Peptide binding prediction for the human class II MHC allele HLA-DP2:a molecular docking approach

MHC class II proteins bind oligopeptide fragments derived from proteolysis of pathogen antigens, presenting them at the cell surface for recognition by CD4+ T cells. Human MHC class II alleles are grouped into three loci: HLA-DP, HLA-DQ and HLA-DR. In contrast to HLA-DR and HLA-DQ, HLA-DP proteins have not been studied extensively, as they have been viewed as less important in immune responses than DRs and DQs. However, it is now known that HLA-DP alleles are associated with many autoimmune diseases. Quite recently, the X-ray structure of the HLA-DP2 molecule (DPA*0103, DPB1*0201) in complex with a self-peptide derived from the HLA-DR a-chain has been determined. In the present study, we applied a validated molecular docking protocol to a library of 247 modelled peptide-DP2 complexes, seeking to assess the contribution made by each of the 20 naturally occurred amino acids at each of the nine binding core peptide positions and the four flanking residues (two on both sides).

Integrating in silico and in vitro analysis of peptide binding affinity to HLA-Cw*0102:a bioinformatic approach to the prediction of new epitopes

Predictive models of peptide-Major Histocompatibility Complex (MHC) binding affinity are important components of modern computational immunovaccinology. Here, we describe the development and deployment of a reliable peptide-binding prediction method for a previously poorly-characterized human MHC class I allele, HLA-Cw*0102.

Identification of the HLA-DM/HLA-DR interface

Human leukocyte antigen (HLA)-DM is a critical participant in antigen presentation that catalyzes the dissociation of the Class II-associated Invariant chain-derived Peptide (CLIP) from the major histocompatibility complex (MHC) Class II molecules. There is competition amongst peptides for access to an MHC Class II groove and it has been hypothesised that DM functions as a 'peptide editor' that catalyzes the replacement of one peptide for another within the groove. It is established that the DM catalyst interacts directly with the MHC Class II but the precise location of the interface is unknown. Here, we combine previously described mutational data with molecular docking and energy minimisation simulations to identify a putative interaction site of >4000A2 which agrees with known point mutational data for both the DR and DM molecule. The docked structure is validated by comparison with experimental data and previously determined properties of protein-protein interfaces. A possible dissociation mechanism is suggested by the presence of an acidic cluster near the N terminus of the bound peptide.

The classification of HLA supertypes by GRID/CPCA and hierarchical clustering methods

Biological experiments often produce enormous amount of data, which are usually analyzed by data clustering. Cluster analysis refers to statistical methods that are used to assign data with similar properties into several smaller, more meaningful groups. Two commonly used clustering techniques are introduced in the following section: principal component analysis (PCA) and hierarchical clustering. PCA calculates the variance between variables and groups them into a few uncorrelated groups or principal components (PCs) that are orthogonal to each other. Hierarchical clustering is carried out by separating data into many clusters and merging similar clusters together. Here, we use an example of human leukocyte antigen (HLA) supertype classification to demonstrate the usage of the two methods. Two programs, Generating Optimal Linear Partial Least Square Estimations (GOLPE) and Sybyl, are used for PCA and hierarchical clustering, respectively. However, the reader should bear in mind that the methods have been incorporated into other software as well, such as SIMCA, statistiXL, and R.

Peptide binding to the HLA-DRB1 supertype:a proteochemometrics analysis

A proteochemometrics approach was applied to a set of 2666 peptides binding to 12 HLA-DRB1 proteins. Sequences of both peptide and protein were described using three z-descriptors. Cross terms accounting for adjacent positions and for every second position in the peptides were included in the models, as well as cross terms for peptide/protein interactions. Models were derived based on combinations of different blocks of variables. These models had moderate goodness of fit, as expressed by r2, which ranged from 0.685 to 0.732; and good cross-validated predictive ability, as expressed by q2, which varied from 0.678 to 0.719. The external predictive ability was tested using a set of 356 HLA-DRB1 binders, which showed an r2(pred) in the range 0.364-0.530. Peptide and protein positions involved in the interactions were analyzed in terms of hydrophobicity, steric bulk and polarity.

Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide:can the α3 and β2m domains be neglected?

Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histo-compatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVY-DGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide–MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the α1–α2 domain, the α3 and β2m domains cannot be neglected. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1803–1813, 2004

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.

The HLA-A2-supermotif:a QSAR definition

Identification of epitopes capable of binding multiple HLA types will significantly rationalise the development of epitope-based vaccines. A quantitative method assessing the contribution of each amino acid at each position was applied to over 500 nonamer peptides binding to 5 MHC alleles — A*0201, A*0202, A*0203, A*0206 and A*6802 — which together define the HLA-A2-like supertype. FXIGXI (L)IFV was identified as a supermotif for the A2-supertype based on the contributions of the common preferred amino acids at each of the nine positions. The results indicate that HLA-A*6802 is an intermediate allele standing between A2 and A3 supertypes: at anchor position 2 it is closer to A3 and at anchor position 9 it is nearer to A2. Models are available free on-line at http://www.jenner.ac.uk/MHCPred and can be used for binding affinity prediction.

Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0:a quantitative molecular docking study

Background: HLA-DPs are class II MHC proteins mediating immune responses to many diseases. Peptides bind MHC class II proteins in the acidic environment within endosomes. Acidic pH markedly elevates association rate constants but dissociation rates are almost unchanged in the pH range 5.0 - 7.0. This pH-driven effect can be explained by the protonation/deprotonation states of Histidine, whose imidazole has a pKa of 6.0. At pH 5.0, imidazole ring is protonated, making Histidine positively charged and very hydrophilic, while at pH 7.0 imidazole is unprotonated, making Histidine less hydrophilic. We develop here a method to predict peptide binding to the four most frequent HLA-DP proteins: DP1, DP41, DP42 and DP5, using a molecular docking protocol. Dockings to virtual combinatorial peptide libraries were performed at pH 5.0 and pH 7.0. Results: The X-ray structure of the peptide - HLA-DP2 protein complex was used as a starting template to model by homology the structure of the four DP proteins. The resulting models were used to produce virtual combinatorial peptide libraries constructed using the single amino acid substitution (SAAS) principle. Peptides were docked into the DP binding site using AutoDock at pH 5.0 and pH 7.0. The resulting scores were normalized and used to generate Docking Score-based Quantitative Matrices (DS-QMs). The predictive ability of these QMs was tested using an external test set of 484 known DP binders. They were also compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0 and showed significantly improved predictions for three of the four DP proteins, when compared to the existing servers. They are able to recognize 50% of the known binders in the top 5% of predicted peptides. Conclusions: The higher predictive ability of DS-QMs derived at pH 5.0 may be rationalised by the additional hydrogen bond formed between the backbone carbonyl oxygen belonging to the peptide position before p1 (p-1) and the protonated ε-nitrogen of His 79β. Additionally, protonated His residues are well accepted at most of the peptide binding core positions which is in a good agreement with the overall negatively charged peptide binding site of most MHC proteins. © 2012 Patronov et al.; licensee BioMed Central Ltd.

An overview on Human Leukocyte Antigen (HLA) region gene expression during Pseudomonas aeruginosa infection

The human leukocyte antigen (HLA) complex is an extensively studied cluster of genes with immunoregulatory function. Pseudomonas aeruginosa is capable of infecting individuals with weakened immune systems, and is associated with a high mortality rate. Previous genetic studies of the HLA region have found correlations between bacterial infection and its effect on regulating HLA gene expressions to establish their infection. This project analyzes the expression of classical HLA loci (A, B, C, DR, DQ, DP) in human B cells and macrophage cells during the infection of virulent strains of P. aeruginosa. Cells were cultured and infected with different virulent live, and heat-killed strains of P. aeruginosa for different time periods. The mRNA was extracted and converted into cDNA followed by real-time quantitative PCR and data analysis. The Western Blot technique was used to identify the targeted protein’s cell surface expression. Infection with P. aeruginosa was found to inhibit the expression of HLA proteins. The PA14 strain inhibited expression of all targeted genes in all experiments. Infections with PA01 and PA103 showed different patterns depending on the incubation time and the targeted gene. These differences suggest that the three strains use various mechanisms to inhibit HLA protein expression.

Molécula HLA-G y su importancia en la inmunorregulación de la unidad feto-materna. Aplicaciones en inmunoterapia celular

OBJETIVOS El objetivo principal de esta tesis doctoral consiste en determinar la presencia de la proteína HLA-G en la superficie celular de células madre CD34/CD133, células dendríticas mieloides y plasmacitoides, células dendríticas derivadas de células CD34/CD133 y derivadas de monocitos de sangre de cordón umbilical y sangre periférica materna, por técnicas de citometría de flujo y la expresión de la proteína HLA-G soluble en plasma de sangre de cordón umbilical por técnicas de ELISA. MATERIALES Y METODOS Se obtuvo un total de 35 unidades de sangre de cordón umbilical y 35 muestras de sangre periférica de gestantes a término que acudieron al Servicio de Ginecología y Obstetricia del Hospital Clínico Universitario San Carlos con cesáreas programadas, según aprobación de Comité Ético. Se realizaron técnicas de cultivo celular, citometría de flujo, Elisa y anticuerpos monoclonales, según protocolo, para la obtención de las células madre CD34+, células dendríticas mieloides y plasmacitoides del cordón umbilical y células dendríticas derivadas de células madre CD34+, y determinación de la molécula HLA-G, isoformas, nuevos alelos y polimorfismos...

Estudio genético HLA en poblaciones iraníes: epidemiología, antropología y farmacogenética

The HLA system is the most polymorphic genetic system described in humans. It consists of several closely linked loci encoding cell surface glycoproteins whose best known function is activating immune system response through antigenic presentation. New loci and new alleles have been described since the discovery of this genetic system and the presently available DNA typing and sequencing of these new alleles have increased the variety of HLA allelism. Due to the fact that HLA gene frequencies have a large degree of variability and a remarkable geographical correlation, HLA genes are an important and useful tool to infer genetic background and ethnical composition of modern human populations and also for tracing migration of ancient ones. In addition, certain combinations of contiguous alleles due to the strong linkage disequilibrium between HLA neighbouring loci show a characteristic frequency or are distinctive in many present day populations. Thus, HLA genetic system is a unique tool for studying the origin of relatively isolated groups, like Turkmen, Azeri and Kurd people, the populations under study, living in North Iran, in the surrounding area of Caspian Sea. Finally, HLA polymorphism is crucial for the compatibility between donor and receptor in organ transplantation and several HLA alleles have been linked to diseases and to response to drug treatments, which accomplishes relationships of certain variants with different pathologies treatment including AIDS. This is important in personalized treatments design. Turkmen could be descendants of Oghuz tribes from Seljuq branch coming from Transoxiana region (Central Asia) contemporarily to the foundation of the Seljuk Empire in 10th century AD. Conversely, this people could belong to another group within the Oghuz, arriving to Iran five centuries later. Migrations of this people were initially developed peacefully, being vassals of the Safavid Empire, and later by violent raids. They speak a language belonging to the Turkish-Oghuz group. In Iran, Turkmen live in Golestan province, mainly in Türkmensähra (“Turkmen plain”) area and amount 1.5 million people (2% of Iranian population). Most of this people are Sunni Muslims...

Régulation de la présentation antigénique par la chaîne invariante Iip35 et la molécule non-classique HLA-DO

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Analyse structure-fonction de la molécule non classique du CMH de classe II HLA-DO

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Modulation de la présentation antigénique par le CMH de classe II : utilisation de HLA-DO dans les cellules dendritiques

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.