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Advances in computational design methods have made possible extensive engineering of soluble proteins, but designed β-barrel membrane proteins await improvements in our understanding of the sequence determinants of folding and stability. A subset of the amino acid residues of membrane proteins interact with the cell membrane, and the design rules that govern this lipid-facing surface are poorly understood. We applied a residue-level depth potential for β-barrel membrane proteins to the complete redesign of the lipid-facing surface of Escherichia coli OmpA. Initial designs failed to fold correctly, but reversion of a small number of mutations indicated by backcross experiments yielded designs with substitutions to up to 60% of the surface that did support folding and membrane insertion.
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http://dx.doi.org/10.1073/pnas.1501836112 | DOI Listing |
Acc Chem Res
March 2025
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.
Enveloped viruses encode ion-conducting pores that permeabilize the host cell membranes and mediate the budding of new viruses. These viroporins are some of the essential membrane proteins of viruses, and have high sequence conservation, making them important targets of antiviral drugs. High-resolution structures of viroporins are challenging to determine by X-ray crystallography and cryoelectron microscopy, because these proteins are small, hydrophobic, and prone to induce membrane curvature.
View Article and Find Full Text PDFVirus Res
November 2024
Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, 145 Xingda Road, Taichung 402, Taiwan.; The iEGG and Animal Biotechnology Center, National Chung Hsing University, 250 Kuo Kuang Road, Taichung 40227, Taiwan. Electronic address:
Coronaviruses (CoVs) are significant animal and human pathogens, characterized by being enveloped RNA viruses with positive-sense single-stranded RNA. The Coronaviridae family encompasses four genera, among which gammacoronaviruses pose a major threat to the poultry industry, which infectious bronchitis virus (IBV) being the most prominent of these threats. Particularly, IBV adversely affects broiler growth and egg production, causing substantial losses.
View Article and Find Full Text PDFMolecules
June 2024
Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298-0540, USA.
A method is described to deconstruct the network of hydropathic interactions within and between a protein's sidechain and its environment into residue-based three-dimensional maps. These maps encode favorable and unfavorable hydrophobic and polar interactions, in terms of spatial positions for optimal interactions, relative interaction strength, as well as character. In addition, these maps are backbone angle-dependent.
View Article and Find Full Text PDFProtein Sci
October 2023
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
The SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined.
View Article and Find Full Text PDFFront Mol Biosci
March 2023
Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States.
The aliphatic hydrophobic amino acid residues-alanine, isoleucine, leucine, proline and valine-are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms.
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