Inherent Structure Analysis of Protein Folding

2007 ◽  
Vol 111 (10) ◽  
pp. 2647-2657 ◽  
Author(s):  
Jaegil Kim ◽  
Thomas Keyes
Keyword(s):  
Protein Folding ◽  
Structure Analysis ◽  
Inherent Structure

Inherent structure analysis of defect thermodynamics and melting in silicon

2012 ◽  
Vol 38 (8-9) ◽  
pp. 659-670 ◽  
Author(s):  
Alex M. Nieves ◽  
Claire Y. Chuang ◽  
Talid Sinno
Keyword(s):  
Structure Analysis ◽  
Inherent Structure

scholarly journals Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

2006 ◽  
Vol 20 (5,6) ◽  
pp. 229-251 ◽  
Author(s):  
Peiqiang Yu
Keyword(s):  
Protein Structure ◽  
Structure Analysis ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
Biological Tissues ◽  
Plant Tissues ◽  
Protein Structure Analysis ◽  
Advanced Technique ◽  
Inherent Structure ◽  
Pure Protein

Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advanced synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in biological tissues at ultraspatial resolutions.

scholarly journals Molecular Dynamics Folding Simulation of β-hairpin Protein (1E0Q)

2014 ◽  
Vol 7 (2) ◽  
Author(s):  
Nur Shima Fadhilah Mazlan ◽  
Nurul Bahiyah Ahmad Khairudin
Keyword(s):  
Molecular Dynamics ◽  
Protein Folding ◽  
Secondary Structure ◽  
Force Field ◽  
Structure Analysis ◽  
Md Simulation ◽  
Folding Pathway ◽  
Mutant Peptide ◽  
Secondary Structure Analysis ◽  
Folding Simulation

The structure and trajectories of the mutant peptide of ubiquitin (PDB ID: 1E0Q) has been studied using Molecular Dynamics (MD) simulation. The simulation was performed using AMBER 11 utilizing force field 99 for 50 ns at constant temperature 325 K. The purpose of this study is to investigate the protein folding pathway of protein 1E0Q. In this simulation, the protein 1E0Q has folded into its near native β-hairpin structure within 5 ns. The RMSD value as compared to the NMR structure from the first residue to 17 residues is 2.17 Å. It has been observed that Gly 10 had been responsible to promote β-turn which caused the structure to turn into β-hairpin. In secondary structure analysis, it is shown that the residue from Thr 6 to Lys 11 has formed a bend in the structure. Two beta strands has also been found comprising residues Glu 2 to Lys 5 and Ile 13 to Glu 16.

Sign in / Sign up

Export Citation Format

Share Document