Proteins Structure Predictions Structural Bioinformatics

Reminder Final date to chose a project 10.1 Submission project overview (one page) -Title -Main question -Major Tools you are planning to use to answer the questions 11.1 /18.1– meetings on projects 9.3 Poster submission 16.3 Poster presentation

3 In there were 114,402 protein structures in the protein structure database. Was solved in 1958 by Max Perutz John Kendrew of Cambridge University. (Won the 1962 and Nobel Prize in Chemistry ) The first high resolution structure of a protein-myoglobin

The 3D structure of a protein is stored in a coordinate file Each atom is represented by a coordinate in 3D (X, Y, Z)

The coordinate file can be viewed graphically RBP

6 Predicting the three dimensional structure from sequence of a protein is very hard (some times impossible) However we can predict with relative high precision the secondary structure MERFGYTRAANCEAP…. What can we do to bridge the gap?? >10,000,000>100,000

What do we mean by Secondary Structure ? Secondary structure are the building blocks of the protein structure: =

8 What do we mean by Secondary Structure ? Secondary structure is usually divided into three categories: Alpha helix Beta strand (sheet) Anything else – turn/loop

9 The different secondary structures are combined together to form the Tertiary Structure of the Proteins

10 RBP Globin Tertiary Secondary ? ? ?

Secondary Structure Prediction Given a primary sequence ADSGHYRFASGFTYKKMNCTEAA what secondary structure will it adopt (alpha helix, beta strand or random coil) ? 11

12 Secondary Structure Prediction Methods Statistical methods –Based on amino acid frequencies –HMM (Hidden Markov Model) Machine learning methods –SVM, Neural networks

13 Chou and Fasman (1974) Name P(a) P(b) P(turn) Alanine Arginine Aspartic Acid Asparagine Cysteine Glutamic Acid Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine The propensity of an amino acid to be part of a certain secondary structure (e.g. – Proline has a low propensity of being in an alpha helix or beta sheet  breaker) Not very useful for predictions Statistical Methods for SS prediction

What is missing? 14

15 HMM enables us to calculate the probability of assigning a sequence to a specific secondary structure TGTAGPOLKCHIQWML HHHHHHHLLLLBBBBB p = ? HMM (Hidden Markov Model) An approach for predicting Secondary Structure considering dependency between the position

16 The probability of observing a residue which belongs to an α-helix followed by a residue belonging to a turn = 0.15 The probability of observing Alanine as part of a β- sheet Table built according to large database of known secondary structures α-helix followed by α-helix Beginning with an α- helix

Example What is the probability that the sequence TGQ will be in a helical structure?? TGQ HHH p = 0.45 x x 0.8 x x 0.8x = What can we learn from secondary structure predictions??

csc Mad Cow Disease PrP c to PrP sc PRP c PRP sc

Predicting 3D Structure based on homology Comparative Modeling/homology modeling Similar sequences suggests similar structure

Sequence and Structure alignments of two Retinol Binding Protein

How do we evaluate structure similarity?? Structure Alignment

Structure Alignments The outputs of a structural alignment are a superposition of the atomic coordinates and a minimal Root Mean Square Distance (RMSD) between the structures. There are many different algorithms for structural Alignment.

Atoms in Protein V Atoms in Protein W Atom N (x, y, z) The RMSD of two aligned structures indicates their divergence from one another. Low values of RMSD mean similar structures

24 Different sequences can result in similar structures 1ecd2hhd RMSD<1

25 We can learn about the important features which determine structure and function by comparing the sequences and structures ?

26 The Globin Family

27 Why is Proline 36 conserved in all the globin family ?

28 Where are the gaps?? The gaps in the pairwise alignment are mapped to the loop regions

29 How are remote homologs related in terms of their structure? b-lactoglobulin RBD

30 PSI-BLAST alignment of RBP and  -lactoglobulin: iteration 3 Score = 159 bits (404), Expect = 1e-38 Identities = 41/170 (24%), Positives = 69/170 (40%), Gaps = 19/170 (11%) Query: 3 WVWALLLLAAWAAAERD CRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQ 54 V L+ LA A + S V+ENFD ++ G WY + K Sbjct: 1 MVTMLMFLATLAGLFTTAKGQNFHLGKCPSPPVQENFDVKKYLGRWYEIEKIPASFE-KG 59 Query: 55 DNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQ I A +S+ E G + K V PAK Sbjct: 60 NCIQANYSLMENGNIEVLNKELSPDGTMNQVKGE--AKQSNVSEPAKLEVQFFPL Query: 115 KGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEA 164 +WI+ TDY+ YA+ YSC + ++ R+P LPPE Sbjct: 113 MPPAPYWILATDYENYALVYSCTTFFWL--FHVDFFWILGRNPY-LPPET 159

31 The Retinol Binding Proteinb-lactoglobulin

32 MERFGYTRAANCEAP…. Taken together FUNCTION

Comparative Modeling Builds a protein structure model based on its alignment (sequence) to one or more related protein structures in the database Similar sequence suggests similar structure

Comparative Modeling General algorithm Modeling of a sequence based on known structures Consist of four major steps : 1.Finding a known structure(s) related to the sequence to be modeled (template), using sequence comparison methods such as PSI-BLAST 2. Aligning sequence with the templates 3. Building a model 4. Assessing the model

Comparative Modeling Accuracy of the comparative model is usually related to the sequence identity on which it is based >50% sequence identity = high accuracy 30%-50% sequence identity= 90% can be modeled <30% sequence identity =low accuracy (many errors) However other parameters (such as identify length) can influence the results

What is a good model? ModBase- for homology modelling

What is a good model?

Extra Slides (for your interest) 39

residues 5.6 Å Alpha Helix : Pauling (1951) A consecutive stretch of 5-40 amino acids (average 10). A right-handed spiral conformation. 3.6 amino acids per turn. Stabilized by Hydrogen bonds

41 Beta Strand : Pauling and Corey (1951) > An extended polypeptide chains is called β –strand (consists of 5-10 amino acids > The chains are connected together by Hydrogen bonds to form b-sheet β -strand β -sheet

42 Loops Connect the secondary structure elements (alpha helix and beta strands). Have various length and shapes.