Virtual bond representation

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1 Today s subjects: Virtual bond representation Coordination number Contact maps Sidechain packing: is it an instrumental way of selecting and consolidating a fold? ASA of proteins Interatomic distances for hard sphere... PDB

2 Virtual bond representation

3 Virtual bond representation of the protein backbone. Dotted lines are the virtual bonds connecting successive α-carbons. This representation takes advantage of the planarity of the three successive backbone bonds, Cαi-1-Ci, Ci-Ni and Ni-Cαi corresponding to each amino acid. The lengths of the virtual bonds are fixed to the extent that the bond lengths and bond angles are fixed and the amide bond adheres to the trans conformation.

4 Interatomic Distances for Hard-sphere Potentials As used in Ramachandran plots {Ramachandran, Ramakrishnan, et al ID: 501}.

5 Atomic Interactions Strong bonded interactions b Non bonded interactions r U = K( b b ) 0 2 θ U = K( θ θ ) 0 2 U = A r 12 B r 6 q 1 q 2 φ U = K( 1 cos( nφ)) = q1q r U 2

6 One could also include soft potentials (attractions) to the hard sphere potentials the intrinsic torsional potentials of the respective bonds N-Cα and Cα- C. They are threefold symmetric with minima at trans, gauche+ and gauche- states. repulsive attractive ionic

7 Number distribution of virtual bond torsions NA(ϕi, ϕi+1) for A = Gly, and Pro.

8 Coupling between virtual bond torsion and bending angles. The surfaces represent the number distributions from 150 PDB structures, irrespective of residue type.

Amino acid sidechains prefer angles near their ideal rotational isomeric states In addition to φ and ψ angles, proteins also have freedom in the side chain

; Two examples, Trp and Lys, illustrating the definition of the torsion angles χ1, χ2, etc.

9 Amino acid sidechains prefer angles near their ideal rotational isomeric states In addition to φ and ψ angles, proteins also have freedom in the side chain rotational angles. Moving along the side chain away from the backbone defines carbons identified as Cβ, Cγ, etc., and rotational angles as χ1, χ2, etc.; Two examples, Trp and Lys, illustrating the definition of the torsion angles χ1, χ2, etc. of amino acid side chains in proteins, along with the labels α, β, γ δ, etc. assigned to successive atoms for distinguishing their position along the sidechain. Nitrogen atoms are shown in black. Backbone atoms are on the right end in each case.

Distribution of the χ1 sidechain torsion angles for amino acids in α-helical and β-sheet regions compiled from 150 high resolution protein structures.

11 Distribution of the χ1 sidechain torsion angles for amino acids in α-helical and β-sheet regions compiled from 150 high resolution protein structures. The ordinate represents the total number of observations for each interval of size χ1 = 100. Note the relatively low probability of the gauchestate (χ1 = 60 o) for side chains on α-helices.

12 Coordination number (z) defines the number of neighbors (nonbonded) on the first coordination shell Distance from the center of the residue 6.8 Å Z = 7 in the core Z is 4 on the surface Z is smaller in small size proteins

14 Contact maps Gives information about the structure of the protein

15 x 8 x x 7 x x 6 x x 5 x x 4 x x x 3 x x x 2 x x helix Antiparallel strand Parallel strand Residues i and j are in contact if distance between their alpha carbons is less than 7 A

16 Accesible surface areas (ASA)

17 (A) (B)

18 Hydrophobicity of proteins

19 Where do protein structures live: Protein Data Bank

20 Yearly added structures to PDB As of Tuesday Feb 28, 2006, there are Structures

25 Get the structure file

26 HEADER MICROTUBULES 23-SEP-97 1TUB TITLE TUBULIN ALPHA-BETA DIMER, ELECTRON DIFFRACTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUBULIN; COMPND 3 CHAIN: A, B; COMPND 4 BIOLOGICAL_UNIT: DIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGAN: BRAIN KEYWDS MICROTUBULES, ALPHA-TUBULIN, BETA-TUBULIN, GTPASE EXPDTA ELECTRON DIFFRACTION AUTHOR E.NOGALES,K.H.DOWNING REVDAT 3 18-NOV-98 1TUBB 3 HET REMARK TITLE HETATM REVDAT DBREF HEADER LINK SOURCE REVDAT KEYWDS HELIX REVDAT 2 21-OCT-98 1TUBA 3 REMARK HETATM CONECT LINK REVDAT 1 07-OCT-98 1TUB 0 JRNL AUTH E.NOGALES,S.G.WOLF,K.H.DOWNING JRNL TITL STRUCTURE OF THE ALPHA BETA TUBULIN DIMER BY JRNL TITL 2 ELECTRON CRYSTALLOGRAPHY JRNL REF NATURE V JRNL REFN ASTM NATUAS UK ISSN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.NOGALES,S.G.WOLF,K.H.DOWNING REMARK 1 TITL ERRATUM. STRUCTURE OF THE ALPHA BETA TUBULIN DIMER REMARK 1 TITL 2 BY ELECTRON CRYSTALLOGRAPHY REMARK 1 REF NATURE V REMARK 1 REFN ASTM NATUAS UK ISSN REMARK 1 REFERENCE 2 REMARK 1 AUTH E.NOGALES,K.H.DOWNING,L.A.AMOS,J.LOWE REMARK 1 TITL TUBULIN AND FTSZ FORM A DISTINCT FAMILY OF GTPASES REMARK 1 REF NAT.STRUCT.BIOL. V REMARK 1 REFN ASTM NSBIEW US ISSN REMARK 2 REMARK 2 RESOLUTION. 3.7 ANGSTROMS. REMARK 3

27 SEQRES 1 A 440 MET ARG GLU CYS ILE SER ILE HIS VAL GLY GLN ALA GLY SEQRES 2 A 440 VAL GLN ILE GLY ASN ALA CYS TRP GLU LEU TYR CYS LEU SEQRES 3 A 440 GLU HIS GLY ILE GLN PRO ASP GLY GLN MET PRO SER ASP SEQRES 4 A 440 LYS THR ILE GLY GLY GLY ASP ASP SER PHE ASN THR PHE SEQRES 5 A 440 PHE SER GLU THR GLY ALA GLY LYS HIS VAL PRO ARG ALA SEQRES 6 A 440 VAL PHE VAL ASP LEU GLU PRO THR VAL ILE ASP GLU VAL SEQRES 7 A 440 ARG THR GLY THR TYR ARG GLN LEU PHE HIS PRO GLU GLN SEQRES 8 A 440 LEU ILE THR GLY LYS GLU ASP ALA ALA ASN ASN TYR ALA SEQRES 9 A 440 ARG GLY HIS TYR THR ILE GLY LYS GLU ILE ILE ASP LEU SEQRES 10 A 440 VAL LEU ASP ARG ILE ARG LYS LEU ALA ASP GLN CYS THR SEQRES 11 A 440 GLY LEU GLN GLY PHE SER VAL PHE HIS SER PHE GLY GLY SEQRES 12 A 440 GLY THR GLY SER GLY PHE THR SER LEU LEU MET GLU ARG SEQRES 13 A 440 LEU SER VAL ASP TYR GLY LYS LYS SER LYS LEU GLU PHE SEQRES 14 A 440 SER ILE TYR PRO ALA PRO GLN VAL SER THR ALA VAL VAL SEQRES 15 A 440 GLU PRO TYR ASN SER ILE LEU THR THR HIS THR THR LEU SEQRES 16 A 440 GLU HIS SER ASP CYS ALA PHE MET VAL ASP ASN GLU ALA.... HET GTP A HET GDP B HET TXL B 1 58 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM TXL TAXOTERE FORMUL 3 GTP C10 H16 N5 O14 P3 FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 TXL C43 H53 N1 O14

28 HELIX 1 1 ALA A 12 LEU A HELIX 2 2 VAL A 74 ARG A HELIX 3 3 GLY A 111 ASP A HELIX 4 4 GLY A 146 TYR A HELIX 5 5 VAL A 182 THR A HELIX 6 6 ASN A 206 ARG A HELIX 7 7 THR A 225 THR A HELIX 8 8 LEU A 252 LEU A HELIX 9 9 VAL A 288 CYS A HELIX PRO A 325 THR A HELIX ALA A 385 LEU A HELIX PHE A 418 GLU A HELIX CYS B 12 VAL B HELIX THR B 74 ARG B HELIX GLY B 111 GLU B HELIX GLY B 146 TYR B HELIX VAL B 182 GLN B HELIX ASN B 206 ARG B HELIX GLY B 225 THR B HELIX LEU B 252 MET B HELIX VAL B 288 MET B HELIX MET B 325 ASN B HELIX GLN B 385 ALA B HELIX PHE B 418 GLN B SHEET 1 A 6 ILE A 93 LYS A 96 0 SHEET 2 A 6 ALA A 65 LEU A 70 1 N VAL A 66 O ILE A 93 SHEET 3 A 6 GLU A 3 HIS A 8 1 N CYS A 4 O ALA A 65 SHEET 4 A 6 GLY A 134 SER A N PHE A 135 O GLU A 3 SHEET 5 A 6 LYS A 166 ILE A N LEU A 167 O GLY A 134 SHEET 6 A 6 CYS A 200 VAL A N ALA A 201 O LYS A 166 SHEET 1 B 4 HIS A 266 ALA A SHEET 2 B 4 ARG A 373 ASN A N ALA A 374 O HIS A 266 SHEET 3 B 4 ALA A 314 ARG A N CYS A 315 O ARG A 373 SHEET 4 B 4 PHE A 351 ASN A N LYS A 352 O ALA A 314 SHEET 1 C 6 VAL B 93 GLN B 96 0 SHEET 2 C 6 ALA B 65 LEU B 70 1 N ILE B 66 O VAL B 93

29 ATOM 1 N MET A N ATOM 2 CA MET A C ATOM 3 C MET A C ATOM 4 O MET A O ATOM 5 CB MET A C ATOM 6 CG MET A C ATOM 7 SD MET A S ATOM 8 CE MET A C ATOM 9 N ARG A N ATOM 10 CA ARG A C ATOM 11 C ARG A C ATOM 12 O ARG A O ATOM 13 CB ARG A C ATOM 14 CG ARG A C ATOM 15 CD ARG A C ATOM 16 NE ARG A N ATOM 17 CZ ARG A C ATOM 18 NH1 ARG A N ATOM 19 NH2 ARG A N ATOM 20 N GLU A N ATOM 21 CA GLU A C ATOM 22 C GLU A C ATOM 23 O GLU A O ATOM 24 CB GLU A C ATOM 25 CG GLU A C ATOM 26 CD GLU A C ATOM 27 OE1 GLU A O ATOM 28 OE2 GLU A O ATOM 29 N CYS A N ATOM 30 CA CYS A C ATOM 31 C CYS A C ATOM 32 O CYS A O ATOM 33 CB CYS A C ATOM 34 SG CYS A S

31 Sequence information

32 >1TUB:A PDBID CHAIN SEQUENCE MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRT GTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVD YGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYR GDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYA KRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSV >1TUB:B PDBID CHAIN SEQUENCE MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVPRAILVDLEPGTMDSVRSGP FGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYP DRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGR MSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTG EGMDEMEFTEAESNMNDLVSEYQQYQD

33 Looking at Protein Structures Quick and dirty Rasmol Chime Cn3D (NCBI) More powerful Swiss PDB Viewer, PyMol (free! Many platforms) Insight, Quanta ($$$, nice interface, powerful) Publication quality graphics, but not easy to manipulate Molscript/Raster3D Chimera Midas VMD

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