Molecular modeling of protein-ligand interactions: Detailed simulations of a biotin-streptavidin complex

Prof. Terry P. LybrandVanderbilt University

Center for Structural Biology &Departments of Chemistry and Pharmacology

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Streptavidin

• Protein isolated from Streptomyces species

• Binds biotin with extremely high affinity

• Tetramer - ~500 amino acids

• One biotin binding site per monomer

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Biotin

HN

NH

SO

CO2-

• One of the B-complex vitamins

• Necessary for CO2 addition reactions in biosynthesis

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

General Strategy

• Protein engineering

• Microcalorimetry

• X-ray crystallography

• Molecular simulation

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Molecular Dynamics

€

Fi = mia i = mi

∂ri

∂t 2; i = 1,N

Fi = -∂

∂ri

V r1, r2, ...,rN( )

• • AMBER version for distributed parallel computationAMBER version for distributed parallel computation (Swanson & Lybrand, (Swanson & Lybrand, J. Comput. Chem.J. Comput. Chem. 1616:1131-40 (1995):1131-40 (1995)

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Potential Function

V r1, r2, ..., rN( ) = 12

Kb R- R0( )bonds∑

2

+ 12

Ka θ -θ0( )angles∑

2

+ Kd 1+cosnφ-γ( )[ ]dihedrals∑

+ A ij

rij

⎛

⎝ ⎜

⎞

⎠ ⎟

12

- Cij

rij

⎛

⎝ ⎜

⎞

⎠ ⎟

6

+ qiqj

rij

⎡

⎣ ⎢

⎤

⎦ ⎥

i, j∑

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Potential of Mean Force

rc is a reaction coordinate that defines a physical path for the process of interest

W rc( ) =−kBTlnρ r( )

P : L → P + L

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Calculated vs. Measured Free Energies (Kcal/mol)

PMF Expt.*

G˚ 17.0 ± 3.0 18.3 ± 1.0 (H˚ = 24.5 ± 0.5; TS = 6.2 ± 0.5)

G‡ 22.0 ± 3.0 24.4 ± 2.4 (H‡ = 32.0 ± 2.1; TS‡ = 7.6 ± 2.1)

*Chilkoti & Stayton, J. Am. Chem. Soc. 117:10622-8 (1995)

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Freitag, Chu, Penzotti, Klumb, To, Le Trong, Lybrand, Stenkamp, & Stayton Proc. Natl. Acad. Sci. USA 96:8384-8389 (1999)

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Hyre, Amon, Penzotti, LeTrong, Stenkamp, Lybrand, & Stayton Nature Struct. Biol. 9:582-585(2002)

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

QuickTime™ and a decompressor

are needed to see this picture.

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Conclusions

• Detailed simulations can reproduce quantitatively the experimental thermodynamic results

• Contributions of specific protein residues to net thermodynamic changes can be characterized

• Simulations can provide detailed insight into dynamics of complex formation and dissociation

• Specific water molecules may play a crucial role in complex formation and in stabilization of intermediates on the dissociation reaction coordinate

• Streptavidin appears to have evolved a “back door” water channel, possibly to facilitate solvent evacuation of the binding site during complex formation

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003

Dr. Julie E. PenzottiDr. Lynn AmonDr. David HyreDr. Stephanie FreitagDr. Lisa KlumbDr. Richard ToDr. Ashok ChilkotiVano ChuIsolde LeTrong

Prof. Patrick StaytonProf. Ronald Stenkamp

NIH NS33290NIH DK49655NIH AI44609NIH GM56307NSF MCB9405405

ZymoGenetics

T. P. Lybrand SURA 2003T. P. Lybrand SURA 2003