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.Excited States and Photochemistry of Chromophores in the Photoactive Proteins Explored by the Combined Quantum Mechanical and Molecular Mechanical Calculations
Publication date: Available online 13 August 2015 Source:Advances in Protein Chemistry and Structural Biology 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 surro...
Source: Advances in Protein Chemistry and Structural Biology - August 16, 2015 Category: Biochemistry Source Type: research
Evolution and Coevolution of PRC2 Genes in Vertebrates and Mammals
This study analyzes the evolution and coevolution of seven PRC2 genes in 29 Deuterostomia. These genes, previously assumed highly conserved, are found to have obtained multiple insertions in vertebrates and mammals and undergone significant positive selections in marsupials and prosimians, indicating adaptions to substantially increased lncRNAs (long noncoding RNAs) in mammals and in primates. Some insertions occur notably in homologous sequences of human nonsense-mediated decay (NMD) transcripts. Moreover, positive selections and signals of convergent evolution imply the independent increase of lncRNAs in mammals and in p...
Source: Advances in Protein Chemistry and Structural Biology - August 5, 2015 Category: Biochemistry Source Type: research
Chapter One Type-3 Copper Proteins
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 - July 28, 2015 Category: Biochemistry Source Type: research
Chapter Nine Food-Grade Protein-Based Nanoparticles and Microparticles for Bioactive Delivery
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 98 Author(s): Gabriel Davidov-Pardo, Iris J. Joye, David Julian McClements Proteins can be used to fabricate nanoparticles and microparticles suitable for use as delivery systems for bioactive compounds in pharmaceutical, food, cosmetic, and other products. Food proteins originate from various animal or vegetal sources and exhibit a wide diversity of molecular and physicochemical characteristics, e.g., molecular weight, conformation, flexibility, polarity, charge, isoelectric point, solubility, and interactions. As a result...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Chapter Seven Polysaccharide Nanoparticles for Protein and Peptide Delivery
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 98 Author(s): Marlise A. dos Santos, Ana Grenha Finding adequate carriers for protein and peptide delivery has become an urgent need, owing to the growing number of macromolecules identified as having therapeutic potential. Nanoparticles have emerged in the field as very promising vehicles and much work has been directed to testing the capacity of different materials to compose the matrix of these carriers. Natural materials and, specifically, polysaccharides have been taking the forefront of the challenge, because of several...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Chapter One Protein– and Peptide–Drug Conjugates
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 98 Author(s): Imran Vhora, Sushilkumar Patil, Priyanka Bhatt, Ambikanandan Misra Protein– and peptide–drug conjugates hold a promising stance in the delivery of therapeutic agents by providing distinct advantage of improving therapeutic potential of drugs. Recent advancements in the proteomics and recombinant DNA technology, by enabling identification of distinct structural features of proteins and making it feasible to introduce specific functionalities in protein/peptide structure, has made it possible to synthesize...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Chapter One Peptide Immunotherapy in Vaccine Development
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 99 Author(s): Hyun Yang, Dong Seok Kim Vaccines are designed to educate the host immune system to prevent infectious disease or to fight against various diseases such as cancers. Peptides were first employed to provide specific immune responses while minimizing unintended allergenic or reactogenic adverse effects. Discoveries of virus or cancer-specific antigens and the advanced knowledge of immunology accelerate the peptide vaccine development. Despite the overwhelming research pipelines, a very few of them reached to market...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
QM and QM/MM Methods Compared: Case Studies on Reaction Mechanisms of Metalloenzymes
Publication date: Available online 3 July 2015 Source:Advances in Protein Chemistry and Structural Biology 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 w...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems
Publication date: Available online 4 July 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Juan Torras, B.P. Roberts, G.M. Seabra, S.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 external ...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Enzymatic Halogenases and Haloperoxidases: Computational Studies on Mechanism and Function
Publication date: Available online 8 July 2015 Source:Advances in Protein Chemistry and Structural Biology 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...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc Hydrolases
Publication date: Available online 15 July 2015 Source:Advances in Protein Chemistry and Structural Biology 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 st...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules
Publication date: Available online 15 July 2015 Source:Advances in Protein Chemistry and Structural Biology 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 sampli...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
QM/MM Studies Reveal How Substrate–Substrate and Enzyme–Substrate Interactions Modulate Retaining Glycosyltransferases Catalysis and Mechanism
Publication date: Available online 15 July 2015 Source:Advances in Protein Chemistry and Structural Biology 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 mec...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations: Applications to Enzymatic Reactions
Publication date: Available online 17 July 2015 Source:Advances in Protein Chemistry and Structural Biology Author(s): Eric A.C. Bushnell, Victoria E.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-lipoxygena...
Source: Advances in Protein Chemistry and Structural Biology - July 28, 2015 Category: Biochemistry Source Type: research
Chapter Six Understanding Amino Acid Mutations in Hepatitis B Virus Proteins for Rational Design of Vaccines and Drugs
Publication date: 2015 Source:Advances in Protein Chemistry and Structural Biology, Volume 99 Author(s): Ke Shen , Li Shen , Jing Wang , Zhi Jiang , Bairong Shen The hepatitis B virus (HBV) genome encodes four proteins, i.e., DNA polymerase, surface protein, X, and core proteins. HBV undergoes different selective pressures for drug resistance and immune/vaccine escape and mutations are common for the HBV proteins. We here collected all the reported amino acid mutations happened in these four HBV proteins and studied their patterns. The relationship between the mutations and epitopic functions are investigated with...
Source: Advances in Protein Chemistry and Structural Biology - June 10, 2015 Category: Biochemistry Source Type: research
