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Structural Biology 2018 & STD AIDS 2018
Journal of Genetics and Molecular Biology
|
Volume 2
S e p t e m b e r 0 3 - 0 4 , 2 0 1 8 | B a n g k o k , T h a i l a n d
allied
academies
STD-AIDS AND INFECTIOUS DISEASES
STRUCTURAL BIOLOGY AND PROTEOMICS
&
International Conference on
International Conference on
Joint Event on
J Genet Mol Biol 2018, Volume 2
DECODING THE AMINO ACID SEQUENCE OF A PROTEIN TO EXTRACT ITS
FOLDING INFORMATION
Takeshi Kikuchi
Ritsumeikan University, Japan
T
he problem how a unique and complex protein 3D structure forms is a long-standing problem in structural biology. It is very
interesting how the folding information of a protein can be extracted from its sequence. When we make a plot of a pair of
residues with the shorter average distance on a contact map so that the average distance of a residue pair <r> shows a scaling
rule N1/3 in an implicit way, a region to be compact can be predicted along the amino acid sequence of a protein. Furthermore,
an effective inter-residue potential can be defined based on the inter-residue average distance statistics. The contact frequency
of a residue with other residues will provide information of a site of the initial folding events of a protein. We call the contact
frequency F value. Thus, we consider that conserved hydrophobic residues during the evolution around a peak of the contact
frequency plot of a protein have a significant role on the folding of a protein. In this study, the effectiveness of the present method
is examined taking proteins with characteristic 3D structures such as lysozyme related proteins,
β
-trefoil proteins and so on. The
results are compared with those of HD-exchange or Φ-value experiments. A, F, L, M, V, Y, W are taken as hydrophobic residues
in this study. Furthermore, evolutionary analysis is also conducted with the phylogenetic tree of proteins in a superfamily. The
common mechanisms of the proteins in a superfamily are discussed. We also discuss the general mechanism of protein folding.