How does it work Structure Prediction from sequence P9 Extra Discussion Slides

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How does it work Structure Prediction from sequence P9 Extra Discussion Slides

Blessing-Rieman College of Nursing, US has reference to this Academic Journal, * P9 Extra Discussion Slides Sequence-Structure-Function Relationships Proteins of similar sequences fold into similar structures in addition to perform similar biological functions. The protein sequence has the intrinsic information so that encode the protein structure. From Nobel Lecture, December 11, 1972, by Christian Anfinsen The protein sequence is sufficient so that specify its 3D structure

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Structure Prediction from sequence Homology (or comparative) modelling Threading Ab initio calculations Homology modelling is most accurate in addition to powerful What is Homology Modeling? Homology modeling also known as comparative modeling uses homologous sequences alongside known 3D structures in consideration of the modelling in addition to prediction of the structure of a target sequence Homology modeling is one of the most best performing prediction methods that gives ?accurate? predicted models. How does it work A homology modeling routine needs three items of input: The sequence of the protein alongside unknown 3D structure, the “target sequence”. A 3D template is chosen by virtue of having the highest sequence identity alongside the target sequence. The 3D structure of the template must be determined by reliable empirical methods such as crystallography or NMR, in addition to is typically a published atomic coordinate “PDB” file from the Protein Data Bank. An alignment between the target sequence in addition to the template sequence. First, the homology modeling routine arranges the backbone identically so that that of the template. This means that not only the positions of alpha carbons, but also the phi in addition to psi angles in addition to secondary structure, are made identical so that the template. Next, the more sophisticated homology modeling packages adjust side chain positions so that minimize collisions, in addition to may offer further energy minimization or molecular dynamics in an attempt so that improve the model. * Taken from: umass /molvis/workshop/homolmod.htm

Homology modelling practical steps, in brief Retrieving the sequence so that be modeled (target sequence) Identifying suitable templates from PDB using BLAST Go in consideration of the best hit (> 30 – 40% identity) No need so that do modeling if hit is 100% identical so that target Aligning target sequence alongside template sequences Remove gapped positions Remove residues in target that are missing in template Final alignment should be in PIR format Performing homology modeling using MODELLER Change the aligned PIR file so that add additional information required by MODELLER Mind the syntax (most errors occur because of not following the syntax) Model quality check ? WHATIF, PROCHECK, VERIFY3D, ERRAT Quantitative comparison of model alongside experimental structure Assess RMSD using SUPERPOSE Quantitative comparison between model in addition to experimental 3D structure using RMSD 0.0-0.5  < 5.0  5.0-7.0  > 7.0  > 12.0  Essentially Identical Very good fit Moderately good fit Structurally related Dubious relationship Completely unrelated Taken from: redpoll.pharmacy.ualberta.ca/bioinfo301/Bioinf301-3Dvisualize.ppt

Surface Enhanced Infrared Absorption (SEIRA) Spectroscopy The Theory Attenuated Total Reflection (ATR) Spectroscopy First Finding of SEIRA in 1980 On Low Reflective Surfaces The Importance of Metal Morphology H2@C60?

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