Structure & Sequence Flashcards
what type of proteins retain a large common core and why?
helical proteins - helix is inflexible.
What is the RMSD and what do the valies tell us?
Measure of degree of structural overlap between 2 proteins.
Less than 1 angstrons shows two proteins are very similar (less than 1 A will share more than 50% sequence identity and HAVE common cores.)
Calculated for optimal alignment using residues within common core.
what rule must be imposed when looking at assignment of structure similarities?
10-20 residue fragments –> no level of sequence identity sufficient to establish structural similarity reliably.
SS probable when sequence identity of LONG fragments (~100 residues) is above 25%.
how do the BLOSUM score and environmental score differ?
in the former scores matches between AAs and AAs whereas latter scores matches between AAs and environmental descriptors.m
give the environmental preferences of Phe, Trp and Gly.
Mainly buried
mainly buried.
mainly exposed
How is the gloving fold an example of conservation of structure over sequence?
Only 28 of 150 residues in alpha and beta Hb subunits are identical but food is preserved.
What is the sequence identity between alpha and;
Beta
Myoglobin
And Beta with myoglobin?
45%
30%
26%
Outline fold recognition.
In given alignments AAs corresponding to sequence of unknown structure mapped into corresponding positions along PP chain of known structure.
Likelihood of position evaluated in terms of what is known about Aa properties in p structures.
What small changes can be seen in Globin fold geometry?
Distance between G and H helices ranges from 8-12 A
Angle omega between helices ranges from -10 to -35 in different globins.
What is topology in the CATH database?
As elements connected in same order (b-lactamase
What is H in CATH?
Homologous fold superfamily
High structural and functional similarity.
(Types of flavodoxins).
What is H in CATH?
Homologous fold superfamily
High structural and functional similarity.
(Types of flavodoxins).
