Flashcards
protein structure
Cards in this deck (10)
- 1Are Alpha helical or -stranded proteins better suited for allosteric regulation? Why?In allosteric regulation e.g. for haemoglobin, conformational changes often take place in order to achieve functional activity. Conformational changes in proteins are made possible by their intrinsic flexibility.
In alpha helices, hydrogen bonding from residues I to residue i+4 - 7 residue repeats where every 4th residues is hydrophobic - form a sticky hydrophobic surface on one side of an alpha helix - directionality of the helix give it an overall dipole moment - can help with binding e.g. nucleotide binding in rossman fold is facilitated by helical dipole moment - positive end of helix interacts with the phosphate in the nucleotide
B strands - alternating H bond acceptors and doors to neighbouring strands -parallel or anti-parallel orientation - pleated conformation for the backbone - side chains project alternatively to different sides of the sheet - sheets are seldom flat and straight - often show twisting and behind - free edfe of the shoe can form H-bonding further - often used for binding other proteins - often much longer loops with variable structure connect - flexi - 22. What information about protein structure is provided by circular dichroism?Measures the difference in absorption of left and right handed circularly polarised light and (created by two perpendicular polarised beams which differ in phase by 90 degrees)- deltaA = deltaAR- delta AL.
Peptide bonds of chiral AAS show conformation dependent difference in the ability to absorb left and right circularly polarised light - can be used to assess 2nd structure - generally CD signal at 215nm indicates sheet content and signal at 208 nm and 222nm are used to calculate helical content - as an approx, CD spec of protein can be treated as a sum of alpha, beta and random coil contributions - accurate estimate requires careful determination of protein conc - 3Why do protein oligomers assemble into symmetrical structures? Suggest some structures for a tetramer.Honomers with close symmetry are finite in space - most of them form with cyclic or dihedral symmetry - specificity of protein-protein interfaces favours symmetrical complexes, the maximum number of intersubunit interactions are formed in closed complexes.
Symmetry is favoured because of stability and a finite control of assembly. Several functions limit symmetry, such as interaction with DNA or membranes, and directional motion. Symmetry is broken or modified in many forms: quasisymmetry, in which identical subunits adopt similar but different conformations; pleomorphism, in which identical subunits form different complexes; pseudosymmetry, in which different molecules form approximately symmetrical complexes; and symmetry mismatch, in which oligomers of different symmetries interact along their respective symmetry axes.
See slide 105 for pictures - 4Explain how Saccharomyces cerevisiae can be used to identify specific protein-protein interactions.Yeast two-hybrid method - use S.cerevisiae to screen a library of genes encoding known proteins for proteins that interact with a protein whose gene you've already cloned - most common versions uses the transcription factor GAL4 - 2 domains - a DNA binding and an activation domain - when joined together they can activate transcription - but don't have to be joined directly - a hybrid Is made encoding a fusion between the DNA binding domain from GAL4 and the protein you've already cloned (the bait) - cloned into a plasmid e.g. yeast episcomal plasmid - the library you're screening is cloned into a suitable vector generating fusion proteins pf the activation domain and the library members - each member of the library is introduced to different cells which contain the bait plasmid and the DNA-binding site upstream of a reporter gene e.g. HIS3 - when interaction of protein occurs - the 2 domains are joined together, activating transcription - reporter translated - e.g. synthesis of histidine - ability for cell to grow in the absence of histidine
- 5Why do some amino acid residues have special conformational preference in peptide backbones?Peptide bond is planar due to the double bond character of the c-o and c-n bond, but there is still some rotational freedom in the backbone - resulting in phi/psi angles
Glycine has no side chains and so has increased flexibility
Proline is cyclised - reduced flexibility - much restricted ramachandran area.
Peptide bonds are usually trans-configuration to minimise steric clashes of R groups, but proline has a similar steric penalty for both cis and trans form so can be found in either - 6Explain how proteins catalyse the folding of nascent and misfolded proteins.Protein disulphide isomerase - shuffles links, prolyl peptide isomerases - catalyse the cis-trans isomerisation of many Xaa-Pro peptide in proteins, lower in the activation barrier to the isomerization by 16kcal. Chaperonins do not catalyse the folding process themselves but simply binds to stoichometric around of newly-synthesised, unfolded proteins to prevent aggregation. small chaperones of the stress protein DnaJ and DnaK families bind as monomer to 40 kDa and 70 kDA to short runs of hydrophobic residues and appear on elongating nascent pp chains from ribosomes - binding is transient and regulated by slow hydrolysis of ATP by DnaK - the prevent pre-mature folding before a complete folding unit has been synthesised and prevent unwanted interactions with hydrophobic residues
- 7The GroEL/ES familyGroEL - 7 subunits stack back to back - two large central cavities each killed by the apical domains of 7 ATPase subunits - create an initially HP environment in which a folding intermediate with exposed hydrophobic surfaces can be sequestered - cavity then cooed by heptameric ring of the GroES co-chaperone and binding of ATP - the cause CC in apical domains of the GroEL - enlarging it and turning the binding cavity hydrophilic - unhindered folding of the sequestered protein can now take place - release triggered by ATP hydrolysis which weaken the GroEL/ES interaction
- 8Apart from non-covalent interactions between amino acid residues, what additional stabilizing mechanisms are found in proteins?Disulphide links, metal co-factors e.g. zinc finger, iron-c;usters in haemoglobin, co-factors, post-translational modification
- 9otheB barrel = green fluorescent protein
linear repeats = leucine-rich repeats-ab horseshoe fold-extracellular receptor 20-30 AAs capped with disulphide link , RING AND HEAT closed structure - b-propellers - compare sequence to itself
Bossman gold -Nad+ binding enzymes e.g. lac dehydo or alcho dehydrogenase or gap
P-loop in atp binding proteins e.g. rase, prtein kinase, actin
actin and hsp-70 both bind atp similar fold
serine - diff folds but same function
NMR proteins labelled with 15N or 13 C in solution - no needs for x-ray - requires purified, stable, homogenous sample
NOE - transfer of magnetism from one nucleus to another
unstructuredd - lack of proteins that can form hydrophobic core
Large proteins - accuracy in synthesis, morphological advantages, increases stability, co-localisation, increased regulation of activity - 10Otherchange of the position of iron in the porphyrin ring upon oxygen binding - in plane
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- Biology (SAQS) Flashcards on protein structure , created by Jenna Robinson on 18/01/2017.
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