Broadening the cofactor specificity of a thermostable alcohol dehydrogenase using rational protein design introduces novel kinetic transient behavior

2010 ◽  
Vol 107 (5) ◽  
pp. 763-774 ◽  
Author(s):  
Elliot Campbell ◽  
Ian R. Wheeldon ◽  
Scott Banta
Keyword(s):  
Alcohol Dehydrogenase ◽  
Protein Design ◽  
Transient Behavior ◽  
Cofactor Specificity ◽  
Rational Protein Design

scholarly journals Probing active-site residues of pyranose 2-oxidase fromTrametes multicolorby semi-rational protein design

2009 ◽  
Vol 4 (4) ◽  
pp. 535-543 ◽  
Author(s):  
Clara Salaheddin ◽  
Oliver Spadiut ◽  
Roland Ludwig ◽  
Tien-Chye Tan ◽  
Christina Divne ◽  
...  
Keyword(s):  
Protein Design ◽  
Active Site ◽  
Active Site Residues ◽  
Rational Protein Design

Cofactor specificity engineering of a long-chain secondary alcohol dehydrogenase from Micrococcus luteus for redox-neutral biotransformation of fatty acids

2019 ◽  
Vol 55 (96) ◽  
pp. 14462-14465 ◽  
Author(s):  
Eun-Ji Seo ◽  
Hye-Ji Kim ◽  
Myeong-Ju Kim ◽  
Jeong-Sun Kim ◽  
Jin-Byung Park
Keyword(s):  
Fatty Acids ◽  
Alcohol Dehydrogenase ◽  
Micrococcus Luteus ◽  
Secondary Alcohol ◽  
Cofactor Specificity ◽  
Secondary Alcohol Dehydrogenase ◽  
Long Chain

Structure-based cofactor specificity engineering of an alcohol dehydrogenase (mLSADH) enables a redox-neutral biotransformation of C18 fatty acids into C9 fatty acids.

Rational Protein Design of Paenibacillus barcinonensis Esterase EstA for Kinetic Resolution of Tertiary Alcohols

ChemCatChem ◽  
2010 ◽  
Vol 2 (8) ◽  
pp. 962-967 ◽  
Author(s):  
Arnau Bassegoda ◽  
Giang-Son Nguyen ◽  
Marlen Schmidt ◽  
Robert Kourist ◽  
Pilar Diaz ◽  
...  
Keyword(s):  
Protein Design ◽  
Kinetic Resolution ◽  
Tertiary Alcohols ◽  
Rational Protein Design ◽  
Paenibacillus Barcinonensis

scholarly journals Crystallization of interleukin-18 for structure-based inhibitor design

2015 ◽  
Vol 71 (6) ◽  
pp. 710-717
Author(s):  
Brian Krumm ◽  
Xiangzhi Meng ◽  
Yan Xiang ◽  
Junpeng Deng
Keyword(s):  
Protein Design ◽  
Immune Defense ◽  
Interleukin 18 ◽  
Structure Based Drug Design ◽  
Binding Interface ◽  
Naturally Occurring ◽  
Rational Protein Design ◽  
Entropy Reduction ◽  
Low Ionic Strength

Interleukin-18 (IL-18) is a pleiotropic pro-inflammatory cytokine belonging to the IL-1 superfamily. IL-18 plays an important role in host innate and acquired immune defense, with its activity being modulatedin vivoby its naturally occurring antagonist IL-18 binding protein (IL-18BP). Recent crystal structures of human IL-18 (hIL-18) in complex with its antagonist or cognate receptor(s) have revealed a conserved binding interface on hIL-18 representing a promising drug target. An important step in this process is obtaining crystals of apo hIL-18 or hIL-18 in complex with small-molecule inhibitors, preferably under low ionic strength conditions. In this study, surface-entropy reduction (SER) and rational protein design were employed to facilitate the crystallization of hIL-18. The results provide an excellent platform for structure-based drug design.

Functional tuning and expanding of myoglobin by rational protein design

2014 ◽  
Vol 57 (3) ◽  
pp. 346-355 ◽  
Author(s):  
YingWu Lin ◽  
JiangYun Wang ◽  
Yi Lu
Keyword(s):  
Protein Design ◽  
Rational Protein Design

scholarly journals Non-native fold of the putative VPS39 zinc finger domain

2020 ◽  
Vol 5 ◽  
pp. 154
Author(s):  
Benjamin G. Butt ◽  
Edward J. Scourfield ◽  
Stephen C. Graham
Keyword(s):  
Zinc Finger ◽  
Protein Design ◽  
Zinc Finger Domain ◽  
Native Structure ◽  
Binding Region ◽  
Late Endosomes ◽  
Rational Protein Design ◽  
Membrane Tethering ◽  
New Gene ◽  
Native Fold

Background: The multi-subunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is involved in regulating the fusion of late endosomes and autophagosomes with lysosomes in eukaryotes. The C-terminal regions of several HOPS components have been shown to be required for correct complex assembly, including the C-terminal really interesting new gene (RING) zinc finger domains of HOPS components VPS18 and VPS41. We sought to structurally characterise the putative C-terminal zinc finger domain of VPS39, which we hypothesised may be important for binding of VPS39 to cellular partners or to other HOPS components. Methods: We recombinantly expressed, purified and solved the crystal structure of the proposed zinc-binding region of VPS39. Results: In the structure, this region forms an anti-parallel β-hairpin that is incorporated into a homotetrameric eight-stranded β-barrel. However, the fold is stabilised by coordination of zinc ions by residues from the purification tag and an intramolecular disulphide bond between two predicted zinc ligands. Conclusions: We solved the structure of the VPS39 C-terminal domain adopting a non-native fold. Our work highlights the risk of non-native folds when purifying small zinc-containing domains with hexahistidine tags. However, the non-native structure we observe may have implications for rational protein design.

scholarly journals Non-native fold of the putative VPS39 zinc finger domain

2020 ◽  
Vol 5 ◽  
pp. 154
Author(s):  
Benjamin G. Butt ◽  
Edward J. Scourfield ◽  
Stephen C. Graham
Keyword(s):  
Zinc Finger ◽  
Protein Design ◽  
Zinc Finger Domain ◽  
Native Structure ◽  
Binding Region ◽  
Late Endosomes ◽  
Rational Protein Design ◽  
Membrane Tethering ◽  
New Gene ◽  
Native Fold

Background: The multi-subunit homotypic fusion and vacuole protein sorting (HOPS) membrane-tethering complex is involved in regulating the fusion of late endosomes and autophagosomes with lysosomes in eukaryotes. The C-terminal regions of several HOPS components have been shown to be required for correct complex assembly, including the C-terminal really interesting new gene (RING) zinc finger domains of HOPS components VPS18 and VPS41. We sought to structurally characterise the putative C-terminal zinc finger domain of VPS39, which we hypothesised may be important for binding of VPS39 to cellular partners or to other HOPS components. Methods: We recombinantly expressed, purified and solved the crystal structure of the proposed zinc-binding region of VPS39. Results: In the structure, this region forms an anti-parallel β-hairpin that is incorporated into a homotetrameric eight-stranded β-barrel. However, the fold is stabilised by coordination of zinc ions by residues from the purification tag and an intramolecular disulphide bond between two predicted zinc ligands. Conclusions: We solved the structure of the VPS39 C-terminal domain adopting a non-native fold. Our work highlights the risk of non-native folds when purifying small zinc-containing domains with hexahistidine tags. However, the non-native structure we observe may have implications for rational protein design.

scholarly journals Common substructures and sequence characteristics of sandwich-like proteins from 42 different folds

2020 ◽  
Author(s):  
A.E. Kister
Keyword(s):  
Protein Design ◽  
Structural Classification ◽  
Hydrophobic Residues ◽  
Rational Protein Design ◽  
The Common ◽  
Database Comparison ◽  
Two Stages ◽  
Sequence Characteristics ◽  
Common Sequence

AbstractThis study addresses the following fundamental question: Do sequences of protein domains with sandwich architecture have common sequence characteristics even though they belong to different superfamilies and folds? The analysis was carried out in two stages: determination of substructures in the domains that are common to all sandwich proteins; and detection of common sequence characteristics within the substructures. Analysis of supersecondary structures in domains of proteins revealed two types of four-strand substructures that are common to sandwich proteins. At least one of these common substructures was found in proteins of 42 sandwich-like folds (as per structural classification in the CATH database). Comparison of the sequence fragments corresponding to strands that make up the common substructures revealed specific rules of distribution of hydrophobic residues within these strands. These rules can be conceptualized as grammatical rules of beta protein linguistics. Understanding of the structural and sequence commonalities of sandwich proteins may also be useful for rational protein design.

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