Studying proteins
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17 Terms
what are the three different experimental environments
in silico
in vitro
in vivo
what is in silico?
computer simulation / modelling
what is in vitro
in test tubes, cells (outside of living organisms)
what is in vivo
studies with living organisms e.g. mice
what are the limitations of studying proteins in experimental environments?
biological functions only emerge in context
protein may act differently in real, living organisms
what is the strength of studying proteins in experimental environments?
able to study in isolation - understanding of precise folding …
what are the three major techniques used to study protein structure?
x-ray crystallography
cryogenic electron microscopy
NMR
how is x-ray crystallography used?
crystal produces diffraction pattern which can be turned into an electron density map to see structure
how is cryo EM used?
combining 2D images to create a 3D image
how does NMR work?
produces a spectra
how can knowledge about protein structure be applied?
in drug designing
in protein engineering (improving proteins)
in denovo protein design (creating new proteins)
to study evolution
how can protein structure be used to study evolution?
looking at sequence alignments and motifs
looking at conserved sequences
looking at phylogenetic tree/relationships
looking at homologs, paralogs, orthologs
what are homologs?
proteins that have diverged from common ancestral gene
what are paralogs?
homologous proteins within same genome
arise by gene duplication
diverged in function
what are orthologs?
homologous proteins found in different species and evolved from common ancestral gene by speciation (retain same function)
what can be used to compare protein sequences?
multiple sequene alignments
sequence of a protein in different species are compared to see what amino acids are the same/different to see level of conservation
what are motifs?
small amino acid sequences e.g. Active sites, binding sites, post translational modification sites, repeats