Molecular Modeling 2018

Transcription

1 Molecular Modeling 2018 A course about proteins protein language protein energy landscapes protein conformation protein evolution protein shape protein interactions

2 Administrative stuff Decide on office hours. (F ok?) Inspect the syllabus. Get a 3-button mouse. heck out the course website: Take notes.

3 1.1 What is Molecular modeling? The use of stereochemical and energetic information to predict conformations, interactions and dynamic behavior of a chemical system. 3

4 ow do you think? Are you a biologist or a chemist? Q: What determines the structure/ function of a protein? 1. Evolution -- protein sequences are selected for function. 2. Energy -- biochemical systems seek the lowest free energy state.

5 Bioinformaticist s view of a protein MSAIQASWPSGTEIAKYNFGTAEQDLPF KGDVLTIVAVTKDPNWYKAKNKVGREGIIPA NYVQKREGV A 1D sequence of amino acids. A character string. Biologist s view of a protein substrates, cofactors products A node in a signaling pathway. An enzyme.

6 Biochemist s view of a protein Branched linear heteropolymer of 20 monomer types. Sometimes disulfide cross-linked. Sometimes oligomeric. 6

7 A more accurate renderings. ompact (usually), flexible (maybe). as shape, charge.

8 To be a molecular modeler, you must think like a chemist, not a biologist. A protein is a covalent chain of chemical moieties, a spontaneously folding heteropolymer. It has shape and charge and flexibility. It s not just a gene product! 8

9 Amino acid states Free amino acid, solid phase R Zwitterionic form, aqueous, p7 R Polymer repeating unit ( residue ) R N 2 + N 3 N The chemical nature of the AA backbone depends on the context. Usually we are talking about AAs in the polymer (polypeptide) context.

10 the side chains The shape and chemical nature of these 20 side chains account for the folding and function of proteins.

11 Venn diagram of AA side chains Study this! Which AA s are found on the surface? In turns? In the core? 11 Based on a paper by W. Taylor.

12 Edman degradation: Why we call AAs residues Thin layer chromotography used to identify the PT-amino acid, product of the Edman degradation, a stain, or residue, on the plate. 12

13 peptide bond formation is dehydrating R 1 + N - R 2 + N 3 R 1 δ- N + N δ+ R 2 Rx is catalyzed by the ribosome.

14 the polypeptide backbone peptide bond R 2 N N R 1 N R 3 N Backbone atom names are N, -alpha and (or N,A,). xygen is also considered a backbone atom, though strictly speaking it is a side chain. All atoms in all amino acids have conventional atom names.

15 The Protein Data Bank (PDB) Go to Search for "1A2" Display PDB file (appears as plain text file) EADER, MPND, REMARK : reference information. ET, FRMUL, ETNAM : ligands, non-standard groups. ELIX, SEET, TURN : secondary structure elements. ATM : coordinates, names, numbering. ETATM : coordinates, names, numbering, for ET groups There is no explicit information about what atoms are bonded to what. (This is determined by distances and atom names.) No direct information about the formal or partial charges on atoms. (These are calculated by the force field.)

16 PDB ATM lines 1-6 keyword ATM ATM 1 N VAL A 101B DFR atom number atom name 17 altloc indicator Z-coordinate residue name 21 not used 22 chain identifier (optional) Y-coordinate residue number* 27 insertion code (optional) X-coordinate** not used B=Temperature factor ccupancy factor footnotes and labels * Usually, but not always, residues are numbered sequentially 1,2,3 etc. ften the numbering starts from a number other than 1. ** oordinates are in orthogonal angstroms by convention. May be converted to crystallographic coordinates using RYST lines. Mean square displacement <u 2 > is proportional to B: <u 2 > = B/(8π 2 )

17 In class exercise 1.1 Try Jmol lick on PDB image 3D View. rotate > drop-down hierarchical menu translate To install JML locally: Manual (very useful) jmol.sourceforge.net/docs shift + zoom 17

18 In class exercise 1.1 JML: Display an amino acid View 1A2.pdb in Jmol Right-click, select console lick on one of the displayed residues. onsole shows its residue number.! restrict nnn (where nnn is the residue number)! wireframe 0.4! label %a (%a shows atoms names, also try label %n, label %r)

19 ow to check L-amino acid chirality R α N The is toward you.. R. the RN crib N When an L-amino acid is drawn with the alpha- forward and the R-group in the back, the letters read clockwise spell RN. The orn rib is a good way to remember which side the R-group (i.e. sidechain) goes on.

20 atom names: tryptophan Z3 2 E3 Z2 rotatable single bonds D2 G E2 NE1 B D1 A PDB convention atom names follow the formula: <element><greek letter><alt posit> -bond acceptor : N polar A = Alpha arbon, B = Beta arbon, G = Gamma xygen, Delta.., Epsilon.., Zeta..,

21 ydrogen bonding holds it all together 2.8Å δ- donor δ+ Donor and acceptor both must be electronegative, usually N or : acceptor δ- Acceptor must have a free electron pair. ydrogen bonds are a linear arrangement of three atoms, two electronegative ( or N) and an electropositive hydrogen in the middle. The atoms are closer together than expected for a non-bonded interaction, but not close enough for a covalent interaction. In that sense, they exist in the limbo world between covalent and non-covalent interactions.

22 -bond stabilized backbone enol resonance structure. N δ- N N δ+ -bonds between backbone atoms define secondary structure like buttons on a shirt, in the sense that donors match acceptors like buttons to button-holes. δ+ These four atoms are arranged in a line, approximately. some orbital overlap δ- resonance double bonds

23 In class exercise 1.2 JML: Display hydrogen bonds To view the core beta sheet of 1A2:!select all!cartoon off!labels off!wireframe 0.30! restrict backbone and sheet! hbonds calculate! hbonds 0.25! color hbonds yellow

24 Protein flexibility is due to rotations around single bonds, backbone and side chain. xdi Torsion angles 4 atoms define two planes Angle atom1 atom2 atom3 atom4 Φ i-1 Ni Ai i Ψ Ni Ai i Ni+1 Ω Ai i Ni+1 Ai+1 Bi xgi χ2 χ1 χ1 i Ai Bi xgi χ2 Ai Bi xgi xdi χ = chi 4 Ai+1 Ni+1 Ω i Ψ Ai Φ Ni i

25 Measuring a torsion angle by eye -90 = Use the right-hand rule Positive torsion is in the direction of the fingers on the thumb-side of the rotation axis.

26 Ramachandran Plot maps allowable phi, psi regions Ramachandran used a physical model of dipeptides to determine the allowed (dark) and disallowed (white)combinations of phi and psi backbone angles. The observed frequencies roughly agree with R s allowed regions. Ramachandran & Sasisekharan (1968) non-glycine, non-proline allowed regions glycine allowed regions glycine, observed Ni+1 Bi Ai non-glycine, non-proline observed Ai+1 i Ψ Φ i-1 Ni 26

27 In class exercise 1.3!select all!cartoon off!spacefill off JML: phi-by-eye!labels off!wireframe 0.01!select gly!spacefill [click on one of the glycines. Residue number appears in console window. Select that residue and the one before it. For example, if you clicked gly183]!restrict !wireframe 0.2 [Line up your eye with the phi bond. Move back bone to 12-noon. What is the phi angle?]

28 Exercise 1.4: Draw all 20 amino acids A D E F G I K L M N P Q R S T V W Y Draw all AA s on one page. 1-letter alphabetical order. Write 3-letter and 1-letter abbreviations Use -chem style: line bonds + non-carbon elements. mit all s except -bond donors Draw a lone-pair : for -bond acceptors Mark chiral centers on Thr, Ile side chains. Draw side chain formal charges + or - on {DEKR} Label side chain chi (χ1, χ2, etc). Turn this page in at the beginning of next class.

29 INSTALL ME This week Get a 3-button mouse: Read elp->mouse... Familiarize yourself with the graphical user interface (GUI): elp-->tutorials-->getting Started..., then click on GUI Run first part of MoeTour (elp-->tutorials-->getting Started)

30 Review questions Is this course more of a biology course or more of a chemistry course? What is a residue? What is a position? What is a sequence? What atoms make up the polypeptide backbone? ow do I know an amino acid is L or D by looking at it? ow is a substitution matrix like a Venn diagram? What do we find in a PDB file? ow are amino acid side chain atoms named? What is a Rakmachandran plot? What is a hydrogen bond made of? ow do I measure a torsion angle? Is there any difference between a torsion angle and a dihedral angle? 30

31 Supplementary 31

32 an oft-forgotten genetically encoded non-canonical amino acid Selenocysteine (3-letter code Sec, one-letter code U) Se The presence of a selenocysteine insertion sequence, SEIS, signals the cell to translate UGA Stop codons with a special, modified trna. Initially charged with serine, Ser-tRNA(Sec) is then converted to Sec-tRNA(Sec) by selenocysteine synthase. Selenocysteine is not formed if no selenium (Se) is present, leading to translation stop. SEIS is located within the coding sequence (bacteria) or in the 3 -UTR (eukaryotes, archea). Walczak, R; Westhof E, arbon P, Krol A (1996). "A novel RNA structural motif in the 32 selenocysteine insertion element of eukaryotic selenoprotein mrnas". RNA 2:

33 Further reading

34 Two degrees of freedom per amino acid alpha carbon φ ψ the peptide bond ω does not rotate easily ne amino acid N α N α N α

35 Sidechain rotamers 1-4 interactions differ greatly in energy depending on the moieties involved. More later in the semester... N N N G A B A B G A B = = = G "m" "t" "p" -60 gauche 180 anti/trans +60 gauche