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.Chapter Nine Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Lihong Liu, Ganglong Cui, Wei-Hai Fang A photoactive protein usually contains a unique chromophore that is responsible for the initial photoresponse and functions of the photoactive protein are determined by the interaction between the chromophore and its protein surroundings. The combined quantum mechanical and molecular mechanical (QM/MM) approach is demonstrated to be a very useful tool for exploring structures and functions of a photoactive protein with the chromophore and its protein surroundings treated...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Eight QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Hansel Gómez, Fernanda Mendoza, José M. Lluch, Laura Masgrau Glycosyltransferases (GTs) catalyze the biosynthesis of glycosidic linkages by transferring a monosaccharide from a nucleotide sugar donor to an acceptor substrate, and they do that with exquisite regio- and stereospecificity. Retaining GTs act with retention of the configuration at the anomeric carbon of the transferred sugar. Their chemical mechanism has been under debate for long as conclusive experimental data to confirm the mechanism have b...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Seven QM and QM/MM Methods Compared
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Tomasz Borowski, Matthew Quesne, Maciej Szaleniec The review focus is a comparison of QM and QM/MM modeling techniques applied to study of metalloenzymes. The chapter aim is to highlight many of the advantages and potential pitfalls of the exciting and revolutionary QM/MM techniques using both large QM/MM systems and QM-only modeling as references. The review is illustrated by case studies for isopenicillin N synthase, ethylbenzene dehydrogenase, cytochrome P450 enzyme, AlkB DNA repair enzyme as well as 4-hyd...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Six The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Eric André C. Bushnell, Victoria Erica J. Berryman, James W. Gauld, Russell J. Boyd In this chapter, we discuss the influence of an anisotropic protein environment on the reaction mechanisms of saccharopine reductase and uroporphyrinogen decarboxylase, respectively, via the use of a quantum mechanical and molecular mechanical (QM/MM) approach. In addition, we discuss the importance of selecting a suitable DFT functional to be used in a QM/MM study of a key intermediate in the mechanism of 8R-lipoxygenase, ...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Five Enzymatic Halogenases and Haloperoxidases
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Amy Timmins, Sam P. de Visser Despite the fact that halogenated compounds are rare in biology, a number of organisms have developed processes to utilize halogens and in recent years, a string of enzymes have been identified that selectively insert halogen atoms into, for instance, a CH aliphatic bond. Thus, a number of natural products, including antibiotics, contain halogenated functional groups. This unusual process has great relevance to the chemical industry for stereoselective and regiospecific synthesis o...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Four Explicit Drug Re-positioning
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Ankur Omer, Venkatesan Suryanarayanan, Chandrabose Selvaraj, Sanjeev Kumar Singh, Poonam Singh With the demand to enhance the speed of the drug discovery process there has been an increased usage of computational approaches in drug discovery studies. However because of their probabilistic outcomes, the challenge is to exactly mimic the natural environment which can provide the exact charge polarization effect while estimating the binding energy between protein and ligand. There has been a large number of ...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Three A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Jesús I. Mendieta-Moreno, Iñigo Marcos-Alcalde, Daniel G. Trabada, Paulino Gómez-Puertas, José Ortega, Jesús Mendieta Quantum mechanics/molecular mechanics (QM/MM) methods are excellent tools for the modeling of biomolecular reactions. Recently, we have implemented a new QM/MM method (Fireball/Amber), which combines an efficient density functional theory method (Fireball) and a well-recognized molecular dynamics package (Amber), offering an excellent balance between accuracy and sampling capabiliti...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter Two Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorithm
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Juan Manuel Romero, Mariano Martin, Claudia Lilián Ramirez, Victoria Gisel Dumas, Marcelo Adrián Marti Determination of the free energy profile for an enzyme reaction mechanism is of primordial relevance, paving the way for our understanding of the enzyme's catalytic power at the molecular level. Although hybrid, mostly DFT-based, QM/MM methods have been extensively applied to this type of studies, achieving accurate and statistically converged results at a moderate computational cost is still an open c...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Chapter One PUPIL
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 100 Author(s): Juan Torras, Benjamin P. Roberts, Gustavo M. Seabra, Samuel B. Trickey PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the ext...
Source: Advances in Protein Chemistry and Structural Biology - October 19, 2015 Category: Biochemistry Source Type: research
Porous Alumina as a Promising Biomaterial for Public Health
Publication date: Available online 26 September 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Nicola Luigi Bragazzi, Roberto Gasparini, Daniela Amicizia, Donatella Panatto, Claudio Larosa Porous aluminum is a nanostructured material characterized by unique properties, such as chemical stability, regular uniformity, dense hexagonal porous lattice with high aspect ratio nanopores, excellent mechanical strength, and biocompatibility. This overview examines how the structure and properties of porous alumina can be exploited in the field of public health. Porous alumina can be employe...
Source: Advances in Protein Chemistry and Structural Biology - September 27, 2015 Category: Biochemistry Source Type: research
Antitumor Lipids—Structure, Functions, and Medical Applications
Publication date: Available online 26 September 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Aneliya Kostadinova, Tanya Topouzova-Hristova, Albena Momchilova, Rumiana Tzoneva, Martin R. Berger Cell proliferation and metastasis are considered hallmarks of tumor progression. Therefore, efforts have been made to develop novel anticancer drugs that inhibit both the proliferation and the motility of tumor cells. Synthetic antitumor lipids (ATLs), which are chemically divided into two main classes, comprise (i) alkylphospholipids (APLs) and (ii) alkylphosphocholines (APCs). They repre...
Source: Advances in Protein Chemistry and Structural Biology - September 27, 2015 Category: Biochemistry Source Type: research
Quartz-Crystal Microbalance (QCM) for Public Health: An Overview of Its Applications
Publication date: Available online 26 September 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Nicola Luigi Bragazzi, Daniela Amicizia, Donatella Panatto, Daniela Tramalloni, Ivana Valle, Roberto Gasparini Nanobiotechnologies, from the convergence of nanotechnology and molecular biology and postgenomics medicine, play a major role in the field of public health. This overview summarizes the potentiality of piezoelectric sensors, and in particular, of quartz-crystal microbalance (QCM), a physical nanogram-sensitive device. QCM enables the rapid, real time, on-site detection of pat...
Source: Advances in Protein Chemistry and Structural Biology - September 27, 2015 Category: Biochemistry Source Type: research
SHOPIN: Semantic Homogeneity Optimization in Protein Interaction Networks
Publication date: Available online 24 August 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Kire Trivodaliev, Slobodan Kalajdziski, Ilinka Ivanoska, Biljana Risteska Stojkoska, Ljupco Kocarev Protein interaction networks (PINs) are argued to be the richest source of hidden knowledge of the intrinsic physical and/or functional meanings of the involved proteins. We propose a novel method for computational protein function prediction based on semantic homogeneity optimization in PIN (SHOPIN). The SHOPIN method creates graph representations of the PIN augmented by inclusion of the sem...
Source: Advances in Protein Chemistry and Structural Biology - August 25, 2015 Category: Biochemistry Source Type: research
Theory, Methods, and Applications of Coevolution in Protein Contact Prediction
Publication date: Available online 18 August 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Jianzhu Ma, Sheng Wang Coevolution is a fundamental mechanism of evolution to maintain structural or functional constraints on proteins. The increasing availability of protein sequences allows the efficient detecting of those coevolutionary couplings between residues in proteins and addresses the long-standing challenge to accurately predict protein contacts from amino acid alone. A wide range of theoretical and computational methods have been invested in studying the coevolution of pairs of posi...
Source: Advances in Protein Chemistry and Structural Biology - August 21, 2015 Category: Biochemistry Source Type: research
Alterations in Gene Expression in Depression: Prospects for Personalize Patient Treatment
Publication date: Available online 19 August 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Rossen Donev, Khaled Alawam The number of people around the world suffering from depression has dramatically increased in last few decades. It has been predicted that by 2020 depression will become the second most common cause of disability. Furthermore, depression is often misdiagnosed and confused with other psychiatric disorders showing similar symptoms, i.e., anxiety and bipolar disorder, due to the fact that diagnosing is often carried out by medical workers who are not psychiatrically train...
Source: Advances in Protein Chemistry and Structural Biology - August 21, 2015 Category: Biochemistry Source Type: research
