9 - Friday October 9th 2009 Biochemistry 405 Lecture#5 Kane...

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1 Friday, October 9 th, 2009 Biochemistry 405 ± Lecture #5 Kane Hall 130 7:30- 8:20 am Lecturer: Wim Hol Slide Set #1.
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2 Protein Structure Outline 1. The main chain -The d ihedra ls Øand Ȍ per amino acid residue , Ȍ )p lot 2. Secondary Structure. - Į -helix. - ȕ -structures. -F ibrous prote ins 3. Tertiary Structure. -Domains -Classes of protein folds -Membrane proteins -Packing of atoms in proteins. 4. Conformational change
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The structural hierarchy of proteins.
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Linking amino acids together via peptide bonds An extended chain of a polypeptide Emphasizing the planar peptide units. (It is a healthy exercise to figure out the possible amino acid sequence of the peptide shown ±realize that there is no color or size difference in the side chains between C, O, S and N; but the side chain hydrogen is smaller than the C, O, S or N. Could it be that the artist has made an error?)
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Two main chain torsional angles per residue: Ø and Ȍ If one peptide unit is kept fixed, Øand Ȍ define the orientation of the second peptide unit. So, in a first approximation, the course of a polypeptide chain is defined by a pair of dihedral angles (Ø and Ȍ ) per amino acid residue. C Į n+1 C Į n-1 (You need to know which peptide atoms are in one plane)
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Two main chain torsional angles per residue: Ø and Ȍ If one peptide unit is kept fixed, Øand Ȍ define the orientation of the second peptide unit. So, in a first approximation, the course of a polypeptide chain is defined by a pair of dihedral angles (Ø and Ȍ ) per amino acid residue. C Į n+1 C Į n-1 The four dot-circled atoms define the dihedral angle ĭ
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Two main chain torsional angles per residue: Ø and Ȍ If one peptide unit is kept fixed, Øand Ȍ define the orientation of the second peptide unit. So, in a first approximation, the course of a polypeptide chain is defined by a pair of dihedral angles (Ø and Ȍ ) per amino acid residue. C Į n+1 C Į n-1 These four dot-circled atoms define the dihedral angle Ȍ
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Steric clashes pose restrictions on Ø and Ȍ Not all combinations of Ø and Ȍ are possible due to clashes between atoms from subsequent residues. For 18 amino acids the so-called (Ø, Ȍ ) ±plot is the same (next slide). For Gly, which has no side chain, the (Ø, Ȍ ) ±plot is less restricted.
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9 - Friday October 9th 2009 Biochemistry 405 Lecture#5 Kane...

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