scholarly journals Grafted biomembranes containing membrane proteins – the case of the leucine transporter

Soft Matter ◽  
2015 ◽  
Vol 11 (39) ◽  
pp. 7707-7711 ◽  
Author(s):  
Vivien Jagalski ◽  
Robert D. Barker ◽  
Mikkel B. Thygesen ◽  
Kamil Gotfryd ◽  
Mie B. Krüger ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulation ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Dynamics Simulation ◽  
Membrane Protein Structure ◽  
Neutron Reflection

Together neutron reflection and molecular dynamics simulation offer a powerful tool to study the membrane protein structure in native-like environment.

Membrane protein structure quality in molecular dynamics simulation

2005 ◽  
Vol 24 (2) ◽  
pp. 157-165 ◽  
Author(s):  
Richard J. Law ◽  
Charlotte Capener ◽  
Marc Baaden ◽  
Peter J. Bond ◽  
Jeff Campbell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Structure ◽  
Molecular Dynamics Simulation ◽  
Membrane Protein ◽  
Dynamics Simulation ◽  
Membrane Protein Structure ◽  
Structure Quality

scholarly journals Molecular Dynamics Simulation of a Spin-Labeled Membrane Protein

2011 ◽  
Vol 100 (3) ◽  
pp. 225a
Author(s):  
Alexandra M. Zudova ◽  
Bengt Svensson ◽  
Michel Espinoza-Fonseca ◽  
David D. Thomas
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Membrane Protein ◽  
Dynamics Simulation

scholarly journals Structures of membrane proteins

2010 ◽  
Vol 43 (1) ◽  
pp. 65-158 ◽  
Author(s):  
Kutti R. Vinothkumar ◽  
Richard Henderson
Keyword(s):  
Protein Structure ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Membrane Protein Structure ◽  
Expression Systems ◽  
Genome Sequences ◽  
Conformational Variability ◽  
Efficient Expression

AbstractIn reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. We group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. The first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure determined was a major landmark. With the advent of complete genome sequences and efficient expression systems, there has been an explosion in the rate of membrane protein structure determination, with many classes represented. New structures are published every month and more than 150 unique membrane protein structures have been determined. This review analyses the reasons for this success, discusses the challenges that still lie ahead, and presents a concise summary of the key achievements with illustrated examples selected from each class.

scholarly journals Molecular Dynamics Simulation-assisted Ionic Liquid Screening for Deep Coverage Proteome Analysis

2020 ◽  
Vol 19 (10) ◽  
pp. 1724-1737
Author(s):  
Fei Fang ◽  
Qun Zhao ◽  
Huiying Chu ◽  
Mingwei Liu ◽  
Baofeng Zhao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ionic Liquid ◽  
Molecular Dynamics Simulation ◽  
Membrane Proteins ◽  
Sample Preparation ◽  
Proteomic Analysis ◽  
Dynamics Simulation ◽  
Dominant Factor ◽  
Label Free ◽  
Compound Libraries

In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic proteins and low-abundance proteins, which play critical roles in signaling networks, are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously satisfy the requirements on strong solubilizing ability to membrane proteins and good enzyme compatibility. Thus, it is urgent to screen out ideal extractant from the huge compound libraries in a fast and effective way. Herein, by investigating the interior mechanism of extractants on the membrane proteins solubilization and trypsin compatibility, a molecular dynamics simulation system was established as complement to the experimental procedure to narrow down the scope of candidates for proteomics analysis. The simulation data shows that the van der Waals interaction between cation group of ionic liquid and membrane protein is the dominant factor in determining protein solubilization. In combination with the experimental data, 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) is on the shortlist for the suitable candidates from comprehensive aspects. Inspired by the advantages of C12Im-Cl, an ionic liquid-based filter-aided sample preparation (i-FASP) method was developed. Using this strategy, over 3,300 proteins were confidently identified from 103 HeLa cells (∼100 ng proteins) in a single run, an improvement of 53% over the conventional FASP method. Then the i-FASP method was further successfully applied to the label-free relative quantitation of human liver cancer and para-carcinoma tissues with obviously improved accuracy, reproducibility and coverage than the commonly used urea-based FASP method. The above results demonstrated that the i-FASP method could be performed as a versatile tool for the in-depth coverage proteomic analysis of biological samples.

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