Advances in Protein Chemistry and Structural Biology 
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.
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.Chapter Four Applications of Quantum Mechanical/Molecular Mechanical Methods to the Chemical Insertion Step of DNA and RNA Polymerization
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 97 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 complexes and conti...
Source: Advances in Protein Chemistry and Structural Biology - November 29, 2014 Category: Biochemistry Source Type: research
Chapter Three Catalytic Mechanisms of Metallohydrolases Containing Two Metal Ions
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 97 Author(s): Nataša Mitić , Manfredi Miraula , Christopher Selleck , Kieran S. Hadler , Elena Uribe , Marcelo M. Pedroso , Gerhard Schenk At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii) the ability to ...
Source: Advances in Protein Chemistry and Structural Biology - November 29, 2014 Category: Biochemistry Source Type: research
Chapter Two Biophysical Studies of Matrix Metalloproteinase/Triple-Helix Complexes
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 97 Author(s): Gregg B. Fields Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. The structures of MMPs, in solution and solid state and in the presence and absence of triple-helical collagen models, have been assessed by NMR spectroscopy, small-angle X-ray scattering, and X-ray crystallography. Structures observed in solution exhibit flexibility between the MMP catalytic (CAT) and hemopexin-like (HPX) domains, while solid-state structures are relatively compact. Evaluation...
Source: Advances in Protein Chemistry and Structural Biology - November 29, 2014 Category: Biochemistry Source Type: research
Chapter One Type-3 Copper Proteins Recent Advances on Polyphenol Oxidases
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 97 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 yellow snapdragon (...
Source: Advances in Protein Chemistry and Structural Biology - November 29, 2014 Category: Biochemistry Source Type: research
Chapter Nine High-Resolution Modeling of Protein Structures Based on Flexible Fitting of Low-Resolution Structural Data
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Wenjun Zheng , Mustafa Tekpinar To circumvent the difficulty of directly solving high-resolution biomolecular structures, low-resolution structural data from Cryo-electron microscopy (EM) and small angle solution X-ray scattering (SAXS) are increasingly used to explore multiple conformational states of biomolecular assemblies. One promising venue to obtain high-resolution structural models from low-resolution data is via data-constrained flexible fitting. To this end, we have developed a new method based on a coar...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Eight CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Sunhwan Jo , Xi Cheng , Shahidul M. Islam , Lei Huang , Huan Rui , Allen Zhu , Hui Sun Lee , Yifei Qi , Wei Han , Kenno Vanommeslaeghe , Alexander D. MacKerell Jr. , Benoît Roux , Wonpil Im CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contai...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Seven Insights in the Mechanism of Action and Inhibition of N-Acylethanolamine Acid Amidase by Means of Computational Methods
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Alessio Lodola , Silvia Rivara , Marco Mor Computer-aided approaches are widely used in modern medicinal chemistry to improve the efficiency of the discovery phase. N-Acylethanolamine acid amidase (NAAA) is a cysteine amidase belonging to the N-terminal nucleophile (Ntn) hydrolases that primarily degrades anti-inflammatory and analgesic lipid amide palmitoylethanolamide. In this chapter, we review our contribution to (i) the determination of the reaction mechanism of amide hydrolysis catalyzed by cysteine Ntn-hyd...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Six 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 - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Five Recent Advances in Transferable Coarse-Grained Modeling of Proteins
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Parimal Kar , Michael Feig Computer simulations are indispensable tools for studying the structure and dynamics of biological macromolecules. Biochemical processes occur on different scales of length and time. Atomistic simulations cannot cover the relevant spatiotemporal scales at which the cellular processes occur. To address this challenge, coarse-grained (CG) modeling of the biological systems is employed. Over the last few years, many CG models for proteins continue to be developed. However, many of them are ...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Four Stability of Amyloid Oligomers
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Workalemahu M. Berhanu , Ulrich H.E. Hansmann Molecular simulations are now commonly used to complement experimental techniques in investigating amyloids and their role in human diseases. In this chapter, we will summarize techniques and approaches often used in amyloid simulations and will present recent success stories. Our examples will be focused on lessons learned from molecular dynamics simulations in aqueous environments that start from preformed aggregates. These studies explore the limitations that arise ...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Three New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 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 experimental data, molecular ...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter Two Computational Study of Putative Residues Involved in DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): Angela A. Elias , G. Andrés Cisneros A fidelity-checking site for DNA polymerase I has been proposed based on recent single-molecule Förster resonance energy transfer studies. The checking site is believed to ensure proper base pairing of the newly inserted nucleotide. Computational studies have been utilized to predict residues involved in this putative checking site on the Klenow and Bacillus fragments. Here, we employ energy decomposition analysis, electrostatic free energy response, and noncovalent interacti...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
Chapter One The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery
Publication date: 2014 Source:Advances in Protein Chemistry and Structural Biology, Volume 96 Author(s): José L. Medina-Franco , Oscar Méndez-Lucio , Karina Martinez-Mayorga Protein–ligand and protein–protein interactions play a fundamental role in drug discovery. A number of computational approaches have been developed to characterize and use the knowledge of such interactions that can lead to drug candidates and eventually compounds in the clinic. With the increasing structural information of protein–ligand and protein–protein complexes, the combination of molecular modeling and chemoinformatics approach...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
3 Catalytic Mechanisms of Metallohydrolases Containing Two Metal Ions
Publication date: Available online 4 November 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Nataša Mitić , Manfredi Miraula , Christopher Selleck , Kieran S. Hadler , Elena Uribe , Marcelo M. Pedroso , Gerhard Schenk At least one-third of enzymes contain metal ions as cofactors necessary for a diverse range of catalytic activities. In the case of polymetallic enzymes (i.e., two or more metal ions involved in catalysis), the presence of two (or more) closely spaced metal ions gives an additional advantage in terms of (i) charge delocalisation, (ii) smaller activation barriers, (iii...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
2 Biophysical Studies of Matrix Metalloproteinase/Triple-Helix Complexes
Publication date: Available online 7 November 2014 Source:Advances in Protein Chemistry and Structural Biology Author(s): Gregg B. Fields Several members of the zinc-dependent matrix metalloproteinase (MMP) family catalyze collagen degradation. The structures of MMPs, in solution and solid state and in the presence and absence of triple-helical collagen models, have been assessed by NMR spectroscopy, small-angle X-ray scattering, and X-ray crystallography. Structures observed in solution exhibit flexibility between the MMP catalytic (CAT) and hemopexin-like (HPX) domains, while solid-state structures are relatively co...
Source: Advances in Protein Chemistry and Structural Biology - November 12, 2014 Category: Biochemistry Source Type: research
