Polypeptide backbone (or the main chain)

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1 Polypeptide backbone (or the main chain) [IUPA-IUB ommission on Biochemical omenclature, Abbreviations and Symbols for the Description of the onfor mation of Polypeptide hains. Eur. J. Biochem., 969, 7, 93-2] Graham Kemp, halmers University of Technology

2 Dihedral angle A D B Graham Kemp, halmers University of Technology

3 Ramachandran steric map [o, K.., Thomas, A. and Brasseur, R., Protein Science, 23, 2: ] Graham Kemp, halmers University of Technology

4 Protein Data Bank entry (extract) MPD TRISE PSPATE ISMERASE (E ) SURE IKE (GALLUS GALLUS) BREAST MUSLE AUTR D.W.BAER,A..BLMER,G.A.PETSK,D..PILLIPS, AUTR 2 I.A.WILS : JRL AUT D.W.BAER,A..BLMER,G.A.PETSK,D..PILLIPS, JRL AUT 2 I.A.WILS JRL TITL ATMI RDIATES FR TRISE PSPATE ISMERASE JRL TITL 2 FRM IKE MUSLE JRL REF BIEM.BIPYS.RES.MM. V JRL REF ASTM BBRA9 US ISS 6-29X 46 : REMARK 2 RESLUTI. 2.5 AGSTRMS. : SEQRES A 247 ALA PR ARG LYS PE PE VAL GLY GLY AS TRP LYS MET SEQRES 2 A 247 AS GLY LYS ARG LYS SER LEU GLY GLU LEU ILE IS TR : ATM ALA A ATM 2 A ALA A ATM 3 ALA A ATM 4 ALA A ATM 5 B ALA A ATM 6 PR A ATM 7 A PR A ATM 8 PR A ATM 9 PR A : Graham Kemp, halmers University of Technology

5 ydrog en bonds in β-sheets A A A A A A A A A A A A A A A A A A A A A A A A A A A A Graham Kemp, halmers University of Technology

6 DSSP ydrogen bond energy E = q q 2 d() + d() d() d() f Antiparallel bridge: [ hbond(i,j) and hbond(j,i) ] or [ hbond(i-,j+) and hbond(j-,i+) ] Parallel bridge: [ hbond(i-,j) and hbond(j,i+) ] or hbond(j-,i) and hbond(i,j+) ] Graham Kemp, halmers University of Technology

7 DSSP summary codes 4-helix (α-helix) B residue in isolated β-br idge E extended strand, participates in β-ladder G 3-helix I 5-helix T -bonded turn S bend rambin (R) TTPSIVARSFVRLPGTPEAIATYTGIIIPGATPGDYA EE SSTT S EE SSS TTS Graham Kemp, halmers University of Technology

8 Protein stability good stereochemistry; no steric clashes; buried charged atoms must be paired; enough hydrophobic surface must be bur ied, and the interior must be sufficiently densely packed, to provide thermodynamic stability. Modular proteins multi-domain proteins, often with many copies of related domains; domains recur in many proteins in different structural contexts. Graham Kemp, halmers University of Technology

9 3D Transformations Tr anslation T (d x, d y, d z ) = d x d y d z Scaling S(s x, s y, s z ) = s x s y s z Rotation R x (θ) = cos(θ) sin(θ) sin(θ) cos(θ) R y (θ) = cos(θ) sin(θ) sin(θ) cos(θ) R z (θ) = cos(θ) sin(θ) sin(θ) cos(θ) Graham Kemp, halmers University of Technology

10 omparing molecular fragments Set A Set B Fit Set A onto Set B 3-D transfor mation to map Set A onto Set B Root Mean Square (RMS) distance Graham Kemp, halmers University of Technology

11 Domain definitions "The definition of protein domains var ies widely across the discipline of biology. Domains are defined simultaneously as: () regions that display a significant level of sequence homology; (2) a minimal part of the gene that is capable of perfor ming a function; (3) a region of the protein with an exper imentally assigned function; (4) par ts of structures that have significant structural similarity; and (5) compact spatially distinct units of protein structure." [Veretnik S, Bour ne PE, Alexandrov, Shindyalov I. To w ard consistent assignment of structural domains in proteins. J Mol Biol. 24 Jun 4;339(3): ] Graham Kemp, halmers University of Technology

12 DMAK (Dmain MAKer) [Siddiqui AS, Bar ton GJ. ontinuous and discontinuous domains: an algor ithm for the automatic generation of reliable protein domain definitions. Protein Sci. 995 May;4(5): ] Based on the principle that the residues comprising a domain make more contacts between themselves (internal contacts) than they do with the rest of the protein (exter nal contacts). Tw o residues make contact if a heavy atom of one is within 5angstrom of a heavy atom of the other. int A ext AB int B ext AB an deal with domains consisting of two segments. Graham Kemp, halmers University of Technology

13 STRUDL (STRUctural Domain Limits) [Wer nisch L, unting M, Wodak SJ. Identification of structural domains in proteins by a graph heuristic. Proteins. 999 May 5;35(3): ] Algor ithm designed to identify domains with any number of noncontiguous chain segments. Uses the Ker nighan-lin graph heuristic to partition the protein into residue sets which display minimum interactions between them. Interactions are deduced from contact areas between atoms in the weighted Voronoi diagram. The radius of the "accessible sphere" around each atom is the van der Waals radius of the atom increased by.4angstrom. Graham Kemp, halmers University of Technology

14 onflicting domain assignments "The major factors responsible for conflicting domain assignments between methods, both exper ts and automatic, are: () the definition of ver y small domains; (2) splitting secondary str uctures between domains; (3) the size and number of discontinuous domains; (4) closely packed or convoluted domain-domain interfaces; (5) str uctures with large and complex architectures; and (6) the level of significance placed upon structural, functional and evolutionar y concepts in considering structural domain definitions." [Veretnik S, Bour ne PE, Alexandrov, Shindyalov I. To w ard consistent assignment of structural domains in proteins. J Mol Biol. 24 Jun 4;339(3): ] Graham Kemp, halmers University of Technology

Dr. R. Sankar, BSE 631 (2018)

Dr. R. Sankar, BSE 631 (2018) Pauling, Corey and Branson Diffraction of DNA http://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050 In short, stereochemistry is important in determining which helices