intramolecular interactions in globular proteins

17

Upload: boris-fackovec

Post on 15-Jul-2015

109 views

Category:

Science


2 download

TRANSCRIPT

Intramolecular Interactions in Globular Proteins

Boris Fa£kovec

Advisor: RNDr. Ji°í Vondrá²ek, CSc.

Katedra fyzikální a makromolekulové chemie

P°írodov¥decká fakulta UK

21st December 2011

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 1 / 17

Introduction - physical studies of proteins

Sequence-structure-stability-function relationships in globular proteins -central to biochemistry

1931 �rst theory of protein denaturation (Wu)

1958 statistical thermodynamics of polymers (Zimm)

1958 �rst resolved protein X-ray structure (Kendrew)

1961 An�nsen's experiments

1977 �rst protein simulation (Karplus)

1983 Go model

80's-90's intensive development of force �elds (Kollman, Jorgensen)

1985 knowledge-based force �elds (Jernigan, Miyazawa)

90's - extensive calorimetric (DSC) studies (Privalov, Makhatadze)

Denatured state investigations (Shortle)

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 2 / 17

Introduction - recent development

1993 sidechain atlas (Thornton)

90's lattice simulations (Shakhnovich)

1995 energy landscape perspective (Bryngelson, Onuchic)

1995 First force �eld decomposition of interactions (Lazaridis)

2000 Variational theory, spin glasses, principle of minimal frustration(Wolynes)

2005 stabilization of rubredoxin by strong dispersion interactions in itscore (Vondrasek)

2008 identifying stabilizing residues by IEM calculations(Biedermannova)

2010 IEM development - fragmentation and QM calculations ofprotein molecules (Berka)

2010 FF calculations surprisingly good agreement with benchmark QM(Kolar)

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 3 / 17

Introduction - Interaction energy matrix (IEM)

Fragmentation of a protein native structureQM calculationsClassi�cation of fragments - backbone BB, sidechain charged CH,polar PO, non-polar NPPair additivity!

Figure: Interaction energy matrix of backbone-backbone interactions for a shortpeptide

`interaction' = inter-residual non-covalent interaction in single structureBoris Fa£kovec ([email protected]) Protein modeling 21st December 2011 4 / 17

Introduction - Types of intramolecular interactions

Charged ion-ionI high values of IEs in IEMs not in correspondence with real stabilization

e�ectI high compensation of attractive and repulsive interactionsI high compensation of interactions in native and unfolded stateI exceptionally high enthalpic-entropic compensation

Charged multipoles

Backbone

van der Waals, stackingI short ranged - small compensation inI always attractive - small compensationI probably undervalued in IEMsI hydrophobic residues burial - folding driving force

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 5 / 17

Introduction - Objectives

Characterization of magnitudes and distributions of inter-residualnon-covalent interaction energies

Development of uni�ed in silico treatment - solution to problems withcharged residues

Decomposition of stabilizing energy

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 6 / 17

Methods

Structure set selection - X-ray resolution <2 Å, single-stranded, noligands → 1358 structures

Optimization of hydrogen atoms - GROMACS, OPLS FF

Fragmentation and IEM calculation → 10 IEMs

Terminal backbones not considered,

HIS double protonated → charged residue

Only interactions with IE<-0.05 kcal/mol or IE>0.05 kcal/mol weresampled

Subsets - size and secondary structure content

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 7 / 17

Results - Residue interaction energy distributions

0

0.2

0.4

0.6

0.8

1

-25 -20 -15 -10 -5 0 5 10

BB

0

0.2

0.4

0.6

0.8

1

-80 -60 -40 -20 0 20 40 60

BBCH

0

0.2

0.4

0.6

0.8

1

-25 -20 -15 -10 -5 0 5 10 15 20

BBNP

0

0.2

0.4

0.6

0.8

1

-25 -20 -15 -10 -5 0 5 10

BBPO

0

0.2

0.4

0.6

0.8

1

-250 -200 -150 -100 -50 0 50 100 150

CHCH

0

0.2

0.4

0.6

0.8

1

-100 -80 -60 -40 -20 0 20 40 60

CHNP

0

0.2

0.4

0.6

0.8

1

-50 -40 -30 -20 -10 0 10 20 30

CHPO

0

0.2

0.4

0.6

0.8

1

-20 -15 -10 -5 0 5

NPNP

0

0.2

0.4

0.6

0.8

1

-10 -8 -6 -4 -2 0 2 4

PONP

0

0.2

0.4

0.6

0.8

1

-6 -5 -4 -3 -2 -1 0 1 2 3

POPO

0.15

0.2

0.25

0.3

0.35

0.4

0.45

0.5

0.55

-15 -14 -13 -12 -11 -10

BB

Figure: Distribution of RIE for all types of interactions. Various curves representsecondary structure particular classes.

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 8 / 17

Results - Domain size in globular proteins

E =

{ED(1− kN

13 ) N ≤ ND

E = ED N ≥ ND

(1)

-4

-3.5

-3

-2.5

-2

-1.5

-1

50 100 150 200 250 300

avera

ge R

IE / [kcal/m

ol]

protein chain length

NPNP calculated

model

Figure: Average RIE - size dependence of NPNP interactions}HCIE of BB-BBinteractions.

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 9 / 17

Results - Interaction energy distributions

number of contacts increases immensely with decreasing IE de�nition,diverges to ∞ at IE=0Cumulative distribution of contributions to sum of IEs (DCIE) and itsderivative (HCIE)

0.2

0.4

0.6

0.8

1

1.2

1.4

-4 -3 -2 -1 0 1 2

DC

IE

IE / [kcal/mol]

Figure: Cumulative distribution curve for IE of SER-TYR pair. BIE is the value ofthe interaction energy where the curve intersects 1 for the �rst time (-0.32kcal/mol), BIE0.5 is the value where it intersects 0.5 (-1.58 kcal/mol).

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 10 / 17

Results - Interaction energy distributions

Random energy model:

HCIE = IE

(a0e

−(IE

σ0

)2+

t∑i=1

aie−(IE−IEi

σi

)2)(2)

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

-7 -6 -5 -4 -3 -2 -1 0

HC

IE

IE / [kcal/mol]

Figure: HCIE of BB-BB interactions. Red line represents calculated data, greenline represents �t using 8 Gaussians.

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 11 / 17

Results - Optimum de�nition of interresidual contact basedon interaction energy matrix calculations

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

-7 -6 -5 -4 -3 -2 -1 0

BB-BB

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

-30 -25 -20 -15 -10 -5 0

BB-CH

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

-8 -7 -6 -5 -4 -3 -2 -1 0

BB-PO

0

0.2

0.4

0.6

0.8

1

1.2

1.4

1.6

1.8

-5 -4 -3 -2 -1 0

BB-NP

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

-140 -120 -100 -80 -60 -40 -20 0

CH-CH

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

0.18

-25 -20 -15 -10 -5 0

CH-PO

0

0.02

0.04

0.06

0.08

0.1

0.12

0.14

0.16

-10 -8 -6 -4 -2 0

CH-NP

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

-4 -3.5 -3 -2.5 -2 -1.5 -1 -0.5 0

PO-PO

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

0.45

-3 -2.5 -2 -1.5 -1 -0.5 0

PONP

0

0.05

0.1

0.15

0.2

0.25

0.3

0.35

0.4

-2.5 -2 -1.5 -1 -0.5 0

NPNP

Figure: Contact de�nitions from HCIE curves for each type of interaction

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 12 / 17

Results - Optimum contact de�nitions and their protperties

Table: compens = ratio of the sum of all negative IEs to the sum of all IEs.Columns 3�6 show the order contributions of a particular type of interaction to aparticular fragment type. x(BIEx) is the ratio of the energy content of theproductive and all the interactions.

IE type CD BBCO CHCO POCO NPCO BIE compens x(BIEx)

BBBB -1.6 1.08 -0.28 1.14 0.72BBCH -10 0.09 0.32 -3.5 4.04 0.39BBPO -3 0.1 0.37 -0.4 1.26 0.28BBNP -1.8 0.07 0.15 -0.1 1.05 0.08CHCH -82 0.16 -69 11.7 0.81CHPO -12 0.1 0.11 -4 3.03 0.47CHNP -3 0.16 0.1 -1.37 2.5 0.44POPO -0.8 0.33 -0.5 1.29 0.9PONP -0.4 1.44 0.82 -0.1 1.06 0.82NPNP -0.3 1.48 -0.19 1.09 0.96

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 13 / 17

Conclusion

RIE characterized by magnitudes and distributions

No correlation between sidechain IEs and secondary structure content

Typical one-domain protein length - 110 residues

Random energy model can be very successfully applied for IE statistics

Compensation of positive and negative interactions characterized

Contact de�nitions for each type of IEs → contact orders 1.34 for BB,0.74, 2.25 and 2.56 for the CH, PO and NP sidechains

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 14 / 17

Future directions

Web application on IOCB's site - IEM calculation, contact matrix

Hydrophobic core de�nition - clusters in contact graphs

Scaling factors → energy functions

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 15 / 17

References

�Decomposition of Intramolecular Interactions Between Amino-Acidsin Globular Proteins - A Consequence for Structural Classes ofProteins and Methods of Their Classi�cation�, Fackovec B andVondrasek J, 2011, chapter 20, �Systems and Computational Biology -Molecular and Cellular Experimental Systems�

�Optimal de�nition of inter-residual contact in globular proteins basedon pairwise interaction energy calculations�, Fackovec B andVondrasek J, Bioinformatics, submitted

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 16 / 17

Acknowledgement

Ji°í Vondrá²ek Ji°í Vym¥tal Karel BerkaJi°í Kysilka

Boris Fa£kovec ([email protected]) Protein modeling 21st December 2011 17 / 17