elastic network model, which has shown excellent agreement with …
Protein–protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces
Polar residue hot spots have been observed at protein–protein binding sites. Here we show
that hot spots occur predominantly at the interfaces of macromolecular complexes …
that hot spots occur predominantly at the interfaces of macromolecular complexes …
Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations
By representing the high-resolution crystal structures of a number of enzymes using the
elastic network model, it has been shown that only a few low-frequency normal modes are …
elastic network model, it has been shown that only a few low-frequency normal modes are …
Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function
In order to study the inferences of structure for mechanism, the collective motions of the
retroviral reverse transcriptase HIV-1 RT (RT) are examined using the Gaussian network …
retroviral reverse transcriptase HIV-1 RT (RT) are examined using the Gaussian network …
Dynamics of large proteins through hierarchical levels of coarse‐grained structures
Elastic network models have been successful in elucidating the largest scale collective
motions of proteins. These models are based on a set of highly coupled springs, where only …
motions of proteins. These models are based on a set of highly coupled springs, where only …
Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T↔ R2 transition
Information on protein dynamics has been usually inferred from spectroscopic studies of
parts of the proteins, or indirectly from the comparison of the conformations assumed in the …
parts of the proteins, or indirectly from the comparison of the conformations assumed in the …
[HTML][HTML] Specificity of trypsin and chymotrypsin: loop-motion-controlled dynamic correlation as a determinant
Trypsin and chymotrypsin are both serine proteases with high sequence and structural
similarities, but with different substrate specificity. Previous experiments have demonstrated …
similarities, but with different substrate specificity. Previous experiments have demonstrated …
Identification of core amino acids stabilizing rhodopsin
AJ Rader, G Anderson, B Isin… - Proceedings of the …, 2004 - National Acad Sciences
Rhodopsin is the only G protein-coupled receptor (GPCR) whose 3D structure is known;
therefore, it serves as a prototype for studies of the GPCR family of proteins. Rhodopsin …
therefore, it serves as a prototype for studies of the GPCR family of proteins. Rhodopsin …