Assume a fragment of two-stranded antiparallel β-structure is 3.3 nm long. What is the approximate number of amino acids in this fragment?
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Assume a fragment of two-stranded antiparallel β-structure is 3.3 nm long. What is the approximate number of amino acids in this fragment?
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- Like a helices, B sheets often have one side facing the surface of the protein and one side facing the interior, giving rise to an amphiphilic sheet with one hydrophobic surface. From the sequences listed below, pick the one that could form a strand in an amphiphilic B sheet. Think about the way side chains are arranged in a strand of a ß sheet (See Figure below). a) ALSCDVETYWLI b) DKLVTSIAREFM c) DSETKNAVFLIL d) TLNISFQMELDV e) VLEFMDIASVLD IINIIConsider a short peptide that forms an alpha-helix within a larger protein structure. Suppose that one glutamate residue at some specific position in the helix were mutated to a leucine residue. The mutation could either make the helix more stable, or less stable. i) Describe two situations in which a Glu-to-Leu mutation could make the helix more stable. ii) Describe two situations in which the Glu-to-Leu mutation could make the helix less stable. Explain briefly the basis for the stabilizing and destabilizing effect in all cases.Consider the peptide with the sequence SANTACLAUSISASTALKER. Assume this entire pepide were a single a-helix. With which two amino acids would the L closest to the N- terminus form hydrogen bonds to help create the a-helix? Consider the peptide with the sequence SANTACLAUSISASTALKER. Assume this entire peptide was a single a-helix. With which two amino acids would the L closest to the N-terminus form hydrogen bonds to help create the a-helix? I and T T and U N and I S and R
- A synthetic polypeptid made up of L-glutamic acid residues is in a random coil configuration at pH 7.0 but changes to alpha helical when the pH is lowered to 2.0. Explain this pH-dependent conformational transition.For the structure shown on the figure - qualitatively draw Ramachandran plot. Assume a mixture of right and left handed helices. How would the plot change if only left handed helices were present?Remembering that the amino acid side chains projecting from each polypeptide backbone in a β sheet point alternately above and below the plane of the sheet, consider the following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg- Leu-Lys-Ile-Arg-Phe-Glu. Do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a β sheet? Can you make any predictions as to how the β sheet might be arranged in a protein?
- This is Fos-Jun dimer (1FOS). Is the leucine zipper at the C-terminus or at the N-terminus of the helices? Are the helices parallel or antiparallel?Certain polypeptide sequences that show a pronounced tendency to dimerize in an antiparallel coiled-coil structure exhibit an exact repetition of leucine every 7 residues. If you also know that the a helix is distorted somewhat from its usual 3.6 residues/turn in coiled coils, propose a mechanism for the dimerization. What does this suggest that the residue/turn value might be in a coiled coil?Low-resolution X-ray diffraction analysis of a protein composed of long stretches of the sequence (-Gly-Ser-Gly-Ala-Gly-Ala-)n, where n indicates any number of repeats, shows an extended structure of stacked layers, with a repeat distance between layers that alternates between 3.5 Å and 5.7 Å. Propose a model that explains this scenario.
- PfCRT is found to have 10 peaks on a hydropathy plot given its primary sequence. Researchers also noted that each peak is comprised of about 30 amino acids. The digestive vacuole membrane is 45Å in Plasmodium species. Explain why researchers conclude there are 10 transmembrane helices from these two pieces of data.Shown below are two cartoon views of the small globular protein StrepG inwhich an α helix is packed against a four-strand β sheet. The sheet is madeup of two “β-hairpins” (a β-hairpin is a “β-turn-β” structure). Refer to theimages and answer the questions that follow: (a) Identify the locations of the N- and C-termini of StrepG.(b) Indicate the orientation of the helical macrodipole, showing the (δ+)and (δ-) ends of the macrodipole.(c) How many residues are in the helix?(d) Do you predict that the α helix and β sheet are amphiphilic or not?Briefly explain.(e) The following two peptides are part of the primary sequence of StrepG.Based on your answer to part (d), which one is more likely to correspondto the α helix? Which is most likely to be part of a β-hairpin? Explainyour choice.Peptide #1: DAATAEKVFKQYAND or Peptide #2: VDGEWTYDDATKTFTVSYNZIPS are a-helices that can be used in synthetic biology to create coiled-coil interactions between two different proteins. SYNZIP1 is around 47 amino acids in length. If each turn in an a-helix is 3.6 residues in length and each turn is 5.4 Å in length, how long is SYNZIP1? Keep in mind that 1 Å = 10 nm. Present your answer in nm.