Related ArticlesProtein engineering of venom toxins by synthetic approach and NMR dynamic simulation: status of basic amino acid residues in waglerin I.
Biochem Biophys Res Commun. 1996 Oct 3;227(1):59-63
Authors: Hsiao YM, Chuang CC, Chuang LC, Yu HM, Wang KT, Chiou SH, Wu SH
The tertiary structure of waglerin I has been determined by NMR and dynamic simulated annealing [Chuang et al., Biochim. Biophys. Acta 1292, 145-155 (1996)]. It is believed that the peptide basicity of waglerin may play an important role for its activity due to its high content of basic amino acids. In order to investigate the active site of the toxin, seven analogues of waglerin, [Ala3]-waglerin, [Ala7]-waglerin, [Ala10]-waglerin, [Ala14]-waglerin, [Ala18]-waglerin, [Ala20]-waglerin and [Ala22]-waglerin have been synthesized chemically by single replacement of basic amino acid residues one by one with Ala. By correlation of structures for each analogue with LD50 toxicity bioassays, it is found that the [Ala10]-waglerin exhibits no toxicity and the active site of the native toxin seems to reside in the proximity of the disulfide loop, which is spatially close to His10. Furthermore, the closer is the disulfide loop to the basic amino acid in waglerin, the more influential is the basic amino acid on the toxicity of waglerin. Based on the tertiary structure of waglerin, the structures of all synthetic analogues were derived based on computer-simulated modelling. By the pair-wise structural comparison, the disulfide loop in [Ala10]-waglerin analogue is found to be twisted as compared to the native form, in agreement with the lack of toxicity for this synthetic analogue.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Biophys J. 2010 Nov 17;99(10):3282-9
Authors: Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A
Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to...
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NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101896j/aop/images/medium/bi-2010-01896j_0004.gif
Biochemistry
DOI: 10.1021/bi101896j
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01-14-2011 01:59 AM
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
Biochemistry. 2011 Jan 4;
Authors: Parkesh R, Disney MD, Fountain M
The NMR structure of an RNA with a copy of the 5'CUG/3'GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single...
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01-06-2011 11:21 AM
[NMR paper] Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.
Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.
Related Articles Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution.
J Mol Biol. 2003 Mar 28;327(3):711-7
Authors: Chowdhury S, Lee MC, Xiong G, Duan Y
Here, we report a 100 ns molecular dynamics simulation of the folding process of a recently designed autonomous-folding mini-protein designated as tc5b with a new AMBER force field parameter set developed based on condensed-phase quantum mechanical calculations and a Generalized...
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[NMR paper] A novel approach to the retrieval of structural and dynamic information from residual
A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy.
Related Articles A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy.
J Am Chem Soc. 2002 Oct 9;124(40):12020-30
Authors: Tolman JR
The interpretation of residual dipolar couplings in terms of molecular properties of interest is complicated because of difficulties in...
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[NMR paper] 3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-r
3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.
Related Articles 3 Nsec molecular dynamics simulation of the protein ubiquitin and comparison with X-ray crystal and solution NMR structures.
J Biomol Struct Dyn. 1992 Apr;9(5):935-49
Authors: Braatz JA, Paulsen MD, Ornstein RL
Mainly due to computational limitations, past protein molecular dynamics simulations have rarely been extended to 300 psec; we are not aware of any published results beyond 350 psec. The present...
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08-21-2010 11:41 PM
[NMR paper] Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Related Articles Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Biochemistry. 1991 Dec 17;30(50):11625-36
Authors: Chen Y, Pitzenberger SM, Garsky VM, Lumma PK, Sanyal G, Baum J
The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic...
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08-21-2010 11:12 PM
[NMR paper] Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Related Articles Proton NMR assignments and secondary structure of the snake venom protein echistatin.
Biochemistry. 1991 Dec 17;30(50):11625-36
Authors: Chen Y, Pitzenberger SM, Garsky VM, Lumma PK, Sanyal G, Baum J
The snake venom protein echistatin is a potent inhibitor of platelet aggregation. The inhibitory properties of echistatin have been attributed to the Arg-Gly-Asp sequence at residues 24-26. In this paper, sequence-specific nuclear magnetic...