Homework. A bit about the nature of the atoms of interest. Project. The role of electronega<vity

Transcription

1 Homework Why cited articles are especially useful. citeulike science citation index When cutting and pasting less is more. Project Your protein: I will mail these out this weekend If you haven t gotten from me see me. 2 A bit about the nature of the atoms of interest The role of electronega<vity More electroneg O < N < C < H Less electroneg When bonded atoms will electrons from a less electronega<ve atom; look at the dipolar residues and the amide backbone. This will be important for electrosta<c interac<ons - hydrogen bonds; pkas 6

2

3 Protein primary and secondary structure the backbone backbone

4 Derivation of secondary structure lengths from the rules for five protein topologies.

5 C >N C >N C2 >N6 C1 >N5 2'-341)+,+5.!(/!/'-+!(8!T$P!h!14(5:!.*+!*+4'G!1G'-!C.*+!Y3'.)*Z!(8!.*+!*+4'GD"!6*')*!,+15-!.*1.!.*+!/'-+!3+/!/+-'27+!'-!T$PX<$^!l!#$T!h$!!R+5)+"!8(/!+G1,34+"!15! =*+4'G!<[!h!4(5:! 6(742!)(5.1'5!%[!/+-'27+-$!! What s the pattern? Ci>Ni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move around not quite 120 +G1,34+!-*(65!'5!X.>1('!)*5)J"!.*+!*+4'G!'-!-1'2!.(!9+!$A%#.%$&#.2$!!! trace how you go around the helix! 8.&#!&#'!)P!('4.01'4!4#/8-!$=/7'5!!?#.4!'Q$A%9'!4#/84!$-!$A%#.%$&#.2!#'9.QK!8.&#! %/9$(!$-0!-/-@%/9$(!('4.01'4!/-!/%%/4.&'!4.0'45!!?#'!#'9.2$9!8#''9!.4!&$H'-!3(/A!$! _$7$!,%%9'&!8(.&&'-!=:!U08$(0!`5!IaY'.9!$-0!"#$(9'4!F5!](.4#$A!Cb-.7'(4.&:!/3! c.(>.-.$!.-!"#$(9/&&'47.99'k!c.(>.-.$e+! #&&%+VV2&.5.&25c.(>.-.$5UDbVd2A>VD'A/V8#''9V8#''9,%%5#&A95!! %T Gennis notice up-down-up-down Each side can have different properties All of the amino acids are on the outside 1f3c 31-50

6 the boxes show amino acids

7 Amino Acids One amino acid Building the peptide bond Rotation around bond - Ramachandran Size of amino acids Polarity of amino acids Ionization (pk s amino-acids.html) alpha helix, beta sheet types of residues in side vs. outside

8 H+ amino acids H+ Role of conjuga<on When a electrons are shared over more than 2 atoms the atoms will try to stay in a plane. This will be important for protein secondary structure. See Tyr, Phe, Trp AND the amide backbone. Petsco and Ringe H page no longer available Types of bonds Amino Acid Name 3-letter Code 1-letter Code Mass Surface Volume pk a pi Solubility Crystal Density [dalton] [Å 2 ] [Å 3 ] (sidechain) (at 25 C) [g/100g] (at 25 C) Alanine Ala A Arginine Arg R ~ Aspartic Acid Asp D Asparagine Asn N Cysteine Cys C very high - Glutamic Acid Glu E Glutamine Gln Q Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K very high - Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T very high - Tryptophan Trp W Tyrosine Tyr Y Valine Val V Find the biggest, and smallest residues; which are the most and least soluble?

9 Changing Classification of Amino Acids T C A G TTT Phe (F) TTC " TTA Leu (L) TTG " CTT Leu (L) CTC " CTA " CTG " T C A G TCT Ser (S) TCC " TCA " TCG " CCT Pro (P) CCC " CCA " CCG " ATT Ile (I) ACT Thr (T) ATC " ACC " ATA " ACA " ATG Met (M) ACG " GTT Val (V) GTC " GTA " GTG " GCT Ala (A) GCC " GCA " GCG " TAT Tyr (Y) TAC TAA Ter TAG Ter CAT His (H) CAC " CAA Gln (Q) CAG " AAT Asn (N) AAC " AAA Lys (K) AAG " GAT Asp (D) GAC " GAA Glu (E) GAG " TGT Cys (C) TGC TGA Ter TGG Trp (W) CGT Arg (R) CGC " CGA " CGG " AGT Ser (S) AGC " AGA Arg (R) AGG " GGT Gly (G) GGC " GGA " GGG " See if you can see properties are grouped Chloroplasts and Mitochondria have their own code substitution matrix for amino acids They scanned the BLOCKS database for very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds score for each of the 210 possible substitutions of the 20 standard amino acids. BLOSUM with high numbers are designed for comparing closely related sequences (wikipedia) They scanned the BLOCKS database for a very conserved regions of protein families (that do not have gaps in the sequence alignment) and then counted the relative frequencies of amino acids and their substitution probabilities. Then, they calculated a log-odds score for each of the 210 possible substitution pairs of the 20 standard amino acids. All BLOSUM matrices are based on observed alignments; they are not extrapolated from comparisons of closely related proteins like the PAM Matrices. Scores within a BLOSUM are log-odds scores that measure, in an alignment, the logarithm for the ratio of the likelihood of two amino acids appearing with a biological sense and the likelihood of the same amino acids appearing by chance.[2] The matrices are based on the minimum percentage identity of the aligned protein sequence used in calculating them.[2] Every possible identity or substitution is assigned a score based on its observed frequencies in the alignment of related proteins.[3] A positive score is given to the more likely substitutions while a negative score is given to the less likely substitutions. (wikipedia). Charged residues on surface Blue - Basic (positively charged) Red - Acidic (negative) Yellow non-polar; Green Polar; Cyan Polar backbone