mandatory to put some order in such a vast wealth of structural

knowledge 14. Nucleic acids and proteins in one and more dimensions - second part

Taxonomy (from Ancient Greek: τάξις taxis, "arrangement," and -νομία -nomia,

"method") is the science of defining groups of biological organisms on the basis of

shared characteristics and giving names to those groups. Organisms are grouped

together into taxa (singular: taxon) and given a taxonomic rank; groups of a given rank can be aggregated to form a super group of higher rank and thus create a

taxonomic hierarchy.

24. Nucleic acids and proteins in one and more dimensions - second part

Learning from Biology

34. Nucleic acids and proteins in one and more dimensions - second part

Learning from Biology

44. Nucleic acids and proteins in one and more dimensions - second part

protein structure taxonomy

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protein structure taxonomy

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protein structure taxonomy

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protein structure taxonomy

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protein structure taxonomy

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protein structure taxonomy

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protein structure taxonomy

red: mainly αgreen: mainly βyellow: αβblue: low content of secondary structures

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protein structure taxonomy

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protein structure taxonomy

from http://www.proteinstructures.com/Structure/Structure/protein-fold.html

most of different protein

folds have been

already found?

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comparing protein structure

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comparing protein structure

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comparing protein structure

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1898 proteins representative of the most common fold

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3. genome analysis

Structural genomics

0101#01001010#10111010#01010001#10010#1001#10110010#100100100101011#0

DNA

Algorithm

Residue

THR 0.0 147.7 172.9

THR 107.2 -125.3 187.4

CYS 123.4 63.6 103.7

PRO 60.3 83.9 -116.7

Protein Structure

X Ray

diff

ract

ometr

y

NMR

cryo-electron tomography

18

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from structural knowledge to structural predictions

secondary structure prediction

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secondary structure prediction

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CHOU & FASMANChou, P.Y. & Fasman, G.D. (1974). Biochemistry, 13, 211-222.

secondary structure prediction

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secondary structure prediction

# residues in window: 6

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secondary structure prediction

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secondary structure prediction

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secondary structure prediction

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secondary structure prediction

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secondary structure prediction

PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST).

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secondary structure prediction

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secondary structure prediction

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4. Nucleic acids and proteins in one and more dimensions - second part

31

Sequence Alignment

“Two homologous sequences whisper ... a full multiple alignment shouts out loud.” in Hubbard TJ, Lesk AM, Tramontano A. Gathering them in to the fold. Nat Struct Biol. 1996 Apr;3(4):313.)

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334. Nucleic acids and proteins in one and more dimensions - second part

344. Nucleic acids and proteins in one and more dimensions - second part

Letters corresponding to isolated matches are shown in non-bold type. The longest matching regions, shown in boldface, are the first and last names DOROTHY and HODGKIN. Shorter matching regions, such as the OTH of dorOTHy and crowfoOTHodgkin, or the RO of doROthy and cROwfoot, are noise.

Dotplot showing identities between the palindromic sequence MAX I STAY AWAY AT SIX AM and itself. The palindrome reveals itself as a stretch of matches perpendicular to the main diagonal.

Dotplot showing identities between a repetitive sequence (ABRACADABRACADABRA) and itself. The repeats appear on several subsidiary diagonals parallel to the main diagonal.

From Introduction to Bioinformaticsby Arthur M. Lesk

dotplotThe dotplot is a simple picture that gives an overview of the similarities between two sequences. Less obvious is its close relationship to alignments.The dotplot is a table or matrix. The rows correspond to the residues of one sequence and the columns to the residues of the other sequence. In its simplest form, the positions in the dotplot are left blank if the residues are different, and filled if they match. Stretches of similar residues show up as diagonals in the upper left-lower right (Northwest-Southeast) direction.

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BLOSUM62 matrix does an excellent job detecting similarities in distant sequences, and this is the matrix used by default in most recent alignment applications such as BLAST

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Mutation probability matrix for the evolutionary distance of 250 PAMs

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tertiary structure prediction

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tertiary structure prediction

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tertiary structure prediction

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teminates with >

Amino Acid Code Meaning

A Alanine

B Aspartic acid or Asparagine

C CysteineD Aspartic acidE Glutamic acidF PhenylalanineG GlycineH HistidineI IsoleucineK LysineL LeucineM MethionineN AsparagineO PyrrolysineP ProlineQ GlutamineR ArginineS SerineT ThreonineU SelenocysteineV ValineW TryptophanY Tyrosine

Z Glutamic acid or Glutamine

X any* translation stop

- gap of indeterminate length

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tertiary structure prediction

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tertiary structure prediction

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tertiary structure prediction

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Protein folding

ab initio calculations of protein structure

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MSSPQAPEDGQGCGDRGDPPGDLRSVLVTTV

ROSETTAFrammenti di 9 aa

Sceglie le strutture delle 25 sequenze più vicine

Ottimizzazione e Assemblaggio(Knowledge-based potential)

Metodo Assemblaggio di frammenti: Dividendo la sequenza in frammenti

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Rosetta Fragment Libraries

25-200 fragments for each 3 and 9 residue sequence window

Selected from database of known structures > 2.5Å resolution < 50% sequence identity

Ranked by sequence similarity and similarity of predicted and known secondary structure

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544. Nucleic acids and proteins in one and more dimensions - second part

554. Nucleic acids and proteins in one and more dimensions - second part

RNA structure prediction

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RNA structure prediction

Secondary structure of a telomerase RNAPrimary structure of RNA

Tertiary structure of RNA

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RNA structure prediction