Predicting Important Residues and Interaction Pathways in Proteins Using Gaussian Network Model: Binding and Stability of HLA Proteins

A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed

Structural Model of the Rev Regulatory Protein from Equine Infectious Anemia Virus

Rev is an essential regulatory protein in the equine infectious anemia virus (EIAV) and other lentiviruses, including HIV-1. It binds incompletely spliced viral mRNAs and shuttles them from the nucleus to the cytoplasm, a critical prerequisite for the production of viral structural proteins and genomic RNA. Despite its important role in production of infectious virus, the development of antiviral therapies directed against Rev has been hampered by the lack of an experimentally-determined structure of the full length protein. We have used a combined computational and biochemical approach to generate and evaluate a structural model of the Rev protein. The modeled EIAV Rev (ERev) structure includes a total of 6 helices, four of which form an anti-parallel four-helix bundle. The first helix contains the leucine-rich nuclear export signal (NES). An arginine-rich RNA binding motif, RRDRW, is located in a solvent-exposed loop region. An ERLE motif required for Rev activity is predicted to be buried in the core of modeled structure where it plays an essential role in stabilization of the Rev fold. This structural model is supported by existing genetic and functional data as well as by targeted mutagenesis of residues predicted to be essential for overall structural integrity. Our predicted structure should increase understanding of structure-function relationships in Rev and may provide a basis for the design of new therapies for lentiviral diseases

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD <2.0 Å), the DPM-HMM method performs as well or better than the best templates, demonstrating that our automated method recaptures these canonical loops without inclusion of any IgG specific terms or manual intervention. In cases with poor or few good templates (mean RMSD >7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/

Interaction Pattern of Arg 62 in the A-Pocket of Differentially Disease-Associated HLA-B27 Subtypes Suggests Distinct TCR Binding Modes

The single amino acid replacement Asp116His distinguishes the two subtypes HLA-B*2705 and HLA-B*2709 which are, respectively, associated and non-associated with Ankylosing Spondylitis, an autoimmune chronic inflammatory disease. The reason for this differential association is so far poorly understood and might be related to subtype-specific HLA:peptide conformations as well as to subtype/peptide-dependent dynamical properties on the nanoscale. Here, we combine functional experiments with extensive molecular dynamics simulations to investigate the molecular dynamics and function of the conserved Arg62 of the α1-helix for both B27 subtypes in complex with the self-peptides pVIPR (RRKWRRWHL) and TIS (RRLPIFSRL), and the viral peptides pLMP2 (RRRWRRLTV) and NPflu (SRYWAIRTR). Simulations of HLA:peptide systems suggest that peptide-stabilizing interactions of the Arg62 residue observed in crystal structures are metastable for both B27 subtypes under physiological conditions, rendering this arginine solvent-exposed and, probably, a key residue for TCR interaction more than peptide-binding. This view is supported by functional experiments with conservative (R62K) and non-conservative (R62A) B*2705 and B*2709 mutants that showed an overall reduction in their capability to present peptides to CD8+ T cells. Moreover, major subtype-dependent differences in the peptide recognition suggest distinct TCR binding modes for the B*2705 versus the B*2709 subtype

A bird's eye view of NK cell receptor interactions with their MHC class I ligands

The surveillance of target cells by natural killer (NK) cells utilizes an ensemble of inhibitory and activating receptors, many of which interact with major histocompatibility complex (MHC) class I molecules. NK cell recognition of MHC class I proteins is important developmentally for the acquisition of full NK cell effector capacity and during target cell recognition, where the engagement of inhibitory receptors and MHC class I molecules attenuates NK cell activation. Human NK cells have evolved two broad strategies for recognition of human leukocyte antigen (HLA) class I molecules: (i) direct recognition of polymorphic classical HLA class I proteins by diverse receptor families such as the killer cell immunoglobulin‐like receptors (KIRs), and (ii) indirect recognition of conserved sets of HLA class I‐derived peptides displayed on the non‐classical HLA‐E for recognition by CD94‐NKG2 receptors. In this review, we assess the structural basis for the interaction between these NK receptors and their HLA class I ligands and, using the suite of published KIR and CD94‐NKG2 ternary complexes, highlight the features that allow NK cells to orchestrate the recognition of a range of different HLA class I proteins

The city through its open spaces system: structure, configuration and fragmentation - a case study in Umuarama - PR

Este trabalho relaciona-se à forma urbana, mas não sob a ótica do urbanismo ou do planejamento urbano em stricto sensu: relaciona-se a uma maneira de ver a cidade através dos seus sistemas de espaços livres, onde a paisagem assume o papel de uma \"lente\" pela qual é lida a cidade contemporânea, indicando meios para sua configuração. Neste contexto, a Arquitetura Paisagística enquanto disciplina e atividade profissional constitui-se como o conjunto de teorias, conceitos e métodos que tornam esta \"lente\" operacional. O objetivo deste trabalho, portanto, é recuperar o sentido da adoção de fundamentos do projeto e planejamento paisagístico em qualquer tipo de desenvolvimento, crescimento e gestão de cidade, considerando que os espaços livres, dentre eles ruas, rios, áreas de preservação, praças, parques são os sistemas estruturais que moldam a paisagem urbana. Este trabalho aborda ainda os diferentes agentes que participam deste dinâmico processo de configuração da paisagem, e demonstra que a falta de planejamento e diretrizes de projeto tem como resultado a fragilização e a fragmentação da forma urbana. A legislação, um dos únicos instrumentos de fato operativos, em grande escala, assume o papel principal de mediador e ordenador dos diferentes interesses, e isoladamente não se mostra apropriada para tal fim. Neste sentido, a hipótese central que guia esta tese é a de que o resgate do conceito estrutural do Sistema de Espaços Livres - SEL na paisagem urbana é essencial para uma nova abordagem de planejamento e projeto de cidades. Como estudo de caso, foi escolhida a cidade planejada de Umuarama-PR, que entre o seu plano inicial e as novas áreas de expansão, possibilitou a análise comparativa de dois momentos distintos do processo de formação e de gestão do sistema de espaços livres e sua relação com a forma urbana.This paper is related to urban morphology, but not upon the Urban Design view or the Urban Planning in stricto sensu; instead, it is related to a way of viewing the city through its open spaces systems, where the landscape turns into lens through which the contemporaneous city is read, pointing out ways for its configuration. In this context, the Landscape Architecture as a subject and professional activity is the set of theories, concepts e methods that make these \"lens\" being operational. So, this paper objective is to bring back the meaning of the adoption of fundaments of Landscape design and planning in any kind of development, growth and management of a city, by taking into consideration that the open spaces, such as streets, rivers, which shape the urban landscape. This paper also mentions the diferente agents which take part in this dynamic configuration of landscape process, and it shows that the lack of planning and guideline of a project results in a urban space fragility and fragmentation. The legislation, one of the only tools which is really operative in a large scale, takes the main role of mediator and organizer of different interests, and it does not show itself to be fit for this purpose. In this sense, the central hypothesis that guides this theory is that the bailout of the structural concept of the open system spaces in the urban landscape is essential for a new approach of planning and designning cities. The planned city of Umuarama - PR was chosen as a case preservation areas, squares, parks are the structural systems study, which between its original plan and the new areas of expansion, made possible the comparative analysis of two distinct moments of its open spaces system and its relation with the urban form