We have performed molecular dynamics (MD) simulation of the thermal denaturation of one protein and one peptide - ubiquitin and melittin. To identify the correlation in dynamics among various secondary structural fragments and also the individual contribution of different residues towards thermal unfolding, principal component analysis method was applied in order to give a new insight to protein dynamics by analyzing the contribution of coefficients of principal components. The cross-correlation matrix obtained from MD simulation trajectory provided important information regarding the anisotropy of backbone dynamics that leads to unfolding. Unfolding of ubiquitin was found to be a three-state process, while that of melittin, though smaller and mostly helical, is more complicated. © 2007 American Institute of Physics.

CHAITALI MUKHOPADHYAY

Chemistry

A DAS

Fulltext

University of Calcutta (informally known as Calcutta University or CU) is a collegiate public state university located in Kolkata, West Bengal, India.&nbsp;Within India it is recognized as a &quot;Five-Star University&quot; and accredited &quot;A&quot; Grade by National Assessment and Accreditation Council.

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The University of Calcutta has secured the Fifth position among the Universities of India in the prestigious &quot;Indian University Ranking 2019&quot; list, released by the NIRF of the Ministry of Human Resource Development, Government of India.

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It was established on 24 January 1857, and was one of the first institutions in Asia to be established as a multidisciplinary and Western-style university. Its alumni and faculty include several heads of state, heads of government, social reformers, prominent artists, only academy award winner and Dirac medal winner in India, many Fellows of the Royal Society and five Nobel laureates as of 2019 which is highest in South Asia.

University Of Calcutta

Application of principal component analysis in protein unfolding: an all-atom molecular dynamics simulation study.

Journal of Chemical Physics

An all atom molecular dynamics simulation was used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin. Ubiquitin unfolds through pre-unfolded (intermediate) states, i.e. guanidinium induced unfolding of ubiquitin appears to be a multi-step process, and loss of hydrophobic contacts of C-terminal residues is crucial for ubiquitin unfolding. Free-energy landscapes show that barrier separation between folded and unfolded basins is ∼5.0 kcal mol-1, and both the basins are of comparable energy. It was observed that guanidinium ions interact directly with ubiquitin. Favorable electrostatic interaction is the main driving force for such accumulation of guanidinium ions near protein, but van der Waals energy also contributes. RDF plots show that accumulation of guanidinium ions near specific residues is the main cause for destabilization of intra-residue interactions crucial to maintain the three-dimensional fold of the protein. One salt-bridge interaction between Lys11 and Glu34 appears to be important to maintain the crystal structure of ubiquitin and this salt-bridge can map the unfolding process of ubiquitin. © the Partner Organisations 2014.

Physical Chemistry Chemical Physics

Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin

UDP-N-acetylglucosamine 3-O-acyltransferase is a protein with a left-handed parallel β-helix, which is a natural nanotube. They are associated with unusual high stability. To identify the reason behind the structural stability of β-helical nanotubular structure, we have performed a total of 4 μs molecular dynamics simulations of the protein in implicit solvent at four different temperatures and monitored the unfolding pathway. The correlation in movement between different regions of the nanotubular structure has been identified from the dynamical cross-correlation map and contribution of some specific residues towards unfolding transition has been identified by principal component analysis. Difference in stability of the three loop regions has also been characterized. Construction of the unfolding conformational energy landscape identifies the probable intermediates that can appear in the unfolding pathway of the protein. © 2010 Wiley Periodicals, Inc.

Biopolymers

LpxA: A natural nanotube

Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study

The temperature-induced unfolding pathway of ubiquitin has been investigated by molecular dynamics simulation at four different temperatures. It has been observed that the sequences of the unfolding events are same at all the temperatures. However, the time scale of the dynamics at different temperatures are different. The transition states at various temperatures also possess similar secondary structural elements. The intermediate conformations visited by the protein at different temperatures can help determination of the transition states. The well known "A state" of ubiquitin, hitherto found to be stable only in methanol water mixture, have been observed to be a common transient intermediate conformation in the unfolding path of the protein in water. Our observation about the similarities of the unfolding process at different temperatures strongly recommend for a defined pathway for the unfolding process. © 2005 The American Physical Society.

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Unfolding dynamics of the protein ubiquitin: Insight from simulation

SpringerReference

Meselson-Radding Model Of Recombination (1975 Proc Natl Acad Sci USA 72:358)

Who's Who

Hunter, Dr Tony, (Anthony Rex Hunter), (born 23 Aug. 1943), Professor, since 1982, and Renato Dulbecco Chair, since 2011, Molecular and Cell Biology Laboratory, Salk Institute, La Jolla, California; concurrently Adjunct Professor of Biology, University of California, San Diego

Biophysical Journal

The Mechanical Unfolding of Ubiquitin through All-Atom Monte Carlo Simulation with a Gō-Type Potential

Journal	Journal of Chemical Physics
Publisher	AMER INST PHYSICS
ISSN	0021-9606
Open Access	No