Development of a Novel In Silico Docking Simulation Model for the Fine HIV-1 Cytotoxic T Lymphocyte Epitope Mapping

Introduction: Class I HLA\u27s polymorphism has hampered CTL epitope mapping with laborious experiments. Objectives are 1) to evaluate the novel in silico model in predicting previously reported epitopes in comparison with existing program, and 2) to apply the model to predict optimal epitopes with HLA using experimental results. Materials and Methods: We have developed a novel in silico epitope prediction method, based on HLA crystal structure and a peptide docking simulation model, calculating the peptide-HLA binding affinity at four amino acid residues in each terminal. It was applied to predict 52 HIV best-defined CTL epitopes from 15-mer overlapping peptides, and its predictive ability was compared with the HLA binding motif-based program of HLArestrictor. It was then used to predict HIV-1 Gag optimal epitopes from previous ELISpot results. Results: 43/52 (82.7%) epitopes were detected by the novel model, whereas 37 (71.2%) by HLArestrictor. We also found a significant reduction in epitope detection rates for longer epitopes in HLArestrictor (p = 0.027), but not in the novel model. Improved epitope prediction was also found by introducing both models, especially in specificity (p<0.001). Eight peptides were predicted as novel, immunodominant epitopes in both models. Discussion: This novel model can predict optimal CTL epitopes, which were not detected by an existing program. This model is potentially useful not only for narrowing down optimal epitopes, but predicting rare HLA alleles with less information. By introducing different principal models, epitope prediction will be more precise

Investigation by DFT Methods of the Damage of Human Serum Albumin Including Amino Acid Derivative Schiff Base Zn(II) Complexes by IR-FEL Irradiation

An infrared free electron laser (IR-FEL) can decompose aggregated proteins by excitation of vibrational bands. In this study, we prepared hybrid materials of protein (human serum albumin; HSA) including several new Schiff base Zn(II) complexes incorporating amino acid (alanine and valine) or dipeptide (gly-gly) derivative moieties, which were synthesized and characterized with UV-vis, circular dichroism (CD), and IR spectra. Density functional theory (DFT) and time dependent DFT (TD-DFT) calculations were also performed to investigate vibrational modes of the Zn(II) complexes. An IR-FEL was used to irradiate HSA as well as hybrid materials of HSA-Zn(II) complexes at wavelengths corresponding to imine C=N, amide I, and amide II bands. Analysis of secondary structures suggested that including a Zn(II) complex into HSA led to the structural change of HSA, resulting in a more fragile structure than the original HSA. The result was one of the characteristic features of vibrational excitation of IR-FEL in contrast to electronic excitation by UV or visible light

Example of epitope prediction using the novel <i>in silico</i> docking simulation model.

<p>U_dock scores of the N-terminal (Row N1–N8) and C-terminal (Column C1–C8) was calculated and their sum was scored as the U_dock score (kcal/mol) of each 8 to 11-mer peptide's. The lower score indicated stronger binding between the peptide and HLA. In this example, Gag p24_263–272 KRWIILGLNK (KK10), well-known as one of the best-defined epitopes, scored −137.11 kcal/mol against HLA-B*27:05 and was the lowest (ranked as the 1st) among 26 variants in 15-mer peptide of Gag p24_258–272 VGEIYKRWIILGLNK.</p

Evaluation of best-defined epitope prediction among docking simulation model, HLArestrictor, and positives in dual models.

<p>Evaluation of best-defined epitope prediction among each model and positives in dual models were statistically evaluated, according to their sensitivity, specificity, positive prediction value (PPV) and negative prediction value (NPV) by maximum Fisher's exact test. DSM: Docking simulation model.</p

Prediction of the HLA restriction of Gag p24_276–285 MYSPVSILDI (MI10) and p24_277–285 YSPVSILDI (YI9) using <i>in silico</i> methods.

<p>HLA restriction prediction against two reactive Gag peptides, Gag p24_276–285 MYSPVSILDI (MI10) and p24_277–285 YSPVSILDI (YI9) was performed by the docking simulation model, and the binding motif HLArestrictor 1.2. The U_dock rank by the docking simulation model against MI10 and YI9 was analyzed in the original 15-mer peptides of Gag p24_271–285 NKIVRMYSPVSILDI (NI15) and p24_276–290 MYSPVSILDIRQGPK (MK15). SB: Strong Binder, WB: Weak Binder.</p

Heat shock transcription factor 1-deficiency attenuates overloading-associated hypertrophy of mouse soleus muscle.

Hypertrophic stimuli, such as mechanical stress and overloading, induce stress response, which is mediated by heat shock transcription factor 1 (HSF1), and up-regulate heat shock proteins (HSPs) in mammalian skeletal muscles. Therefore, HSF1-associated stress response may play a key role in loading-associated skeletal muscle hypertrophy. The purpose of this study was to investigate the effects of HSF1-deficiency on skeletal muscle hypertrophy caused by overloading. Functional overloading on the left soleus was performed by cutting the distal tendons of gastrocnemius and plantaris muscles for 4 weeks. The right muscle served as the control. Soleus muscles from both hindlimbs were dissected 2 and 4 weeks after the operation. Hypertrophy of soleus muscle in HSF1-null mice was partially inhibited, compared with that in wild-type (C57BL/6J) mice. Absence of HSF1 partially attenuated the increase of muscle wet weight and fiber cross-sectional area of overloaded soleus muscle. Population of Pax7-positive muscle satellite cells in HSF1-null mice was significantly less than that in wild-type mice following 2 weeks of overloading (p<0.05). Significant up-regulations of interleukin (IL)-1β and tumor necrosis factor mRNAs were observed in HSF1-null, but not in wild-type, mice following 2 weeks of overloading. Overloading-related increases of IL-6 and AFT3 mRNA expressions seen after 2 weeks of overloading tended to decrease after 4 weeks in both types of mice. In HSF1-null mice, however, the significant overloading-related increase in the expression of IL-6, not ATF3, mRNA was noted even at 4th week. Inhibition of muscle hypertrophy might be attributed to the greater and prolonged enhancement of IL-6 expression. HSF1 and/or HSF1-mediated stress response may, in part, play a key role in loading-induced skeletal muscle hypertrophy