Simulations of fatty acid-binding proteins suggest sites important for function. I. Stearic acid

Biophysical Journal
T B Woolf

Abstract

Molecular dynamics simulations of two structurally similar fatty acid-binding proteins interacting with stearic acid are described. The calculations relate to recent ligand binding measurements and suggest similarities and differences between the two systems. Charged and neutral forms of the fatty acid were examined. The charged forms led to rapid trajectory divergence, whereas the protonated forms remained stable over the length of their 1-ns production trajectories. The two protein systems showed similar sets of total interaction energies with the ligand. However, the strengths of individual amino acids interacting with the ligand differ. Furthermore, covariance analysis of the ligand with both protein and water suggests that the stearic acid in the adipocyte fatty acid-binding protein is coupled more strongly to the water than to the protein. The stearic acid in the muscle fatty acid-binding protein is seen to be coupled differentially along the length of the chain to the protein. These differences could help to rationalize the stronger binding affinity for stearic acid in the human muscle fatty acid-binding protein. An importance scale, based on both covariance and interaction energy with the ligand, is proposed to identify...Continue Reading

References

Apr 11, 1995·Proceedings of the National Academy of Sciences of the United States of America·J B ClarageG N Phillips
Dec 1, 1994·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·J M LaLondeL J Banaszak
Jul 15, 1994·The Biochemical Journal·G ZanottiP Spadon
Jan 1, 1994·Advances in Protein Chemistry·L BanaszakT A Jones
Mar 1, 1994·Protein Engineering·J AqvistJ E Samuelsson
Jun 9, 1993·Molecular and Cellular Biochemistry·K R Miller, D P Cistola
Dec 22, 1995·Journal of Medicinal Chemistry· Ajay, M A Murcko
May 10, 1996·The Journal of Biological Chemistry·G V RichieriA M Kleinfeld
Dec 6, 1996·The Journal of Biological Chemistry·G V RichieriA M Kleinfeld

❮ Previous
Next ❯

Citations

Oct 17, 2009·Journal of Molecular Modeling·Lihie Ben-Avraham LevinYossi Tsfadia
Nov 26, 1999·Biochimica Et Biophysica Acta·A Reese-WagonerL Banaszak
Nov 26, 1999·Biochimica Et Biophysica Acta·G Zanotti
Jun 24, 2003·Biochimica Et Biophysica Acta·Emma JakobssonGerard J Kleywegt
Jul 27, 2012·Journal of Biomolecular Structure & Dynamics·Adriana EstevesMargot Paulino Zunini
Aug 19, 1999·Protein Science : a Publication of the Protein Society·V A Likić, F G Prendergast
Aug 10, 2000·Protein Science : a Publication of the Protein Society·L RagonaH Molinari
Jan 24, 2006·Journal of Structural Biology·Eugenia PolveriniPaolo Cavatorta
Jan 29, 2002·Journal of Molecular Biology·Dirk Bakowies, Wilfred F van Gunsteren
May 29, 2014·Biopolymers·Martiniano Bello, Enrique García-Hernández

❮ 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.