Exploring Peptide⁻Solvent Interactions: A Computational Study

Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry
Nadia Elghobashi-Meinhardt

Abstract

The dilemma of reconciling the contradictory evidence regarding the conformation of long solvated peptide chains is the so-called "reconciliation problem". Clues regarding the stability of certain conformations likely lie in the electronic structure at the peptide⁻solvent interface, but the peptide⁻solvent interaction is not fully understood. Here, we study the influence of aqueous solvent on peptide conformations by using classical molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) energy calculations. The model systems include an 11-residue peptide, X 2 A 7 O 2 (XAO), where X, A, and O denote diaminobutyric acid, alanine, and ornithine, respectively, and a 9-mer (Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys). Spectroscopic and MD data present conflicting evidence regarding the structure of XAO in water; some results indicate that XAO adopts a polyproline II (P II ) conformation, whereas other findings suggest that XAO explores a range of conformations. To investigate this contradiction, we present here the results of MD simulations of XAO and the 9-mer in aqueous solution, combined with QM/MM energy calculations.

References

Jan 1, 1968·Advances in Protein Chemistry·G N Ramachandran, V Sasisekharan
Nov 29, 2001·Biochemistry·M A KellyT P Creamer
Jul 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·Zhengshuang ShiNeville R Kallenbach
Jan 22, 2004·Journal of the American Chemical Society·Alexander D MacKerellCharles L Brooks
Apr 23, 2004·Proteins·Alex KentsisRoman Osman
Aug 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Bojan ZagrovicVijay S Pande
Sep 1, 2005·Proceedings of the National Academy of Sciences of the United States of America·Abhishek K JhaTobin R Sosnick
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Feb 1, 2006·Proceedings of the National Academy of Sciences of the United States of America·Joanna MakowskaHarold A Scheraga
May 11, 2006·Chemical Reviews·Ninad Prabhu, Kim Sharp
Sep 14, 2006·Journal of the American Chemical Society·Susana BlancoJosé L Alonso
Feb 6, 2007·Biophysical Journal·Joanna MakowskaHarold A Scheraga
Apr 10, 2007·Proceedings of the National Academy of Sciences of the United States of America·Reinhard Schweitzer-Stenner, Thomas J Measey
Apr 13, 2011·PloS One·Yohann MansiauxAlexandre G de Brevern
Nov 8, 2016·Nature Methods·Jing HuangAlexander D MacKerell

❮ Previous
Next ❯

Citations

Apr 19, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shuai ZhouXiaoying Zhuang

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR
circular dichroism
X-ray

Software Mentioned

CRYSOL
charmm36
CHARMM
charmm22
AMBER
NAMD
SCC
DFTB
XAO
DSSP

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.