A new method to model membrane protein structure based on silent amino acid substitutions

2001 ◽  
Vol 44 (3) ◽  
pp. 370-375 ◽  
Author(s):  
John A.G. Briggs ◽  
Jaume Torres ◽  
Isaiah T. Arkin
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Membrane Protein ◽  
Model Membrane ◽  
New Method ◽  
Amino Acid Substitutions ◽  
Membrane Protein Structure

Order-disorder transitions of cytoplasmic N-termini in the mechanisms of P-type ATPases

2020 ◽  
Author(s):  
Khondker Rufaka Hossain ◽  
Daniel Clayton ◽  
Sophia C Goodchild ◽  
Alison Rodger ◽  
Richard James Payne ◽  
...  
Keyword(s):  
Protein Structure ◽  
Membrane Protein ◽  
Structure And Function ◽  
Membrane Protein Structure ◽  
Protein Structure And Function ◽  
Lipid Environment ◽  
Membrane Pumps ◽  
And Function ◽  
P Type

Membrane protein structure and function are modulated via interactions with their lipid environment. This is particularly true for the integral membrane pumps, the P-type ATPases. These ATPases play vital roles...

Effect of conserved intersubunit amino acid substitutions on Hfq protein structure and stability

2014 ◽  
Vol 79 (5) ◽  
pp. 469-477 ◽  
Author(s):  
V. N. Murina ◽  
B. S. Melnik ◽  
V. V. Filimonov ◽  
M. Ühlein ◽  
M. S. Weiss ◽  
...  
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Amino Acid Substitutions ◽  
Structure And Stability

scholarly journals Protein structure prediction and design in a biologically-realistic implicit membrane

2019 ◽  
Author(s):  
Rebecca F. Alford ◽  
Patrick J. Fleming ◽  
Karen G. Fleming ◽  
Jeffrey J. Gray
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Structure Prediction ◽  
Protein Design ◽  
Structure Prediction ◽  
De Novo ◽  
Computational Design ◽  
Amino Acid Distribution

ABSTRACTProtein design is a powerful tool for elucidating mechanisms of function and engineering new therapeutics and nanotechnologies. While soluble protein design has advanced, membrane protein design remains challenging due to difficulties in modeling the lipid bilayer. In this work, we developed an implicit approach that captures the anisotropic structure, shape of water-filled pores, and nanoscale dimensions of membranes with different lipid compositions. The model improves performance in computational bench-marks against experimental targets including prediction of protein orientations in the bilayer, ΔΔG calculations, native structure dis-crimination, and native sequence recovery. When applied to de novo protein design, this approach designs sequences with an amino acid distribution near the native amino acid distribution in membrane proteins, overcoming a critical flaw in previous membrane models that were prone to generating leucine-rich designs. Further, the proteins designed in the new membrane model exhibit native-like features including interfacial aromatic side chains, hydrophobic lengths compatible with bilayer thickness, and polar pores. Our method advances high-resolution membrane protein structure prediction and design toward tackling key biological questions and engineering challenges.Significance StatementMembrane proteins participate in many life processes including transport, signaling, and catalysis. They constitute over 30% of all proteins and are targets for over 60% of pharmaceuticals. Computational design tools for membrane proteins will transform the interrogation of basic science questions such as membrane protein thermodynamics and the pipeline for engineering new therapeutics and nanotechnologies. Existing tools are either too expensive to compute or rely on manual design strategies. In this work, we developed a fast and accurate method for membrane protein design. The tool is available to the public and will accelerate the experimental design pipeline for membrane proteins.

scholarly journals Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure

2018 ◽  
Vol 1860 (2) ◽  
pp. 378-383 ◽  
Author(s):  
Mayuriben Parmar ◽  
Shaun Rawson ◽  
Charlotte A. Scarff ◽  
Adrian Goldman ◽  
Timothy R. Dafforn ◽  
...  
Keyword(s):  
Protein Structure ◽  
Membrane Protein ◽  
Single Particle ◽  
Membrane Protein Structure
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