Summary of information
PROJECT
3-(2-naphthyl)-L-alanine

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Upload 05-06-2009 11:59 (Day-Month-Year, Paris time)



Information about the Author (who submitted the project in R.E.DD.B.)

Firstname Arturas

Lastname Ziemys

Institute UT at Houston

City Houston, tx

Country US


General information about the Project

Molecule keywords

New amino acid 3-(2-naphthyl)-L-alanine central fragment N-terminal fragment C-terminal fragment


Abstract

RESP atomic charges embedded in force field libraries for the N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide dipeptide (or ACE-NAP-NME capped amino acid), as well as for the central, (+)NH3-terminal and (-)OOC-terminal fragments of the 3-(2-naphthyl)-L-alanine amino acid. All atom force field libraries suitable for MD simulations using the Cornell et al. AMBER force field (and/or its successive adaptations: Kollman et al., Cheatham et al., Wang et al. & Hornak et al. force fields). A single conformation for the N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide dipeptide (φ = -157.2, ψ = 150.8, χ = -166.7) was considered in the procedure. Charge derivation and force field library building for the central fragment of 3-(2-naphthyl)-L-alanine (or NAP fragment) were carried out by using N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide, and setting two intra-molecular charge constraints to a value of zero for the ACE and NME residues during the charge fitting step. Charge derivation and force field library building for the N-terminal fragment of 3-(2-naphthyl)-L-alanine (or NNAP fragment) were performed by using two molecules: methylammonium and N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide, and setting two different constraints to a value of zero during the fitting step: (i) an inter-molecular charge constraint between the methyl group of methylammonium and the CH3CO-NH group of atoms of the capped amino acid, and (ii) an intra-molecular charge constraint for the NME residue of the capped amino acid. Charge derivation and force field library building for the C-terminal fragment of 3-(2-naphthyl)-L-alanine (or CNAP fragment) were carried out by using two molecules: acetate and N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide, and setting to a value of zero two different constraints during the fitting step: (i) an inter-molecular charge constraint between the methyl group of acetate and the CO-NHCH3 group of atoms of the capped amino acid, and (ii) an intra-molecular charge constraint for the ACE residue of the capped amino acid (Scheme 1).


Scheme 1
Multiple orientation single conformation and multiple molecule charge derivation and force field library building for the N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide dipeptide and the corresponding central, H3N(+)-terminal and (-)OOC-terminal molecular fragments carried out using R.E.D. Server and the R.E.D. IV program. (A) Description of the different molecules involved in the procedure. Dashed line box: symbolisation of intra-molecular charge constraints used during the fitting step within the dipeptide; Plain line box: symbolisation of inter-molecular charge constraints used during the fitting step between the dipeptide and methylammonium or acetate. ACE chemical group = CH3CO; NME chemical group = NHCH3. (B) Selection of force field libraries generated in the Tripos mol2 file format.

Geometry optimization, frequency calculation and molecular electrostatic potential (MEP) computation were carried out using the Gaussian 03 program, while charge fitting was performed using the RESP program. For all the structures, the HF method and the 6-31G* basis set in gas phase were used in geometry optimization and frequency calculation. MEP computation was carried out using the HF/6-31G* theory level in gas phase, and the Connolly surface algorithm. The molecular orientation of each optimized structure was controlled using the rigid-body re-orientation algorithm implemented in the R.E.D. program. Four molecular orientations for N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide (based on the NAP nitrogen, NAP α-carbon, NAP β-carbon; NAP β-carbon, NAP α-carbon, NAP nitrogen; NAP nitrogen, NAP α-carbon, NAP carbonyl-carbon; NAP carbonyl-carbon, NAP α-carbon, NAP nitrogen atoms), and two molecular orientations for methylammonium (based on the methyl carbon, nitrogen, anti nitrogen hydrogen atoms; anti nitrogen hydrogen, nitrogen, methyl carbon atoms) and acetate (based on the methyl carbon, naphtalenelate carbon, terminal oxygen atoms; terminal oxygen, naphtalenelate carbon, methyl carbon atoms)] were involved in MEP computation. A RRMS (relative root mean square value between the MEP values calculated by quantum mechanics, and those generated using the derived charge values) of 0.036 was obtained for the fitting step.

Is the project published NOT YET

"Whole molecule" or "Molecule fragment" type project MOLECULE FRAGMENT

Interface R.E.D. used ? YES


Charge derivation procedure

Number of Tripos mol2 file(s) provided by the author(s) 4

Contain charge values & information about molecular topology

No Name Download Wikipedia 3D visualization
1 Fragment NAP Link Wiki Logo Jmol Logo
2 Fragment NNAP Link Wiki Logo Jmol Logo
3 Fragment CNAP Link Wiki Logo Jmol Logo
4 N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide Link Wiki Logo Jmol Logo


Number of molecule(s) used in the charge derivation procedure 6

File(s) provided to the PDB format

No Molecule name Conformation No Reorientation procedure Mol. orientation No Download Wikipedia
1 N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide 1 Rigid Body Reorient Algo 4 Link Wiki Logo
2 Methylammonium 1 Rigid Body Reorient Algo 2 Link Wiki Logo
3 N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide 1 Rigid Body Reorient Algo 4 Link Wiki Logo
4 Acetate 1 Rigid Body Reorient Algo 2 Link Wiki Logo
5 N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide 1 Rigid Body Reorient Algo 4 Link Wiki Logo
6 N-Acetyl-3-(2-naphthyl)-L-alanine-N'-methylamide 1 Rigid Body Reorient Algo 4 Link Wiki Logo



Information regarding Quantum Calculations

Geometry optimization

Program 1 GAUSSIAN 2003

Theory level 1 HF

More information 1 Opt=Tight

Basis set 1 6-31G*

Molecular electrostatic potential computation

Program 2 GAUSSIAN 2003

Theory level 2 HF

More information 2 IOp(6/33=2) NoSymm

Basis set 2 6-31G*

Algorithm CONNOLLY SURFACE


Information about the charge fit

Program RESP

Number of stage(s) 2

input of stage 1 Link

input of stage 2 Link



Files the author of the project wishes to provide...

A script to convert Tripos mol2 file(s) into LEaP OFF library(ies) (for AMBER)...Link
A script to convert Tripos mol2 file(s) into RTF or PSF library(ies) (for CHARMM)...Link
A file to provide new force field parameters compatible with the Tripos mol2 file(s)...Link
A file (choice made by the author) to provide more information about the project...Link
A file (choice made by the author) to provide more information about the project...Link

Download the whole project... Link



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