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).

Peptide length significantly influences in vitro affinity for MHC class II molecules

Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules.

Static energy analysis of MHC class I and class II peptide-binding affinity

Antigenic peptide is presented to a T-cell receptor (TCR) through the formation of a stable complex with a major histocompatibility complex (MHC) molecule. Various predictive algorithms have been developed to estimate a peptide's capacity to form a stable complex with a given MHC class II allele, a technique integral to the strategy of vaccine design. These have previously incorporated such computational techniques as quantitative matrices and neural networks. A novel predictive technique is described, which uses molecular modeling of predetermined crystal structures to estimate the stability of an MHC class II-peptide complex. The structures are remodeled, energy minimized, and annealed before the energetic interaction is calculated.

EpiTOP—a proteochemometric tool for MHC class II binding prediction

Motivation: T-cell epitope identification is a critical immunoinformatic problem within vaccine design. To be an epitope, a peptide must bind an MHC protein. Results: Here, we present EpiTOP, the first server predicting MHC class II binding based on proteochemometrics, a QSAR approach for ligands binding to several related proteins. EpiTOP uses a quantitative matrix to predict binding to 12 HLA-DRB1 alleles. It identifies 89% of known epitopes within the top 20% of predicted binders, reducing laboratory labour, materials and time by 80%. EpiTOP is easy to use, gives comprehensive quantitative predictions and will be expanded and updated with new quantitative matrices over time.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Towards the in silico identification of class II restricted T-cell epitopes:a partial least squares iterative self-consistent algorithm for affinity prediction

Motivation: The immunogenicity of peptides depends on their ability to bind to MHC molecules. MHC binding affinity prediction methods can save significant amounts of experimental work. The class II MHC binding site is open at both ends, making epitope prediction difficult because of the multiple binding ability of long peptides. Results: An iterative self-consistent partial least squares (PLS)-based additive method was applied to a set of 66 pep- tides no longer than 16 amino acids, binding to DRB1*0401. A regression equation containing the quantitative contributions of the amino acids at each of the nine positions was generated. Its predictability was tested using two external test sets which gave r pred =0.593 and r pred=0.655, respectively. Furthermore, it was benchmarked using 25 known T-cell epitopes restricted by DRB1*0401 and we compared our results with four other online predictive methods. The additive method showed the best result finding 24 of the 25 T-cell epitopes. Availability: Peptides used in the study are available from http://www.jenner.ac.uk/JenPep. The PLS method is available commercially in the SYBYL molecular modelling software package. The final model for affinity prediction of peptides binding to DRB1*0401 molecule is available at http://www.jenner.ac.uk/MHCPred. Models developed for DRB1*0101 and DRB1*0701 also are available in MHC- Pred

EpiDOCK:a molecular docking-based tool for MHC class II binding prediction

Cellular peptide vaccines contain T-cell epitopes. The main prerequisite for a peptide to act as a T-cell epitope is that it binds to a major histocompatibility complex (MHC) protein. Peptide MHC binder identification is an extremely costly experimental challenge since human MHCs, named human leukocyte antigen, are highly polymorphic and polygenic. Here we present EpiDOCK, the first structure-based server for MHC class II binding prediction. EpiDOCK predicts binding to the 23 most frequent human, MHC class II proteins. It identifies 90% of true binders and 76% of true non-binders, with an overall accuracy of 83%. EpiDOCK is freely accessible at http://epidock.ddg-pharmfac. net. © The Author 2013. Published by Oxford University Press. All rights reserved.

MHC class II binding prediction by molecular docking

Proteins of the Major Histocompatibility Complex (MHC) bind self and nonself peptide antigens or epitopes within the cell and present them at the cell surface for recognition by T cells. All T-cell epitopes are MHC binders but not all MCH binders are T-cell epitopes. The MHC class II proteins are extremely polymorphic. Polymorphic residues cluster in the peptide-binding region and largely determine the MHC's peptide selectivity. The peptide binding site on MHC class II proteins consist of five binding pockets. Using molecular docking, we have modelled the interactions between peptide and MHC class II proteins from locus DRB1. A combinatorial peptide library was generated by mutation of residues at peptide positions which correspond to binding pockets (so called anchor positions). The binding affinities were assessed using different scoring functions. The normalized scoring functions for each amino acid at each anchor position were used to construct quantitative matrices (QM) for MHC class II binding prediction. Models were validated by external test sets comprising 4540 known binders. Eighty percent of the known binders are identified in the best predicted 15% of all overlapping peptides, originating from one protein. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Major Histocompatibility Complex (MHC) Class II sequence polymorphism in long-finned pilot whale (Globicephala melas) from the North Atlantic

Funding Silvia S. Monteiro and Marisa Ferreira were supported by a Ph.D. grant from Fundação para a Ciência e Tecnologia (ref SFRH/BD/38735/2007 and SFRH/BD/30240/2006, respectively). Alfredo López was supported by a postdoctoral grant from Fundação para a Ciência e Tecnologia (ref SFRH/BPD/82407/2011). Catarina Eira is supported by CESAM (UID/AMB/50017), from FCT/MEC through national funds and FEDER (PT2020, Compete 2020). The work related with strandings and tissue collection in Portugal was partially supported by the SafeSea Project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), by the Project MarPro–Life09 NAT/PT/000038 (funded by the European Union–Program Life+) and by the project CetSenti FCT RECI/AAG-GLO/0470/2012; FCOMP-01-0124-FEDER-027472 (Funded by the Program COMPETE and Fundação para a Ciência e Tecnologia).

Adult orthodontics: internet information and a national survey

Aims: 1. To investigate the reliability and readability of information on the Internet on adult orthodontics. 2. To evaluate the profile and treatment of adults by specialist orthodontists in the Republic of Ireland (ROI). Materials and methods: 1. An Internet search was conducted in May 2015 using three search engines (Google, Yahoo and Bing), with two search terms (“adult orthodontics” and “adult braces”). The first 50 websites from each engine were screened and exclusion criteria applied. Included websites were then assessed for reliability using the JAMA benchmarks, the DISCERN and LIDA tools and the presence of the HON seal. Readability was assessed using the FRES. 2. A pilot-tested questionnaire about adult orthodontics was distributed to 122 eligible specialist orthodontists in the ROI. Questions addressed general and treatment information about adult orthodontic patients, methods of information provision and respondent demographics. Results: 1. Thirteen websites met the inclusion criteria. Three websites contained all JAMA benchmarks and one displayed the HON Seal. The mean overall score for DISCERN was 3.9/5 and the mean total LIDA score was 115/120. The average FRES score was 63.1. 2. The questionnaire yielded a response rate of 83%. The typical demographic profile of adult orthodontic patients was professional females between 25-35 years. The most common incisor relationship and skeletal base was Class II, division 1 (51%) and Class II (61%) respectively. Aesthetic upper brackets and metal lower brackets were the most frequently used appliances. Only 30% of orthodontists advise their adult patients to find extra information on the Internet. Conclusions: 1. The reliability and readability of information on the Internet on adult orthodontics is of moderate quality. 2. The provision of adult orthodontic treatment is common among specialist orthodontists in the Republic of Ireland.

Three-dimensional outcomes of twin-block appliance treatment and the influence of the postured wax bite

Aims 1 To identify the 3D soft tissue volumetric and linear landmark changes following treatment with the Twin-Block Appliance TBA. 2 To estimate the TBA treatment outcome on the soft tissue facial profile volumetric and linear landmark changes from the Postured Wax Bite (PWB). 3 To identify if there is any association between certain soft tissue landmark variables and successful treatment outcome of the TBA as measured by the reduction in overjet. 4 To assess the effects of TBA treatment on facial expressions. Materials and Methods Forty-seven Caucasian subjects with Class II division 1 were recruited. 3D images captured of each subject, pre-treatment (T1), with the PWB (T2) and at the end of treatment (T3). Soft tissue volumetric and linear changes as well as the correlation between facial parameters and successful treatment were calculated. Results The mean soft tissue volumetric change from T1 to T3 was 22.24 ± 16.73 cm³. Soft tissue profile linear changes from T1-T3 for lower facial landmarks were 4-5 mm. From T1-T3, the mean soft tissue volumetric change of the total sample was 60% of the change produced by the PWB (T1 to T2). Correlations were weak for all 3D facial parameters and successful overjet reduction. Facial expression changes were only significant for the lower landmarks. Conclusions 1 TBA treatment, in growing subjects, increased the lower facial soft tissue volume and caused forward movement of the lower soft tissue facial profile landmarks.2 The PWB can be used to estimate the treatment outcome of the TBA on soft tissue profile changes.3 No association was found between soft tissue landmark variables and successful overjet reduction.4 TBA treatment had no effect on the upper facial landmarks for each facial expression but it changed the lower facial expressions significantly except for maximal smile in males.

Tratamento da classe II divisão 1 na dentição mista

Introdução: Os indivíduos portadores da má oclusão de Classe II Divisão 1 possuem diversas etiologias e podem ser encontrados em todas as etnias. As suas características clínicas e radiográficas se agravam com o crescimento e uma vez não tratada, continuam com esta má oclusão por toda sua vida. Para o tratamento ortodôntico na dentição mista recorre-se a dispositivos como aparelhos extra-orais, aparelhos funcionais fixos e removíveis. Objetivo: O objetivo deste trabalho é fazer uma revisão sobre o diagnóstico e tratamento da Classe II Divisão 1 na dentição mista, salientando a importância do tratamento nesta fase. Materiais e Métodos: Para a concretização do presente trabalho foi realizada uma revisão bibliográfica no presente ano, recorrendo-se ao livro “Ortodontia Contemporânea” do autor William Proffit, diversos motores de busca online, nomeadamente, PubMed, Medline, Elsevier e Scholar Google, utilizando como palavras-chave: “Class II Division 1”, “Mixed Dentition”, “Functional Appliance”, “Extra-Oral Appliance”, e revistas de Ortodontia, nomeadamente, American Journal of Orthodontics, Seminars in Orthodontics, The Angle Orthodontist e Dental Press de Ortodontia e Ortopedia Facial. A pesquisa foi realizada sem qualquer tipo de limites temporais, sendo dada uma maior importância a artigos mais recentes. Os artigos foram selecionados segundo o seu rigor científico e interesse para o tema. Numa fase mais avançada de revisão bibliográfica foram usados artigos citados na bibliografia dos artigos selecionados na primeira pesquisa efetuada. Conclusão: A dentição mista é considerada a fase ideal para iniciar o diagnóstico, prevenção, interceção e possível correção dos problemas dentários e/ou esqueléticos associados a uma Classe II Divisão 1. A Ortopedia Funcional dos Maxilares, removível ou fixa, e o uso de aparelhos extra-orais constituem recursos terapêuticos disponíveis para o tratamento desta má oclusão.

Classe II divisão 1

Introdução: A Classe II Divisão 1 trata-se de um tipo de má oclusão com elevada prevalência na população com repercussões tanto físicas como psicológicas que pode ser diagnosticado precocemente em dentição mista, cujo seu tratamento pode ser apenas corretivo em dentição permanente ou bifásico com a primeira fase realizada em dentição mista. Objetivo: O objetivo do trabalho é realizar uma revisão sobre o diagnóstico e tratamento de Classe II Divisão 1 em dentição mista, averiguando qual a melhor metodologia a adotar. Materiais e Métodos: Para a concretização do presente trabalho foi realizada uma revisão bibliográfica, no presente ano, recorrendo-se a diversos motores de busca online, nomeadamente, Pubmed, Scielo, Medline, Science Direct, Elsevier e Scholar Google, utilizando como palavras-chave: “ class II”, “mixed dentition”, “overjet” e “orthodontic treatment”. A pesquisa foi realizada sem limite temporal, no entanto primazia foi conferida a artigos mais recentes. Os artigos foram selecionados mediante o seu rigor científico e interesse para o tema. Conclusão: Após a análise de vários estudos que averiguaram a necessidade de duas fases de tratamento ortodôntico em situações de Classe II Divisão 1 concluiu-se que para um maior conforto do paciente, assim como pelos resultados obtidos, o tratamento apenas em uma fase será o mais indicado. Quanto ao momento mais oportuno para a intervenção ainda existe espaço para debate, ficando claro que dependerá do paciente assim como da metodologia adotada pelo ortodontista.

Tratamento ortopédico com aparelho de Herbst: ocorrem mudanças verticais no padrão de crescimento facial?

OBJETIVO: o objetivo deste estudo prospectivo de 32 adolescentes com má oclusão de Classe II, divisão 1, associada a retrognatismo mandibular, tratados com aparelho de Herbst, construído sobre bandas e coroas metálicas, foi avaliar cefalometricamente as possíveis mudanças no padrão de crescimento facial. METODOLOGIA: as telerradiografias laterais foram obtidas ao início do tratamento (T1) e imediatamente após 12 meses de tratamento com o referido aparelho ortopédico (T2). Foram utilizados o quociente de Jarabak e o VERT de Ricketts (modificado) para determinação do padrão facial em T1 e T2. RESULTADOS: utilizando o quociente de Jarabak, os resultados evidenciaram que 27 casos (84,4%) apresentaram padrões hipodivergentes em T1 e permaneceram da mesma forma em T2. Cinco casos (15,6%) apresentaram padrão neutro em T1 e não exibiram mudanças em T2. Quando avaliado o VERT de Ricketts (modificado), não ocorreram mudanças no padrão facial em 31 pacientes. Em apenas um caso ocorreu mudança do tipo facial. CONCLUSÃO: baseado nos resultados obtidos, pode-se concluir que, após 12 meses de tratamento com aparelho de Herbst, não ocorreram mudanças verticais no padrão de crescimento facial dos pacientes estudados.

Changes in temporomandibular joint disc position and form following Herbst and fixed orthodontic treatment

Objective: To determine the changes in the position and form of the temporomandibular joint articular disc in adolescents with Class II division 1 malocclusion and mandibular retrognathism treated with the Herbst appliance (phase I) and fixed orthodontic appliance (phase II). Materials and Methods: Thirty-two consecutive adolescents went through phase I of treatment and 23 completed phase II. The temporomandibular joints were evaluated qualitatively by means of magnetic resonance images at the beginning of treatment (T1), during phase I (T2), at the end of phase I (T3), and at the end of phase II (T4). Results: Significant changes in disc position were not observed with the mouth closed between T1 X T3 (P = .317), T3 X T4 (P = .287), or T1 X T4 (P = .261). At T2, on average, the disc was positioned regressively. With the mouth open, no difference was observed between T1 X T3 (P = .223) or T1 X T4 (P = .082). We did observe a significant difference between T3 X T4 (P < .05). Significant changes in the disc form were found with the mouth closed between T1 X T2 (P < .001) and T2 X T3 (P < .001). Conclusions: At the end of the two-phase treatment, in general terms, the position and form of the initial articular discs were maintained; however, in some temporomandibular joints some seemingly adverse effects were observed at T4. (Angle Orthod. 2010;80:843-852.)