【PPT】北京大学AMP高级管理课程

Much experimental data can aid the structure prediction process. Some of these are listed below: • Disulphide bonds, which provide tight restraints on the location of cysteines in space • Spectroscopic data, which can give ideas as to the secondary structure content of the protein • Site-directed mutagenesis studies, which can give insights as to residues involved in active or binding sites • Knowledge of proteolytic cleavage sites, post-translational modifications, such as phosphorylation or glycosylation can suggest residues that must be accessible, etc. • Remember to keep all of the available data in mind when doing predictive work. Always ask whether a prediction agrees with the results of experiments. If not, then it may be necessary to modify what has been completed.
http://www.mbb.ki.se/tmap/index.html
COILS - Prediction of Coiled Coil Regions in Proteins
• Does the protein contain coiled-coils? Prediction of coiled coils can be completed at the COILS server or by downloading the COILS program. /software/COILS_form.html • COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. COILS was described in:
• Proteins frequently contain runs of poly-glutamine or polyserine, which do not predict well. To check for this the program SEG (a version of SEG is also contained within the GCG suite of programs) can be employed. ftp:///pub/seg/seg/
Homologous Proteins
• The term of homology as used in a biological context is defined as similarity of structure, physiology, development and evolution of organisms based upon common genetic factors. • The statement that two proteins are homologous implies that their genes have evolved from a common ancestral gene. Usually they might have similar functions. • Two proteins are considered to be homologous when they have identical amino acid residues in a significant number of sequential positions along the polypeptide chains (> 30 %). • Homologous proteins have conserved structural cores and variable loop regions.
• If the answer to any of the above questions is yes, then it is worthwhile trying to break the sequence into pieces or ignore particular sections of the sequence, etc. This is related to the problem of locating domains.
Multiple Sequence Alignment
• • • Alignments can provide: Information to protein domain structure The location of residues likely to be involved in protein function Information of residues likely to be buried in the protein core or exposed to solvent More information on a single sequence for applications like homology modeling and secondary structure prediction.
• • • • • • • • • • Relevant experimental data Sequence data/preliminary analysis Sequence Database searching Domain assignment Multiple sequence alignment Comparative or homology modeling Secondary structure prediction Fold Recognition Analysis of folds and alignment of secondary structures Sequence to structure alignment
Protein Structure Prediction
• Sequence database searching • Domain assignment • Multiple sequence alignment • Comparative or homology modeling • Secondary structure prediction
The Divergence of Amino-acid Sequence and 3D Structure for the Core Region of Homologous Proteins
A Generalized Approach to Predicting Protein Structure
Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coiled Coils from Protein Sequences, Science 252:1162-1164.
Doesow Complexity?
Flow Chart
• This flowchart assumes that the protein is soluble, likely comprises a single domain, and does not contain nonglobular regions.
Experimental Data
• Known structures of 32 pairs of homologous proteins such as globins, serine proteinases, and immunoglobulin domains have been compared. The root mean square deviation of the main-chain atoms of the core regions is plotted as a function of amino acid homology. The curve represents the best fit of the dots to an exponential function. Pairs with high sequence homology are almost identical in threedimensional structure, whereas deviations in atomic positions for pairs of low homology are on the order of 2 Å.
Protein Sequence Data