Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein

Proteins
D van der SpoelH J Berendsen

Abstract

Molecular dynamics (MD) simulations of N-terminal peptides from lactate dehydrogenase (LDH) with increasing length and individual secondary structure elements were used to study their stability in relation to folding. Ten simulations of 1-2 ns of different peptides in water starting from the coordinates of the crystal structure were performed. The stability of the peptides was compared qualitatively by analyzing the root mean square deviation (RMSD) from the crystal structure, radius of gyration, secondary and tertiary structure, and solvent accessible surface area. In agreement with earlier MD studies, relatively short (< 15 amino acids) peptides containing individual secondary structure elements were generally found to be unstable; the hydrophobic alpha 1-helix of the nucleotide binding fold displayed a significantly higher stability, however. Our simulations further showed that the first beta alpha beta supersecondary unit of the characteristic dinucleotide binding fold (Rossmann fold) of LDH is somewhat more stable than other units of similar length and that the alpha 2-helix, which unfolds by itself, is stabilized by binding to this unit. This finding suggests that the first beta alpha beta unit could function as an N-term...Continue Reading

References

Mar 16, 1992·Biochemical and Biophysical Research Communications·B DasC Das Gupta
Oct 20, 1992·Journal of Molecular Biology·D J TobiasC L Brooks
Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·V Daggett, M Levitt
Jun 18, 1991·Biochemistry·D J TobiasC L Brooks
Nov 1, 1990·Trends in Biochemical Sciences·M SarasteA Wittinghofer
Jan 1, 1990·Annual Review of Biochemistry·P S Kim, R L Baldwin
Dec 5, 1987·Journal of Molecular Biology·C Abad-ZapateroM G Rossmann
Jul 20, 1973·Science·C B Anfinsen
Jul 19, 1974·Nature·M G RossmannK W Olsen
Aug 18, 1995·Journal of Molecular Biology·L PuglieseS J Wodak
Mar 1, 1994·Nature Structural Biology·T E Creighton
Mar 1, 1994·Nature Structural Biology·T R SosnickS W Englander
Mar 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·K A DillH S Chan
Jun 13, 1995·Biochemistry·J D Hirst, C L Brooks
Feb 14, 1995·Proceedings of the National Academy of Sciences of the United States of America·A N Fedorov, T O Baldwin
Mar 1, 1994·Protein Science : a Publication of the Protein Society·M JechtR Jaenicke
May 1, 1994·Trends in Biochemical Sciences·D Bossemeyer
Mar 29, 1993·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·R Jaenicke
Jan 1, 1994·Trends in Biochemical Sciences·C M DobsonS E Radford
Oct 1, 1993·Biopolymers·K V SomanD A Case
Nov 1, 1993·Protein Science : a Publication of the Protein Society·N Alexandrov
Jan 1, 1993·Annual Review of Biophysics and Biomolecular Structure·V Daggett, M Levitt
Apr 27, 1993·Biochemistry·J Tirado-Rives, W L Jorgensen

❮ Previous
Next ❯

Citations

Oct 1, 1996·Protein Science : a Publication of the Protein Society·D van der SpoelH J Vogel
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Apr 16, 2013·Biochimie·Jaroslav KubrychtJiří Hudeček
Oct 1, 2011·The Journal of Physical Chemistry. B·Hong-Ze GangBo-Zhong Mu
Jul 17, 2001·The Journal of Peptide Research : Official Journal of the American Peptide Society·M IovinoA Desideri

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.