Please use this identifier to cite or link to this item: https://hdl.handle.net/10356/107356
Title: Ab initio folding of extended α-helix : a theoretical study about the role of electrostatic polarization in the folding of helical structures
Authors: Lazim, Raudah
Wei, Caiyi
Sun, Tiedong
Zhang, Dawei
Keywords: DRNTU::Science::Chemistry::Biochemistry
Issue Date: 2013
Source: Lazim, R., Wei, C., Sun, T., & Zhang, D. (2013). Ab initio folding of extended α-helix : A theoretical study about the role of electrostatic polarization in the folding of helical structures. Proteins : structure, function, and bioinformatics, 81(9), 1610-1620.
Series/Report no.: Proteins : structure, function, and bioinformatics
Abstract: In this work, we report the ab initio folding of three different extended helical peptides namely 2khk, N36, and C34 through conventional molecular dynamics simulation at room temperature using implicit solvation model. Employing adaptive hydrogen bond specific charge (AHBC) scheme to account for the polarization effect of hydrogen bonds established during the simulation, the effective folding of the three extended helices were observed with best backbone RMSDs in comparison to the experimental structures over the helical region determined to be 1.30 Å for 2khk, 0.73 Å for N36 and 0.72 Å for C34. In this study, 2khk will be used as a benchmark case serving as a means to compare the ability of polarized (AHBC) and nonpolarized force field in the folding of an extended helix. Analyses conducted revealed the ability of the AHBC scheme in effectively folding the extended helix by promoting helix growth through the stabilization of backbone hydrogen bonds upon formation during the folding process. Similar observations were also noted when AHBC scheme was employed during the folding of C34 and N36. However, under Amber03 force field, helical structures formed during the folding of 2khk was not accompanied by stabilization thus highlighting the importance of electrostatic polarization in the folding of helical structures. Proteins 2013.
URI: https://hdl.handle.net/10356/107356
http://hdl.handle.net/10220/17946
ISSN: 0887-3585
DOI: 10.1002/prot.24319
Fulltext Permission: none
Fulltext Availability: No Fulltext
Appears in Collections:SPMS Journal Articles

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