Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions.
The RNA-binding N-terminal arm of the coat protein of cowpea chlorotic mottle virus has been studied with five molecular dynamics simulations of 2.0 ns each. This 25-residue peptide (pep25) is highly charged: it contains six Arg and three Lys residues. An alpha-helical fraction of the sequence is stabilized in vitro by salts. The interaction of monophosphate (Pi) ions with pep25 was studied, and it was found that only two Pi ions are bound to pep25 on average, but water-mediated interactions between pep25 and Pi, which provide electrostatic screening for intrapeptide interactions, are abundant. Shielding by the Pi ions of repulsive electrostatic interactions between Arg sidechains increases the alpha-helicity of pep25. A hydrogen bond at the N-terminal end of the alpha-helix renders extension of the alpha-helix in the N-terminal direction impossible, in agreement with evidence from nuclear magnetic resonance experiments.
23 references, click to expand
-
'Random coil' 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG.J Biomol NMR. 1995 Jan;5(1):14-24 PMID: 7881270
-
Conformation and mobility of the RNA-binding N-terminal part of the intact coat protein of cowpea chlorotic mottle virus. A two-dimensional proton nuclear magnetic resonance study.J Mol Biol. 1991 Aug 5;220(3):701-9 PMID: 1908015
-
The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water.J Mol Biol. 1995 Apr 7;247(4):808-22 PMID: 7723032
-
Urea-diketopiperazine interactions: a model for urea induced denaturation of proteins.Biophys Chem. 1993 Apr;46(2):171-7 PMID: 8513118
-
Complete nucleotide sequences of the coat protein messenger RNAs of brome mosaic virus and cowpea chlorotic mottle virus.Nucleic Acids Res. 1982 Jan 22;10(2):703-13 PMID: 6895941
-
Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol.Biopolymers. 1993 Aug;33(8):1159-66 PMID: 8364151
-
Molecular dynamics simulations of the unfolding of apomyoglobin in water.Biochemistry. 1993 Apr 27;32(16):4175-84 PMID: 8476847
-
Formation of an infectious nucleoprotein from protein and nucleic acid isolated from a small spherical virus.Virology. 1967 Jun;32(2):354-6 PMID: 6025882
-
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble.J Biomol NMR. 1995 Sep;6(2):163-70 PMID: 8589605
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.Biopolymers. 1983 Dec;22(12):2577-637 PMID: 6667333
-
Helicity, circular dichroism and molecular dynamics of proteins.J Mol Biol. 1994 Oct 21;243(2):173-8 PMID: 7932747
-
Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach.Science. 1993 Jun 4;260(5113):1491-6 PMID: 8502992
-
Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography.Acta Crystallogr D Biol Crystallogr. 1994 Jan 1;50(Pt 1):24-36 PMID: 15299473
-
On the sensitivity of MD trajectories to changes in water-protein interaction parameters: the potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field.Proteins. 1996 May;25(1):89-103 PMID: 8727321
-
Conformational studies on a peptide fragment representing the RNA-binding N-terminus of a viral coat protein using circular dichroism and NMR spectroscopy.Eur J Biochem. 1991 Oct 15;201(2):489-94 PMID: 1935944
-
Raster3D Version 2.0. A program for photorealistic molecular graphics.Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869-73 PMID: 15299354
-
A structure refinement method based on molecular dynamics in four spatial dimensions.J Mol Biol. 1993 Dec 5;234(3):751-62 PMID: 8254671
-
Simulation of the thermal denaturation of hen egg white lysozyme: trapping the molten globule state.Biochemistry. 1992 Sep 1;31(34):7745-8 PMID: 1510961
-
Role of the N-terminal part of the coat protein in the assembly of cowpea chlorotic mottle virus. A 500 MHz proton nuclear magnetic resonance study and structural calculations.J Mol Biol. 1986 Oct 5;191(3):453-60 PMID: 3820293
-
Conformation of a pentacosapeptide representing the RNA-binding N-terminus of cowpea chlorotic mottle virus coat protein in the presence of oligophosphates: a two-dimensional proton nuclear magnetic resonance and distance geometry study.Biochemistry. 1992 Sep 29;31(38):9177-82 PMID: 1390704
-
Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy.Structure. 1995 Jan 15;3(1):63-78 PMID: 7743132
-
Calibration of ring-current effects in proteins and nucleic acids.J Biomol NMR. 1995 Dec;6(4):341-6 PMID: 8563464
-
Analysis of proton chemical shifts in regular secondary structure of proteins.J Biomol NMR. 1994 Mar;4(2):215-30 PMID: 8019135
Contact
No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong
Qilu Normal University · Genelibs Bioinformatics Lab
750 Shunhua Rd, Jinan
2F, Bldg F, University Science Park
Tel: 0531-88819269
WeChat Official Account
Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.
Business Email
E-mail: [email protected]
Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2
