Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way

doi:10.1002/prot.25495

	Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way
	Wang, Jia 1,2,3; Chen, Jingfei 1,2; Li, Jingwen 1,2,3; An, Liaoyuan 1,2; Wang, Yefei 1,2; Huang, Qingshan 1,2; Yao, Lishan 1,2
刊名	PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
	2018-06-01
卷号	86 期号:6 页码:684-692
关键词	Alpha Helix Arginine Stacking Cooperativity Quantum Mechanical Calculation Stability
ISSN号	0887-3585
DOI	10.1002/prot.25495
文献子类	Article
英文摘要	A combined experimental and computational study is performed for arginine side chain stacking with the protein -helix. Theremostability measurements of Aristaless homeodomain, a helical protein, suggest that mutating the arginine residue R106, R137 or R141, which has the guanidino side chain stacking with the peptide plane, to alanine, destabilizes the protein. The R-PP stacking has an energy of approximate to 0.2-0.4 kcal/mol. This stacking interaction mainly comes from dispersion and electrostatics, based on MP2 calculations with the energy decomposition analysis. The calculations also suggest that the stacking stabilizes 2 backbone-backbone h-bonds (ii-4 and i-3i-7) in a cooperative way. Desolvation and electrostatic polarization are responsible for cooperativity with the ii-4 and i-3i-7 h-bonds, respectively. This cooperativity is supported by a protein -helices h-bond survey in the pdb databank where stacking shortens the corresponding h-bond distances.
WOS关键词	ALANINE-BASED PEPTIDES ; MOLECULAR-DYNAMICS ; AMINO-ACIDS ; 4-OXALOCROTONATE TAUTOMERASE ; PROPENSITIES ; PARAMETERS ; RESIDUES ; SEQUENCE ; POLAR ; SIMULATIONS
WOS研究方向	Biochemistry & Molecular Biology ; Biophysics
语种	英语
出版者	WILEY
WOS记录号	WOS:000431734800009
资助机构	National Natural Science Foundation of China(31400061 ; 31270785)
内容类型	期刊论文
源URL	[http://ir.qibebt.ac.cn/handle/337004/11473]
专题	中国科学院青岛生物能源与过程研究所
通讯作者	Yao, Lishan
作者单位	1.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Shandong Prov Key Lab Synthet Biol, Qingdao 266061, Peoples R China 2.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Lab Biofuels, Qingdao 266061, Peoples R China 3.Chinese Acad Sci, Qingdao Inst Bioenergy & Bioproc Technol, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Wang, Jia,Chen, Jingfei,Li, Jingwen,et al. Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2018,86(6):684-692.
APA	Wang, Jia.,Chen, Jingfei.,Li, Jingwen.,An, Liaoyuan.,Wang, Yefei.,...&Yao, Lishan.(2018).Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,86(6),684-692.
MLA	Wang, Jia,et al."Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 86.6(2018):684-692.