Advances in Protein Chemistry and Structural Biology Advances in Protein Chemistry and Structural Biology RSS feedThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.

Chapter Eight Biology, Mechanism, and Structure of Enzymes in the α-d-Phosphohexomutase Superfamily
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Kyle M. Stiers, Andrew G. Muenks, Lesa J. Beamer Enzymes in the α-d-phosphohexomutases superfamily catalyze the reversible conversion of phosphosugars, such as glucose 1-phosphate and glucose 6-phosphate. These reactions are fundamental to primary metabolism across the kingdoms of life and are required for a myriad of cellular processes, ranging from exopolysaccharide production to protein glycosylation. The subject of extensive mechanistic characterization during the latter half of the 20th century, these e...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Seven Sortase Transpeptidases: Structural Biology and Catalytic Mechanism
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Alex W. Jacobitz, Michele D. Kattke, Jeff Wereszczynski, Robert T. Clubb Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its a...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Six Enzymology of Microbial Dimethylsulfoniopropionate Catabolism
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Mishtu Dey The biochemistry of dimethylsulfoniopropionate (DMSP) catabolism is reviewed. The microbes that catalyze the reactions central to DMSP catabolic pathways are described, and the focus is on the enzymology of the process. Approximately 109 tons of DMSP is released annually by marine eukaryotes as an osmolyte. A vast majority of DMSP is assimilated by bacteria through either a demethylation or lyase pathways, producing either the methane thiol or the volatile dimethylsulfide (DMS), respectively. Enzymatic...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Five Striking Diversity in Holoenzyme Architecture and Extensive Conformational Variability in Biotin-Dependent Carboxylases
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Liang Tong Biotin-dependent carboxylases are widely distributed in nature and have central roles in the metabolism of fatty acids, amino acids, carbohydrates, and other compounds. The last decade has seen the accumulation of structural information on most of these large holoenzymes, including the 500-kDa dimeric yeast acetyl-CoA carboxylase, the 750-kDa α6β6 dodecameric bacterial propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, and geranyl-CoA carboxylase, the 720-kDa hexameric bacterial long-chain ...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Four A Paradigm for CH Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Stephen L. Bearne, Martin St. Maurice Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg2+-dependent, 1,1-proton transfer reaction that racemizes (R)- and (S)-mandelate. MR shares a partial reaction (i.e., the metal ion-assisted, Brønsted base-catalyzed proton abstraction of the α-proton of carboxylic acid substrates) and structural features ((β/α)7β-barrel and N-terminal α + β capping domains) with a vast group of homologous, yet functionally diverse, enzymes in the enolase superfamily. Me...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Three Computational Biochemistry —Enzyme Mechanisms Explored
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Martin Culka, Florian J. Gisdon, G. Matthias Ullmann Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Co...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter Two Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Andrew P. Montgomery, Kela Xiao, Xingyong Wang, Danielle Skropeta, Haibo Yu Carbohydrate-active enzymes (CAZymes) are families of essential and structurally related enzymes, which catalyze the creation, modification, and degradation of glycosidic bonds in carbohydrates to maintain essentially all kingdoms of life. CAZymes play a key role in many biological processes underpinning human health and diseases (e.g., cancer, diabetes, Alzheimer's diseases, AIDS) and have thus emerged as important drug targets i...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Chapter One Collagenolytic Matrix Metalloproteinase Structure –Function Relationships: Insights From Molecular Dynamics Studies
Publication date: 2017 Source:Advances in Protein Chemistry and Structural Biology, Volume 109 Author(s): Tatyana G. Karabencheva-Christova, Christo Z. Christov, Gregg B. Fields Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. Experimental data reveal a collaboration between different MMP domains in order to achieve efficient collagenolysis. Molecular dynamics (MD) simulations have been utilized to provide atomistic details of the collagenolytic process. The triple-helical structure of collagen exhibits local regions of flexibility, with modulation of inte...
Source: Advances in Protein Chemistry and Structural Biology - July 4, 2017 Category: Biochemistry Source Type: research

Enzymology of Microbial Dimethylsulfoniopropionate Catabolism
Publication date: Available online 23 June 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Mishtu Dey The biochemistry of dimethylsulfoniopropionate (DMSP) catabolism is reviewed. The microbes that catalyze the reactions central to DMSP catabolic pathways are described, and the focus is on the enzymology of the process. Approximately 109 tons of DMSP is released annually by marine eukaryotes as an osmolyte. A vast majority of DMSP is assimilated by bacteria through either a demethylation or lyase pathways, producing either the methane thiol or the volatile dimethylsulfide (DMS), respective...
Source: Advances in Protein Chemistry and Structural Biology - June 24, 2017 Category: Biochemistry Source Type: research

A Paradigm for CH Bond Cleavage: Structural and Functional Aspects of Transition State Stabilization by Mandelate Racemase
Publication date: Available online 9 June 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Stephen L. Bearne, Martin St. Maurice Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg2+-dependent, 1,1-proton transfer reaction that racemizes (R)- and (S)-mandelate. MR shares a partial reaction (i.e., the metal ion-assisted, Brønsted base-catalyzed proton abstraction of the α-proton of carboxylic acid substrates) and structural features ((β/α)7β-barrel and N-terminal α + β capping domains) with a vast group of homologous, yet functionally diverse, enzymes in the enolase sup...
Source: Advances in Protein Chemistry and Structural Biology - June 10, 2017 Category: Biochemistry Source Type: research

Sortase Transpeptidases: Structural Biology and Catalytic Mechanism
Publication date: Available online 5 June 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Alex W. Jacobitz, Michele D. Kattke, Jeff Wereszczynski, Robert T. Clubb Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent beca...
Source: Advances in Protein Chemistry and Structural Biology - June 5, 2017 Category: Biochemistry Source Type: research

Computational Biochemistry —Enzyme Mechanisms Explored
Publication date: Available online 27 May 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Martin Culka, Florian J. Gisdon, G. Matthias Ullmann Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimen...
Source: Advances in Protein Chemistry and Structural Biology - May 28, 2017 Category: Biochemistry Source Type: research

Striking Diversity in Holoenzyme Architecture and Extensive Conformational Variability in Biotin-Dependent Carboxylases
Publication date: Available online 23 May 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Liang Tong Biotin-dependent carboxylases are widely distributed in nature and have central roles in the metabolism of fatty acids, amino acids, carbohydrates, and other compounds. The last decade has seen the accumulation of structural information on most of these large holoenzymes, including the 500-kDa dimeric yeast acetyl-CoA carboxylase, the 750-kDa α6β6 dodecameric bacterial propionyl-CoA carboxylase, 3-methylcrotonyl-CoA carboxylase, and geranyl-CoA carboxylase, the 720-kDa hexameric bacterial...
Source: Advances in Protein Chemistry and Structural Biology - May 24, 2017 Category: Biochemistry Source Type: research

Computational Glycobiology: Mechanistic Studies of Carbohydrate-Active Enzymes and Implication for Inhibitor Design
Publication date: Available online 19 May 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Andrew P. Montgomery, Kela Xiao, Xingyong Wang, Danielle Skropeta, Haibo Yu Carbohydrate-active enzymes (CAZymes) are families of essential and structurally related enzymes, which catalyze the creation, modification, and degradation of glycosidic bonds in carbohydrates to maintain essentially all kingdoms of life. CAZymes play a key role in many biological processes underpinning human health and diseases (e.g., cancer, diabetes, Alzheimer's diseases, AIDS) and have thus emerged as important dr...
Source: Advances in Protein Chemistry and Structural Biology - May 21, 2017 Category: Biochemistry Source Type: research

Mechanistic Insights Into Catalytic RNA –Protein Complexes Involved in Translation of the Genetic Code
Publication date: Available online 19 May 2017 Source:Advances in Protein Chemistry and Structural Biology Author(s): Satya B. Routh, Rajan Sankaranarayanan The contemporary world is an “RNA–protein world” rather than a “protein world” and tracing its evolutionary origins is of great interest and importance. The different RNAs that function in close collaboration with proteins are involved in several key physiological processes, including catalysis. Ribosome—the complex megadalton cellular machinery that translates genetic information encoded in nucleotide sequence to amino acid sequence—epitomizes su...
Source: Advances in Protein Chemistry and Structural Biology - May 21, 2017 Category: Biochemistry Source Type: research