MARZINEK Jan

A polar SxxS motif drives assembly of the transmembrane domains of Toll-like receptor 4

Like all members of the Toll-like receptor (TLR) family, TLR4 comprises of a large ectodomain (ECD) involved in ligand recognition at the cell-surface, and a cytosolic Toll/interleukin-1 receptor (TIR) signalling domain, linked by a lipid membrane-anchored transmembrane (TM) domain (TMD).

type: 
Journal Paper
journal: 
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2017 Jul 22;1859(10):2086-2095. doi: 10.1016/j.bbamem.2017.07.010
pubmed: 
28739292
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/?term=28739292
Impact Factor: 
3.498
Date of acceptance: 
2017-07-20

Multiscale Molecular Dynamics Simulation Approaches to the Structure and Dynamics of Viruses

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated.

type: 
Journal Paper
journal: 
Progress in Biophysics and Molecular Biology, Oct 17 2016, doi: 10.1016/j.pbiomolbio.2016.09.010
pubmed: 
27765545
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27765545
Impact Factor: 
2.581
Date of acceptance: 
2016-09-27

South-east Asian Zika virus strain linked to cluster of cases in Singapore, August 2016

Zika virus (ZIKV) is an ongoing global public health emergency with 70 countries and territories reporting evidence of ZIKV transmission since 2015. On 27 August 2016, Singapore reported its first case of local ZIKV transmission and identified an ongoing cluster. Here, we report the genome sequences of ZIKV strains from two cases and find through phylogenetic analysis that these strains form an earlier branch distinct from the recent large outbreak in the Americas.

type: 
Journal Paper
journal: 
Eurosurveillance, Volume 21, Issue 38, 22 September 2016, DOI: http://dx.doi.org/10.2807/1560-7917.ES.2016.21.38.30347
Url: 
http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=22588
Impact Factor: 
5.8
Date of acceptance: 
2016-09-22

Pushing the Envelope: Dengue Viral Membrane Coaxed into Shape by Molecular Simulations

Dengue virus is a flavivirus responsible for millions of infections per year. Its surface contains a phospholipid bilayer, within which are embedded the envelope (E) and membrane (M) proteins, arranged with icosahedral geometry. Exposure to low pH triggers the E proteins to undergo conformational changes, which precede fusion with the host cell membrane and release of the viral genome.

type: 
Journal Paper
journal: 
Structure 2016 Jul 6, doi: 10.1016/j.str.2016.05.014
pubmed: 
27396828
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/27396828
Impact Factor: 
5.618
Date of acceptance: 
2016-05-11

Characterizing the Conformational Landscape of Flavivirus Fusion Peptides via Simulation and Experiment

Conformational changes in the envelope proteins of flaviviruses help to expose the highly conserved fusion peptide (FP), a region which is critical to membrane fusion and host cell infection, and which represents a significant target for antiviral drugs and antibodies. In principle, extended timescale atomic-resolution simulations may be used to characterize the dynamics of such peptides. However, the resultant accuracy is critically dependent upon both the underlying force field and sufficient conformational sampling.

type: 
Journal Paper
journal: 
Scientific Reports 2016, doi: 10.1038/srep19160
Url: 
http://www.nature.com/articles/srep19160
Impact Factor: 
5.578
Date of acceptance: 
2015-11-12

Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations

Free energy prediction of ligand binding to macromolecules using explicit solvent molecular dynamics (MD) simulations is computationally very expensive. Recently, we reported a linear correlation between the binding free energy obtained via umbrella sampling (US) versus the rupture force from steered molecular dynamics (SMD) simulations for epigallocatechin-3-gallate (EGCG) binding to α-helical-rich keratin. This linear correlation suggests a potential route for fast free energy predictions using SMD alone.

type: 
Journal Paper
journal: 
Journal of Chemical Information and Modeling, doi: 10.1021/ci500164q
Url: 
http://pubs.acs.org/doi/abs/10.1021/ci500164q
Impact Factor: 
4.304
Date of acceptance: 
2014-03-14

A Study on Fe2+ – α-Helical-Rich Keratin Complex Formation Using Isothermal Titration Calorimetry and Molecular Dynamics Simulation

Iron binding to protein is common in biological processes of dioxygen transport, electron transfer as well as in stabilizing drug–protein complexes. α-Helix is the most prevalent secondary structure of proteins. In this study, Fe2+ binding to α-helix has been studied by isothermal titration calorimetry (ITC) and explicitly solvated molecular dynamics (MD) simulation. Ferrous gluconate and α-helix-rich keratin are used for the ITC study and the results revealed followed one set of identical sites binding model.

type: 
Journal Paper
journal: 
Journal of Pharmaceutical Sciences, vol. 103, Issue 4, pg 1224-1232, April 2014, doi: 10.1002/jps.23895
Url: 
http://onlinelibrary.wiley.com/doi/10.1002/jps.23895/abstract
Impact Factor: 
3.13
Date of acceptance: 
2014-01-17
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