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Skolan för Bioteknologi

Biokemi (17)

Nanobioteknologi (5)

Molekylär Bioteknik (30)

Bioprocess- teknologi (10)

Genteknologi (30)

Miljömikrobiologi (4)

Proteomik (45)

TeoretiskKemi (52)

Träbioteknik (25)

Stefan Ståhl (Skolchef)16 Professorer90 Forskarstuderanden44 Forskningsledare215 Anställda

Proteins in solution

Proteins in cellsProteins targetingstructures in vivo

Proteins in solution

Lipase B from Candida antarcticais a serine hydrolase belonging to the / hydrolase family with a central -sheetSurrounded by -helixes

Lipase B from Candida antarctica is very active and stable in most organic solvents

Candida antarctica lipase BCandida antarctica lipase B

The active site is deep in theproteinstructure

XET+GLLX complexXET+GLLX complex

XET+XXXGXXXG complexXET+XXXGXXXG complex

VISION :3D Visualisation + Haptic Arms

• Haptic arms for protein interaction and docking.

1 ns in real time – 10 ms in simulation time

-- Coarse Grain Modeling

Interface region

Multiple Length Scales

QM part ~ ~ 100 atoms

~ 400 electrons

MM part part > 1000 solute atoms> 1000 solute atoms > 10000 solvent atoms> 10000 solvent atoms

time evolution of time evolution of a mixed a mixed QM/MMQM/MM system.system.

Galactose oxidase

QM/MM

MMVery fast Transferability problemsNo chemical reactions

QMMM QMMM

QM Accurate physics/chemistryComputer resource intensive

•

Some bio-systems are very large (too large for full QM)

and catalyse complicated reactions

(no force field available) proteins >1000 atoms

solvent >10000 atoms active site ~ 100 atoms

Interface?

Hammerhead Ribozymes: A QM/MM study of the catalytic mechanism

Methodology:Methodology:(i)(i) Classical (Amber98) Classical (Amber98)

MD simulations (3-4 MD simulations (3-4 ns). Previous ns). Previous theoretical studies theoretical studies (Torres and Bruice (Torres and Bruice 2000) show 2000) show Near Near Attack ConformationsAttack Conformations (NAC) in 18% of (NAC) in 18% of simulation time (1.2 simulation time (1.2 ns).ns).11 NAC: 2’O-P-5’O > NAC: 2’O-P-5’O > 150 and 2’O-P < 3.25 150 and 2’O-P < 3.25 Å.Å.

(ii) NAC transfered to (ii) NAC transfered to QM/MM. Constrained QM/MM. Constrained dynamics along dynamics along different reaction paths different reaction paths to study reaction. to study reaction.

(1) (1) R.A. Torres and T.C. Bruice, J. Am. Chem. Soc. 122, 781 (2000).

Ion positions in the Domain V of a group II intron

Highly conserved region of group II introns (ribozymes).

DomainV plays critical role in excision (catalytic) activity.

Bulge and loop regions seen to be metal-ion binding sites.1

Experimental difficulties in revealing metal-ion binding sites in helical stems I and II.

Classical and QM/MM MD study of putative and crystallographic binding sites, and comparison with NMR/X-ray structures.Domain V

Group II intron

(1) R.K.O. Sigel and coworkers, Nature Struct. Biol. 7, 1111 (2000).