Post-genomic Revolution in Life Sciences

15 maggio 2015 1

Neri Niccolai

Dipartimento di Biotecnologie, Chimica e Farmacia

Università degli Studi di Siena

Post-genomic Revolution

in Life Sciences

15 maggio 2015 2

α haemolisin

from staphylococcus aureus

20,324 atoms 2,051 amminoacidi

Protein structure and dynamics…

Something good for Engineers!

Neri Niccolai

Dipartimento di Biotecnologie, Chimica e Farmacia

Università degli Studi di Siena

15 maggio 2015 3

A journey around Life Sciences?

http://it.wikipedia.org/wiki/Legge_di_Moore

15 maggio 2015 4

100100101101101001000100100101001101100100101101101001000100 101001000100101110001010100101001101100100101101101001000100

101110001010100101001101100101001101100100101101101001000100 100101001101100100101101101001000100100100101101101001000101

A journey around Life Sciences?

Meeting point @ Genome data banks !

15 maggio 2015 5

A journey around Life Sciences?

Meeting point in Genome data banks !

15 maggio 2015 6

UniProtKB/TrEMBL: la banca dati delle sequenze di amminoacidi delle proteine individuate genomicamente

Il primo aprile 2015 UniProtKB conteneva la sequenza di 46.714.516 proteine diverse, comprendenti 15.391.501.940 amminoacidi (lunghezza media 329 aa)

15 maggio 2015

From protein sequences to 3D structures

3 experimental techniques to solve molecular structures

X-ray diffraction

1a structure: 1957 deposited in PDB in 1972

Cryo-electronic microscopy

1a structure: 1996 deposited in PDB in 1996

Nuclear Magnetic Resonance Spectroscopy

(NMR)

1a structure: 1985 deposited in PDB in 1988

7

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Protein Data Bank: the only Bank you can rely on

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pdb files: a structural treasure

to be parsed around!

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Databanks New tools +

New insights = ?

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Protein Data Bank: the only Bank you can rely on

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Protein Data Bank: the only Bank you can rely on

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Protein Data Bank: the only Bank you can rely on

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a database of protein singles

In PDB, as of Tuesday May 7, 2013 at 5 PM PDT there are 90,424 Structures Experimental Method: X-RAY (79,770)

Chain Type: Protein (74,456)

Only 1 chain in asym. unit: (28,803) Oligomeric state: 1 (21,193)

Number of Entities: 1 (3,517)

Homologue Removal @ 95% identity (2,410)

2,410 proteins in the dataset 4,657,574 atoms 589,383 residues

0 2 4 6 8 10 12

DOOPS:

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a database of protein singles

2,410 proteins in the dataset 4,657,574 atoms 589,383 residues

DOOPS:

0 2 4 6 8 10 12

Swiss-Prot: 540,052 proteins in the dataset (191 Maa)

0 1000 2000

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Databanks New tools +

New insights = ?

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protein folding Birth of the Earth

Digging inside objects to discover their origins

3D atom depth analysis

Depth index analysis

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atom depth analysis

Atom depth * = atom distance from molecular surface.

* Chakravarty,S. and Varadarajan,R.

(1999) Residue depth: a novel parameter for the analysis of protein structure and

stability. Structure Fold. Des., 7, 723–

732

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atom depth analysis 3D

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Depht index defined as:

exposed volume sphere volume

A0 r

atom depth analysis 3D

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r r i r

i V

D V

, 0

, ,

 2

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3D atom depth analysis

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3D atom depth analysis

1UBQ PDB_SADIC file Di 1UBQ PDB file B

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N 0.19 CA 0.30 C 0.25 O 0.23 CB 0.50 CG 0.68 CD 0.91 CE 1.11

K63

N 0.38 CA 0.52 C 0.50 O 0.52 CB 0.76 CG 0.95 CD 1.17

E24

3D atom depth analysis

N 0.10 CA 0.05 C 0.11

CB 0.02 CG 0.02 CD1 0.02 CD2 0.00

L43

Dima x

Dima x Dima x

from PDB ID 1UBQ

http://www.sbl.unisi.it/prococoa/

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Ln Di % atoms color L0 < 0.2 17,9 violet L1 0.2 - 0.4 17,1 indigo

L2 0.4 -0.6 17,7 blue

L3 0.6 –

0.8

17,4 green

L4 0.8 –

1.0

14,4 yellow

L5 1.0 –

1.2

9,4 orange

L6 > 1.2 5,7 red

L0 L1 L2 L3 L4 L5 L6

Dimax analysis of protein singles

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Ln Di % atoms color L0 < 0.2 17,9 violet L1 0.2 - 0.4 17,1 indigo

L2 0.4 -0.6 17,7 blue

L3 0.6 –

0.8

17,4 green

L4 0.8 –

1.0

14,4 yellow

L5 1.0 –

1.2

9,4 orange

L6 > 1.2 5,7 red

L0

L6

Dimax analysis of protein singles

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Dimax analysis of protein singles

0 2 4 6 8 10

12

DOOPS: all structural layers from 3,515 pdb

%

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Databanks New tools +

New insights = ?

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L0

L6

Dimax analysis of protein singles

protein folding protein – protein

interactions

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Post-genomic Era and System Biology

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Brownian Dynamics simulation of protein motion inside E. coli cell (1,109 molecules selected from

51 different kinds of proteins and RNA

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A caccia di tasche sulla superficie proteica:

una ricerca complessa...

0 10 20 [ns] 30

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A screeshot of PSTP-Finder results window. Histograms refer to the surface pockets found during a 50 ns MD from 1QG7 PDB file

discovering disruptors of

protein-protein interactions

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discovering disruptors of protein-protein interactions

:O

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discovering disruptors of protein-protein interactions

:O

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Codon codes assigned by

chance?

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/ 45 Release 2015_04 of 01-Apr-15 of UniProtKB/Swiss-Prot contains

548,208 sequence entries, comprising 195,282,524 amino acids

Ala (A) 8.26 Gln (Q) 3.93 Leu (L) 9.66 Ser (S) 6.58 Arg (R) 5.53 Glu (E) 6.74 Lys (K) 5.83 Thr (T) 5.34 Asn (N) 4.05 Gly (G) 7.08 Met (M) 2.41 Trp (W) 1.09 Asp (D) 5.46 His (H) 2.27 Phe (F) 3.86 Tyr (Y) 2.92 Cys (C) 1.37 Ile (I) 5.94 Pro (P) 4.71 Val (V) 6.87

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6

6

6 4

4 4 2

3 2 2 4

2 2 2 2

2 1 2

2 1

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The frequencies of DNA bases in human genome (NT 46.742.881) are:

A: 24.54 %; T: 26.39 %; C: 24.27 %; G: 24.79 %

The expected frequency of a particular codon can then be calculated by multiplying the frequencies of each DNA base comprising the codon. The expected frequency of the amino acid can then be calculated by adding the frequencies of each codon that codes for that amino acid.

As an example, the RNA codons for tyrosine are UAU and UAC, so the random expectation for its frequency is (26.39)(24.54)(26.39) + (26.39)(24.54)(24,27) = 32,807.952996

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0 2 4 6 8 10 12

0 2 4 6 8 10 12

SWISS Prot Codoni

S L R

E K

C A

D P

expected codon frequency vs SwissProt_amino acid frequency

expected trend*

* (0.25)3 x (64-3)/20 = 4.76 x 10- 2

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0 2 4 6 8 10

12

amino acid frequency @ proteina-DNA interface (from 209 pdb files)

0 2 4 6 8 10 12

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2.3 Å

2.5 Å

hydrophilic plug

hydrophobic plug

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4YCP

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Lys

Lys NZ

Arg

Arg NH1 + NH2

Leu

DNA P

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Lys

Lys NZ

Arg

Arg NH1 + NH2

Leu

DNA P

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4QVI

Lys NZ RNA O1 + O2 Arg NH1 + NH2

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enjoy structural

Bioinformatics!

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one swallow

doesn't make a

summer