AMBER Parameters for Pseudouridine

Delon WilsonAdvisor: J. SantaLucia

Outline

Introduction and MotivationPseudouridine & Modified Nucleic AcidsAtomic charge in MM

RESP/ MethodThe MEPCharge Fitting with Restraints

Results Conclusion

Nucleic Acid Structure

Base

Sugar

PhosphateG,C,A,T (DNA)

G,C,A,U (RNA)

Deoxyribose (DNA)Ribose (RNA)

PSU and Modified NA’s

Found as natural substances or obtained synthetically

Pseudouridine – 1% in rRNA, tRNA

produced by chemically modifiying one of the four bases (G, C, A, and T in DNA or U in RNA)

Important in biochemical regulation

Used extensively in chemistry, biochemistry, and pharmacology as probes to study biological mechanisms

PSU and Modified NA’s

Major cause of spontaneous mutation in E. coli results from the presence of an unusual base in the DNA.

e.g. 5-MethylCytosine

Successful applications as antibiotics or chemotherapeutic agents

e.g. AZT interferes with the replication of HIV (Human Immunodeficiency Virus)

Molecular Mechanics

Modeling of biological systems

Accurate representation of electrostatic interactions

crucial for force field application

Suitable force field parameters required for molecular

mechanics and dynamics

force constants, atom types, bond distances, atomic

charges

Molecular Mechanics

Amber: A suited of programs developed by Peter

Kollman & Coworkers at UCSF

Force field referred to by same name

Parameters for regular NA’s (A,C,T,G,U) developed

Suitable parameters for modified NA’s not available

An albatross to computations for systems involving

substantial amounts of mod. NA’s

Potential Energy ModelThe force field energy

where

ticelectrostavdwtorsionbendstrFF EEEEEE

2eqbonds

rstr rrKE 2

angleseqbend KE

nK

En

ntorsion cos1

2

ji ij

ij

ij

ijvdw R

B

R

AE

612

ji ij

jiticelectrosta R

qqE

Pseudouridine

Base joined to ribose via C-C,Vs. C-N in regular NA’s

Uridine

Psu

Starting structure from PDB

Perform Geometry Optimization (HF-631G*)

ComputeElectrostatic Potential Charges

(pop=mk)

Fit ESP charges(RESP)

MD simulation (AMBER)

Initial Structure

Gaussian Keywords

#p hf 6/31-g(d) opt pop=mk

geom=connectivity test iop(6/33=2)

Duration: around 5hrs

ESP: Some Common Methods

Mulliken Population Analysis-does not

reproduce ESP closely enough

Natural Population Analysis`

ESP derived using CHelpG scheme

ESP derived using MKS scheme

Calculation of ESP/MEP

10 14i

i i

Q

r

Calculate approximate Ψ from eq geom

Calculate e density from psi

The ESP at point 1 is:

RESP

Least squares algorithm derives atom centered

charges that best reproduces MEP

Potential calculated on large number of points

on 4 shells of surfaces defined by {1.4, 1.6, 1.8,

2.0} x VDW radii

ESP at each point derived from QM

Results .4312(.4295)

-.6135(-.6223)

.0748(.0679)

.0748(.0679)

.0264(.0558)

.0788(.1065)

.1171(.1174)

-.3604(-.3548)

.0461(.0615)

.2808(.2022) .0736

(.0670)

.0974(.0972) -.5962

(-.6139)

.4098(.4186)

.3885(.4376)

-.6271(-.6541)

.0303(-.1081)

.1714(.2405)

-.5332(-.6230)

.3842(.8922)

.0069(-.5317)

-.0759(.3896)

.2104(.1226)

.5173(.9290)

-.5841(-.6096)

-.3407(-.6770)

.3418(.4311)

-.2671(-.7255)

.3402(.3859)

Partial charges on pseudouridine: values in parenthesis from Amber website, std=0.23

Results Calculations performed on a single Pentium IV

processor.

Average CPU time to perform the geometry optimization of each nucleoside in the order of several hours (~5)

Charges for each ribonucleotide are in a good

agreement with AMBER standard reference file (all_nuc94.in).

Calculations on pseudouridine deviate more than expected from the contributed values provided at the AMBER website.

…To do

Investigate the dependence of the charges on conformation

Determine force field parameters for all (~103) of the naturally occurring modified nucleotides that occur in RNA and DNA.

Extend the AMBER force field so that nuclei acids with modifications may be routinely modeled.

Develop a novel force field specifically tailored to nucleic acid applications (NA_FF).

References/Acknowlegment

U. C. Singh and P. A. Kollman

J. Comp. Chem. vol.5, no.2, 129-145 (1984)

B.H. Besler, K.M. Merz Jr., and P.A. Kollman

J. Comp. Chem. vol.11, no.4, 431-439(1990)

JSL Lab

Schlegel Lab

Questions etc…

Thank you