TY - JOUR
T1 - Dynamics based clustering of globin family members
AU - Tobi, Dror
N1 - Publisher Copyright:
© 2018 Dror Tobi. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2018/12
Y1 - 2018/12
N2 - A methodology to cluster proteins based on their dynamics’ similarity is presented. For each pair of proteins from a dataset, the structures are superimposed, and the Anisotropic Network Model modes of motions are calculated. The twelve slowest modes from each protein are matched using a local mode alignment algorithm based on the local sequence alignment algorithm of Smith–Waterman. The dynamical similarity distance matrix is calculated based on the top scoring matches of each pair and the proteins are clustered using a hierarchical clustering algorithm. The utility of this method is exemplified on a dataset of protein chains from the globin family and a dataset of tetrameric hemoglobins. The results demonstrate the effect of the quaternary structure of globin members on their intrinsic dynamics and show good ability to distinguish between different states of hemoglobin, revealing the dynamical relations between them.
AB - A methodology to cluster proteins based on their dynamics’ similarity is presented. For each pair of proteins from a dataset, the structures are superimposed, and the Anisotropic Network Model modes of motions are calculated. The twelve slowest modes from each protein are matched using a local mode alignment algorithm based on the local sequence alignment algorithm of Smith–Waterman. The dynamical similarity distance matrix is calculated based on the top scoring matches of each pair and the proteins are clustered using a hierarchical clustering algorithm. The utility of this method is exemplified on a dataset of protein chains from the globin family and a dataset of tetrameric hemoglobins. The results demonstrate the effect of the quaternary structure of globin members on their intrinsic dynamics and show good ability to distinguish between different states of hemoglobin, revealing the dynamical relations between them.
UR - http://www.scopus.com/inward/record.url?scp=85057765997&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0208465
DO - 10.1371/journal.pone.0208465
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C2 - 30513111
AN - SCOPUS:85057765997
SN - 1932-6203
VL - 13
JO - PLoS ONE
JF - PLoS ONE
IS - 12
M1 - e0208465
ER -