Interactions between neuronal fusion proteins explored by molecular dynamics.

Biophysical Journal
Marie-Pierre DurrieuMarc Baaden

Abstract

In this report, we present features of the neuronal SNARE complex determined by atomistic molecular dynamics simulations. The results are robust for three models, varying force fields (AMBER and GROMOS) and solvent environment (explicit and implicit). An excellent agreement with experimental findings is observed. The SNARE core complex behaves like a stiff rod, with limited conformational dynamics. An accurate picture of the interactions within the complex emerges with a characteristic pattern of atomic contacts, hydrogen bonds, and salt bridges reinforcing the underlying layer structure. This supports the metaphor of a molecular Velcro strip that has been used by others to describe the neuronal fusion complex. No evidence for directionality in the formation of these interactions was found. Electrostatics largely dominates all interactions, with an acidic surface patch structuring the hydration layers surrounding the complex. The interactions within the four-helix bundle are asymmetric, with the synaptobrevin R-SNARE notably exhibiting an increased rigidity with respect to the three Q-SNARE helices. The interaction patterns we observe provide a new tool for interpreting the impact of mutations on the complex.

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Feb 14, 1997·The Journal of Biological Chemistry·D FasshauerA T Brünger
Sep 10, 1998·Nature Structural Biology·M A PoirierM K Bennett
Dec 23, 1998·Proceedings of the National Academy of Sciences of the United States of America·D FasshauerR Jahn
Aug 16, 2000·Proceedings of the National Academy of Sciences of the United States of America·S QuetglasM Seagar
Mar 30, 2001·The Journal of Biological Chemistry·M MargittaiR Langen
May 31, 2001·Journal of Molecular Graphics & Modelling·W CornellD A Case
Jan 12, 2002·Nature Structural Biology·Wolfram AntoninThomas R Schneider
Feb 8, 2002·Neuron·Xiaocheng ChenJosep Rizo
Nov 5, 2002·Biophysical Journal·Sang-Joon ChoBhanu P Jena
Dec 24, 2002·The Journal of Biological Chemistry·James A Ernst, Axel T Brunger
May 13, 2003·Nature Structural Biology·Dae-Hyuk KweonYeon-Kyun Shin
Oct 8, 2003·Neuropharmacology·Maria F MatosThomas C Südhof
Jun 25, 2004·Nucleic Acids Research·Matthias Heinig, Dmitrij Frishman
Jul 13, 2004·The Journal of Biological Chemistry·Fan ZhangYeon-Kyun Shin
Oct 4, 2005·Journal of Computational Chemistry·David A CaseRobert J Woods
Jan 19, 2006·The Journal of Cell Biology·Xue Han, Meyer B Jackson
Apr 29, 2006·Journal of Molecular Graphics & Modelling·Elmar KriegerGert Vriend

❮ Previous
Next ❯

Citations

Mar 5, 2009·The Journal of Biological Chemistry·Katrin Wiederhold, Dirk Fasshauer
Mar 1, 2012·Current Opinion in Structural Biology·Herre Jelger Risselada, Helmut Grubmüller
May 9, 2015·Biophysical Journal·Nicole FortoulAnand Jagota
Mar 25, 2011·Chembiochem : a European Journal of Chemical Biology·Herre Jelger RisseladaHelmut Grubmüller
Apr 9, 2009·Journal of Computational Chemistry·Olivier DelalandeMarc Baaden
Sep 2, 2017·Scientific Reports·Dario De VecchisAntoine Taly
May 30, 2009·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Marie-Pierre DurrieuMarc Baaden
Oct 9, 2012·Journal of Chemical Theory and Computation·Leonardo DarréSergio Pantano
Oct 16, 2014·The Journal of Physical Chemistry. B·Obaidur RahamanFabio Sterpone
Nov 17, 2021·Biochemical Society Transactions·Alzbeta Tuerkova, Peter M Kasson

❮ 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.

Related Papers

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
Marie-Pierre DurrieuMarc Baaden
Biophysical Journal
Yonathan Kozlovsky, Michael M Kozlov
Chembiochem : a European Journal of Chemical Biology
H Jelger RisseladaHelmut Grubmüller
© 2021 Meta ULC. All rights reserved