HDAC Inhibitors as Epigenetic Regulators

The average all-atom RMSD for the complete Fv is in the order of 1.5?? for the unrefined structures (Dreiding-r, CHARMm-r, CHARMm), and improves to approximately 1.41?? for the neighborhood-refined structures (NR-Dreiding-r, NR-CHARMm-r, NR-CHARMm). and previously unpublished antibody crystal structures. Keywords: antibody structure, amino acid sidechain conformation, homology modeling, macromolecular modeling, protein domain orientation, protein engineering, protein structure prediction Abbreviations RMSDroot mean square deviationAMAAntibody Modeling Assessment Introduction Antibodies are proteins that form an integral part of the specific immune response due to their ability to engage extracellular pathogenic structures (or antigens) with high affinity and specificity. Based on the recombination of a limited repertoire of different variable region germline genes, followed by somatic hypermutation and B cell-mediated antigen-dependent affinity maturation, evolution has brought forth an ingenious mechanism that enables the organism to generate a practically unlimited number of different specificities in answer to almost any antigen that this immune system is usually confronted with.1-3 The unique properties of antibodies have made them an important tool in diagnostic and biotechnological applications,4 and, last but not least, an increasingly sought-after therapeutic modality, in particular in the field of oncology.5-7 In order to fulfill the desired drug profile, therapeutic antibodies are often heavily engineered. For example, modifications may be made to modulate target binding and pharmacokinetic properties, increase the degree of humanness, or address developability issues that might affect drug safety and shelf life.8-11 Many of those tasks are enabled, or at least greatly facilitated, by structure-based considerations around the atomic level.12 Ecdysone The large number of publicly available antibody crystal structures that have been solved during the last 25?y is an indicator for the relevance of this class of proteins. As of April 2015, the structural antibody database SAbDab13 counts 2025 entries, a number that is steadily increasing. The demand to accelerate and facilitate the rational design and engineering of antibody-based therapeutics has brought forth a multitude of computational methods aimed at supporting those tasks.12-16 Among these computational methods is a number of homology modeling applications that have been tailored to exclusively generate atomistic models of the antigen-binding (Fv) region of antibodies,17-19 a functionality that is meant to complement and relieve experimental structure elucidation by crystallography. Given the large number of available crystal structures that can serve as templates, antibody Fv homology modeling is usually justifiably considered a less challenging problem than general homology modeling of arbitrary proteins, where often only a single template structure of low homology is available. 20-22 Considering that the overall structure of the Fv region is usually well comprehended and characterized,23 the challenge in Ecdysone antibody homology modeling is to create a model that is sufficiently precise to form a sound basis for structure-based engineering and design, at a level of resolution that rivals that of a crystal structure. The main obstacle in this regard is the fact that the specificity of the antibody is usually mediated by 6 antigen-binding loops (complementarity-determining regions, CDRs) that are hyper-variable in sequence and length.24,25 While Ecdysone 5 of these CDRs are prone to adopt canonical conformations26-28 that to a certain degree can be predicted directly from sequence, the third loop around the variable region of the heavy chain, CDR-H3, is known to form a unique conformation that, in the majority of the known complex structures, constitutes the key contributor to the antibody-antigen interaction. Due to the fact that CDR-H3 is usually by far the most variable of the 6 CDR loops, 29 a template loop structure of acceptable homology is often not available. MMP19 Predicting the conformation of CDR-H3 with acceptable accuracy is usually thus the key challenge in antibody homology modeling.19 The situation is complicated further because the Fv region is composed of 2 individual immunoglobulin domains, the variable region of the heavy chain and the variable region of the light chain (VH and VL), with 3 CDRs distributed on each of the 2. The relative orientation of the 2 2 domains exhibits a notable variability over the known repertoire of antibody crystal structures,30-32 and it has been suggested that VH-VL orientation, in addition to length and sequence of the CDRs, is a co-modulator of antigen specificity and affinity.12 The parameters of.