These are notes.
2020
fn main() {
let number_list = vec![34, 50, 25, 100, 65];
print_max(&number_list);
print_max_1(&number_list);
print_max_2(number_list)
}
fn print_max(number_list: &[u16]) {
let mut largest = &number_list[0];
for number in number_list.iter() {
if number > largest {
largest = number;
}
}
println!("The largest number is {}", largest);
}
fn print_max_1(number_list: &[u16]) {
let mut largest = &number_list[0];
for number in number_list {
if number > largest {
largest = number;
}
}
println!("The largest number is {}", largest);
}
fn print_max_2(number_list: Vec<u16>) {
let mut largest = number_list[0];
for number in number_list {
if number > largest {
largest = number;
}
}
println!("The largest number is {}", largest);
} About the frame
Sometimes we want to use the start/stop codon in the vector for our protein production, especially when tag sequences need to be included. In these cases, we need to check our inserted GOI is in frame with the start/codon on the vector. Frame mismatch can be corrected by adding 1 or 2 random nucleotide(s) to the primer (forward primer to match vector start condon and reverse primer to match the stop codon) between the GOI sequence and the restriction site sequence.
Some vectors have an N-terminal tag and stop codons in all three frames (e.g. TGA C TGA C TGA)
Protein Structure
Homology Modelling
Swiss Model
Model Evaluation
- GMQE (global model quality estimation)
- 0-1, higher better
- combines properties from the target-alignment and the template search method
- replecting the expected accuracy of a model built with that alignment and the template and the coverage of the target
- computed before modelling and after modelling. The latter also takes into account the QMEAN
- QMEAN
- QMEAN z score: around 0: ideal; < -4.0: low quality
- QMEAN is a composite estimator based on different geometrical properties and provides both global and local absolute quality estimates on the basis of one single model
- the QMEAN z-score provides an estimate of the ‘degree of nativeness’ of the structural features observed in the model on a global scale. It indicates whether the QMEAN score of the model is comparable to what one expect from experimental structures of similar size
- 4 terms of the global QMEAN quality score:
- the interaction potential between Cβ atoms only
- and between all atoms
- solvation potential
- torsion angle potential
- the accuracy of local QMEAN scores is enhanced by QMEANDisCo
- below 0.6: low quality
- if downloaded, local score is reported in the B-factor column of the PDB file
- can be visualised by choosing the colour scheme ‘QMEAN’
- QMEANDisco assesses the consistency of observed interatomic distances in the model with ensemble information extracted from experimentally determined protein structures that are homologous to the target sequence. The ‘local quality’ plot shows, for each residue of the model (x-axis), the expected similarity to the native structure (y-axis)
- in the ‘comparison’ plot, model quality scores are related to scores obtained for experimental structures of similar size. The x-axis shows protein length and the y-axis shows the normalized QMEAN score. Every dot represents an experimentally determined structure. The mean and standard deviation of the experimental structures around the x-location of the star (the model) are the basis to calculate the QMEAN z-score of the model.
Paper I
X-ray and EM
“Biomolecular Crystallography” by Bernard Rupp (preferably 2 nd Edition) Garland Science ISBN 978-0815340812 “Outline of Crystallography for Biologists” by David Blow Oxford University Press, ISBN 978-0198510512 “Crystallography Made Crystal Clear” by Gale Rhodes Academic Press ISBN 978-0125870733 Milne JL, Borgnia MJ, Bartesaghi A, Tran EE, Earl LA, Schauder DM, Lengyel J, Pierson J, Patwardhan A, Subramaniam S. Cryo-electron microscopy–a primer for the non-microscopist. FEBS J. 2013 Jan;280(1):28-45. doi:
10.1111/febs.12078.
Kühlbrandt W. Cryo-EM enters a new era. Elife. 2014 Aug 13;3:e03678. doi:
10.7554/eLife.03678 Yong Xiong (2007) From electron microscopy to X-ray crystallography:
molecular-replacement case studies. Elife. 2014 Aug 13;3:e03678.
Paper VI
HT 2020: Protein Purification
- ‘Methods in Enzymology’ volumes 22, 34, and 104 are devoted to techniques of protein purification.
- ‘Protein Purification Methods: A Practical Approach’ IRL Press, Eds ELV Harris and S Angal