Search Results - "Reilly, Peter J."

Computational Studies of Glycoside, Carboxylic Ester, and Thioester Hydrolase Mechanisms: A Review by Reilly, Peter J, Rovira, Carme

“…This article is a review of computational work over the last ∼15 years to elucidate the catalytic mechanisms of three major enzyme classes: glycoside…”
Get full text

Mechanism of Cellulose Hydrolysis by Inverting GH8 Endoglucanases: A QM/MM Metadynamics Study by Petersen, Luis, Ardèvol, Albert, Rovira, Carme, Reilly, Peter J

“…A detailed understanding of the catalytic strategy of cellulases is key to finding alternative ways to hydrolyze cellulose to mono-, di-, and oligosaccharides…”
Get full text

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity by Jing, Fuyuan, Cantu, David C, Tvaruzkova, Jarmila, Chipman, Jay P, Nikolau, Basil J, Yandeau-Nelson, Marna D, Reilly, Peter J

“…Acyl-acyl carrier protein thioesterases (acyl-ACP TEs) catalyze the hydrolysis of the thioester bond that links the acyl chain to the sulfhydryl group of the…”
Get full text

Structural classification and properties of ketoacyl synthases by Chen, Yingfei, Kelly, Erin E., Masluk, Ryan P., Nelson, Charles L., Cantu, David C., Reilly, Peter J.

“…Ketoacyl synthases (KSs) catalyze condensing reactions combining acyl‐CoA or acyl‐acyl carrier protein (acyl‐ACP) with malonyl‐CoA to form 3‐ketoacyl‐CoA or…”
Get full text

Hypocrea jecorina (Trichoderma reesei) Cel7A as a molecular machine: A docking study by Mulakala, Chandrika, Reilly, Peter J.

“…Hypocrea jecorina (formerly Trichoderma reesei) Cel7A has a catalytic domain (CD) and a cellulose‐binding domain (CBD) separated by a highly glycosylated…”
Get full text

Modeling protein recognition of carbohydrates by Laederach, Alain, Reilly, Peter J.

“…We have a limited understanding of the details of molecular recognition of carbohydrates by proteins, which is critical to a multitude of biological processes…”
Get full text

Gibbs free energy correlation for automated docking of carbohydrates by Hill, Anthony D, Reilly, Peter J

“…Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a…”
Get full text

Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures by Chen, Yingfei, Black, Daniel S., Reilly, Peter J.

“…We classified the carboxylic ester hydrolases (CEHs) into families and clans by use of multiple sequence alignments, secondary structure analysis, and tertiary…”
Get full text

Automated docking to explore subsite binding by glycoside hydrolase family 6 cellobiohydrolases and endoglucanases by Mertz, Blake, Hill, Anthony D., Mulakala, Chandrika, Reilly, Peter J.

“…Cellooligosaccharides were computationally docked using AutoDock into the active sites of the glycoside hydrolase Family 6 enzymes Hypocrea jecorina (formerly…”
Get full text

Thioesterases: A new perspective based on their primary and tertiary structures by Cantu, David C., Chen, Yingfei, Reilly, Peter J.

“…Thioesterases (TEs) are classified into EC 3.1.2.1 through EC 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (EC…”
Get full text

Crystal Structure and Evolution of a Prokaryotic Glucoamylase by Aleshin, Alexander E., Feng, Ping-Hua, Honzatko, Richard B., Reilly, Peter J.

“…The first crystal structures of a two-domain, prokaryotic glucoamylase were determined to high resolution from the clostridial species Thermoanaerobacterium…”
Get full text

Tertiary Structure and Characterization of a Glycoside Hydrolase Family 44 Endoglucanase from Clostridium acetobutylicum by Warner, Christopher D, Hoy, Julie A, Shilling, Taran C, Linnen, Michael J, Ginder, Nathaniel D, Ford, Clark F, Honzatko, Richard B, Reilly, Peter J

“…A gene encoding a glycoside hydrolase family 44 (GH44) protein from Clostridium acetobutylicum ATCC 824 was synthesized and transformed into Escherichia coli…”
Get full text

Molecular Mechanism of the Glycosylation Step Catalyzed by Golgi α-Mannosidase II: A QM/MM Metadynamics Investigation by Petersen, Luis, Ardèvol, Albert, Rovira, Carme, Reilly, Peter J

“…Golgi α-mannosidase II (GMII), a member of glycoside hydrolase family 38, cleaves two mannosyl residues from GlcNAcMan5GlcNAc2 as part of the N-linked…”
Get full text

Carbohydrate-binding module tribes by Carvalho, Caio C., Phan, Ngoc N., Chen, Yingfei, Reilly, Peter J.

“…ABSTRACT At present, 69 families of carbohydrate‐binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences…”
Get full text

Mechanism of Xylobiose Hydrolysis by GH43 β-Xylosidase by Barker, Ian J., Petersen, Luis, Reilly, Peter J.

“…Glycoside hydrolases cleave the glycosidic linkage between two carbohydrate moieties. They are among the most efficient enzymes currently known. β-Xylosidases…”
Get full text

Puckering Coordinates of Monocyclic Rings by Triangular Decomposition by Hill, Anthony D, Reilly, Peter J

“…We describe a new method of describing the pucker of an N-member monocyclic ring using N − 3 parameters. To accomplish this, three ring atoms define a…”
Get full text

Molecular Mechanism of a Hotdog-Fold Acyl-CoA Thioesterase by Cantu, David C., Ardèvol , Albert, Rovira , Carme, Reilly, Peter J.

“…Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and…”
Get full text

Ruminal Fermentation of Propylene Glycol and Glycerol by Trabue, Steven, Scoggin, Kenwood, Tjandrakusuma, Siska, Rasmussen, Mark A, Reilly, Peter J

“…Bovine rumen fluid was fermented anaerobically with 25 mM R-propylene glycol, S-propylene glycol, or glycerol added. After 24 h, all of the propylene glycol…”
Get full text

Scoring functions for AutoDock by Hill, Anthony D, Reilly, Peter J

“…Automated docking allows rapid screening of protein-ligand interactions. A scoring function composed of a force field and linear weights can be used to compute…”
Get more information

Phylogenetic analysis of family 6 glycoside hydrolases by Mertz, Blake, Kuczenski, Robert S., Larsen, Robert T., Hill, Anthony D., Reilly, Peter J.

“…Multiple sequence alignment separates members of glycoside hydrolase Family 6 into eight subfamilies: one of mainly actinobacterial endoglucanases (EGs), one…”
Get full text