Advances in Protein Chemistry and Structural Biology 
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This 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.4 Applications of Quantum Mechanical/Molecular Mechanical Methods to the Chemical Insertion Step of DNA and RNA Polymerization
Publication date: Available online 7 November 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Lalith Perera , William A. Beard , Lee G. Pedersen , Samuel H. Wilson We review theoretical attempts to model the chemical insertion reactions of nucleoside triphosphates catalyzed by the nucleic acid polymerases using combined quantum mechanical/molecular mechanical methodology. Due to an existing excellent database of high-resolution X-ray crystal structures, the DNA polymerase β system serves as a useful template for discussion and comparison. The convergence of structures of high-quality co...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Publication date: Available online 30 September 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Enrico Spiga , Matteo Thomas Degiacomi , Matteo Dal Peraro Data reporting on structure and dynamics of cellular constituents are growing with increasing pace enabling, as never before, the understanding of fine mechanistic aspects of biological systems and providing the possibility to affect them in controlled ways. Nonetheless, experimental techniques do not yet allow for an arbitrary level of resolution on cellular processes in situ. By consistently integrating a variety of diverse experiment...
Source: Advances in Protein Chemistry and Structural Biology - October 2, 2014 Category: Biochemistry Source Type: research
Type-3 Copper Proteins: Recent Advances on Polyphenol Oxidases
Publication date: Available online 26 September 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Cornelia Kaintz , Stephan Gerhard Mauracher , Annette Rompel Recent investigations in the study of plant, fungal, and bacterial type-3 copper proteins are reviewed. Focus is given to three enzymes: catechol oxidases (CO), tyrosinases, and aureusidin synthase. CO were mostly found in plants, however, in 2010 the first fungal CO was published. The first plant-originated tyrosinase was published in 2014, before tyrosinases were only reported in fungi, bacteria, and human. Aureusidin synthase from ...
Source: Advances in Protein Chemistry and Structural Biology - September 27, 2014 Category: Biochemistry Source Type: research
Monitoring the Biomolecular Interactions and the Activity of Zn-Containing Enzymes Involved in Conformational Diseases: Experimental Methods for Therapeutic Purposes
Publication date: Available online 26 September 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Giuseppe Grasso Zinc metalloproteases (ZnMPs) participate in diverse biological reactions, encompassing the synthesis and degradation of all the major metabolites in living organisms. In particular, ZnMPs have been recognized to play a very important role in controlling the concentration level of several peptides and/or proteins whose homeostasis has to be finely regulated for the correct physiology of cells. Dyshomeostasis of aggregation-prone proteins causes pathological conditions and the deve...
Source: Advances in Protein Chemistry and Structural Biology - September 27, 2014 Category: Biochemistry Source Type: research
Studying Allosteric Regulation in Metal Sensor Proteins Using Computational Methods
We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through th...
Source: Advances in Protein Chemistry and Structural Biology - September 12, 2014 Category: Biochemistry Source Type: research
