Scaling in Biomolecular Solvation Are Proteins Large?. Ray Luo Molecular Biology and Biochemistry University of California, Irvine. Different levels of abstraction: Approximations in Biomolecules. Quantum description: electronic & covalent structure
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Ray Luo
Molecular Biology and Biochemistry
University of California, Irvine
Mathematical models should be
as realistic as possible
Multiple trajectories, often as many as 10s to 100s, are needed
ru: solute coordinates; rv: solvent coordinates
Mathematical models should be
as realistic as possible
Dielectric
constant
Charge density

ep
Charge of salt ion in solution
+


Electrostatic potential
+
+
+

s
Wrep: Estimated with surface (SES/SAS) or volume (SEV/SAV)
Watt: Approximated by (D. Chandler and R. Levy)
Computational efficiency for alanine dipeptide
Are structureless implicit solvents sufficient?
D. Chandler, Nature, 437, 640647, 2005
3 Biomolecules10 Helix
αHelix
π Helix
How consistent are implicit and explicit solvents on conformation dependent energetics?Tan et al, JPCB, 110, 1868018687, 2006
ε= 80
Linearized PoissonBoltzmann Equation:
where
Atomic cavity radii are responsible for the desolvation penalties of amino acids and nucleotides.
Different cavity radii for PB solvents will result in different agreements with explicit solvent.
Correlation Coefficient:
0.99995
Root Mean Square Deviation:
0.33 kcal/mol
AMBER/TIP3P Error (wrt Expt):
1.06 kcal/mol
AMBER/PB Error (wrt Expt):
0.97 kcal/mol
(neutral side chain analogs)
Tan et al, JPCB, 110, 1868018687, 2006
310 helix α helix π helix
5 Parallel 5 Antiparallel
HD3 HD4 HD5
Tan et al, JPCB, 110, 1868018687, 2006
Correlation Coefficient:
0.997
RMSD:
2.90 kcal/mol
TI statistical uncertainties less than 0.6 kcal/mol.
Tan and Luo, In Prep.
Tan and Luo, In Prep
Tan et al, JPCB, 111, In Press, 2007
Tan et al, JPCB, 111, In Press, 2007
CC: 0.9995
RMSD: 0.16kcal/mol
RMS Rel Dev: 0.01
Tan et al, JPCB, 111, In Press, 2007
Error bars too small to be seen
Tan et al, JPCB, 111,
In Press, 2007
Tan and Luo, In Prep.
CC: 0.983
RMSD: 0.29 kcal/mol
RMS Rel Dev: 0.035
Tan and Luo, In Prep.
Error bars too small to be seen
Tan and Luo, In Prep.
Behavior of Two Estimators for BiomoleculesTYR SideChain Conformations
SAS
SAV
Tan and Luo, In Prep.
Jun Wang, Siang Yip
Chuck Tan, Yuhong Tan
Qiang Lu, MJ Hsieh
Gabe Ozorowski, Seema D’Souza
Morris Chen, Emmanuel Chanco
NIH/GMS
PMEMD simulations at 450K Biomolecules
PBMD simulations at 450K Biomolecules
(C, Tan et al. JPC, 2007 )
Lu and Luo, JCP, 119, 1103511047, 2003
(Hu et al. PROTEINS, 2003)
(Hu et al. PROTEINS, 2003)