Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
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- Ιππόλυτος Παπαδόπουλος
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1 Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field Supplementary Information Michael J. Robertson, Julian Tirado-Rives, and William L. Jorgensen* Department of Chemistry, Yale University, New Haven, Connecticut , United States Figure S1. Two-dimensional Phi-Psi Potential Energy Surfaces pp 3-4 Table S1. Summary of the Force Field Parameters Developed and Tested in this Work for the Alanine and Glycine Peptide Backbone.....pp 4 Table S2. Summary of the 1 Force Field Parameters Developed and Tested in this Work..pp 5-8 Table S3. Summary of the 2 Force Field Parameters Developed and Tested in this Work...pp 9-10 Table S4. Summary of the Results of the Molecular Dynamics Simulations of Blocked Dipeptides Performed in this Work...pp Table S5. Relative Conformer Energies for the Blocked Alanine Dipeptide Calculated with Various Ab Initio Methods and Molecular Mechanics Force Fields pp 13 1
2 Table S6. Relative Conformer Energies for the Blocked Alanine Tetrapeptide Calculated with Various ab initio and DFT Methods pp 14 Table S7. Values of and ψ for the Alanine Tetrapeptides Calculated at the ωb97x-d/ g(p,d) Level of Theory...pp 15 Table S8. Values of and ψ for the Alanine Tetrapeptides Calculated at the M06-2X/6-31+g(d) Level of Theory.pp 16 Table S9. Relative Conformer Energies for the Blocked Proline Dipeptide Calculated with Various ab initio Methods and Molecular Mechanics Force Fields...pp 17 Table S10. Summary of the Force Field Parameters Developed and Tested in this Work for Proline...pp 17 Figure SI2. The Populations of Each Rotamer as a Percentage from Molecular Dynamics Simulations of Blocked Dipeptides Versus the Average Populations from a Library...pp Figure SI3. The RMSD Between the Coordinates of the Backbone Atoms in the MD Simulations Compared to the Starting al Structure..pp
3 Figure S1. Two dimensional phi-psi potential energy surfaces calculated for A) alanine at the B2PLYP-D3BJ/aug-cc-pVTZ// B97X-D/ G(d,p) level of theory, B) glycine at the B2PLYP-D3BJ/aug-cc-pVTZ// B97X-D/ G(d,p) level of theory, C) alanine with the 3
4 original OPLS-AA forcefield, D) glycine with the original OPLS-AA forcefield, E) alanine with the OPLS-AA/L force field, F) glycine with the OPLS-AA/L force field, G) alanine with the newly derived 2000 K parameters, and H) glycine with the newly derived 2000 K parameters. The energies are given in kcal/mol. Table S1. Summary of the Force Field Parameters Developed and Tested in this Work for the Alanine and Glycine Peptide Backbone and their Boltzmann-Weighted Errors Compared to the B2PLYP-D3BJ/aug-cc-pVTZ// B97X-D/ G(d,p) Relative Energies. Parameters Noted with a * are those Selected for the OPLS-AA/M Force Field. Parameters a Boltzmann Weighted Error a V1 V2 V3 500 K 1000 K 2000 K Unweighted OPLS-AA Alanine Glycine OPLS-AA/L Alanine Glycine Optimized Parameters 500 K Alanine Glycine K Alanine Glycine *2000 K Alanine Glycine Unweighted Alanine Glycine a Both the parameters and the RMSD values have units of kcal/mol 4
5 Table S2. Summary of the 1 Force Field Parameters Developed and Tested in this Work and their Boltzmann-Weighted Errors Compared to the B2PLYP-D3BJ/aug-ccpVTZ// B97X-D/ G(d,p) Relative Energies. Parameters Noted with a * are those Selected for the OPLS-AA/M Force Field. Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted Valine OPLS-AA OPLS-AA/L K Val *2000 K Val/Ile K Val/Ile/Leu Isoleucine OPLS-AA OPLS-AA/L K Ile *2000 K Val/Ile K Val/Ile/Leu Leucine OPLS-AA OPLS-AA/L *2000 K Leu K Val/Ile/Leu Serine OPLS-AA OPLS-AA/L K Ser *2000 K Ser Empirical Both the parameters and the error values have units of kcal/mol 5
6 Table S2 Continued Threonine OPLS-AA OPLS-AA/L 2000 K Val/Ile/Leu 1 C Ser 1 O *2000 K Val/Ile 1 C Ser Empirical 1 O Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted C C O O C C O O C C O O C C O O Aspartate OPLS-AA OPLS-AA/L K Asp/Asn K Asp *2000 K Asp Empirical Asparagine OPLS-AA OPLS-AA/L K Asp/Asn *2000 K Asn Glutamine OPLS-AA OPLS-AA/L K Leu K Gln *2000 K Gln/Lys a Both the parameters and the error values have units of kcal/mol 6
7 Table S2 Continued Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted Lysine OPLS-AA OPLS-AA/L K Leu K Lys *2000 K Gln/Lys Glutamate OPLS-AA OPLS-AA/L K Leu K Glu *2000 K Glu Empirical Cysteine OPLS-AA OPLS-AA/L K Cys *2000 K Cys Empirical Methionine OPLS-AA OPLS-AA/L K Leu *2000 K Met Arginine OPLS-AA OPLS-AA/L K Leu *2000 K Arg Phenylalanine OPLS-AA OPLS-AA/L *2000 K Phe a Both the parameters and the error values have units of kcal/mol 7
8 Table S2 Continued Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted Tyrosine OPLS-AA OPLS-AA/L K Tyr *2000 K Phe Tryptophan OPLS-AA OPLS-AA/L K Phe K Trp *2000 K Trp Empirical Histidine-ε OPLS-AA OPLS-AA/L K Hie *2000 K Hie/Hid Histidine-δ OPLS-AA OPLS-AA/L K Hid *2000 K Hie/Hid Protonated His OPLS-AA OPLS-AA/L K Hid/Hie *2000 K Hip a Both the parameters and the error values have units of kcal/mol 8
9 Table S3. Summary of the 2 Force Field Parameters Developed and Tested in this Work and their Boltzmann-Weighted Errors Compared to the B97X-D/ G(d,p) and, where Applicable, B2PLYP-D3BJ/aug-cc-pVTZ// B97X-D/ G(d,p) Relative Energies. Parameters Noted with a * are those Selected for the OPLS-AA/M Force Field. Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted Isoleucine *OPLS-AA K Ile Leucine *OPLS-AA K Ile Serine *OPLS-AA OPLS-AA/L K Ser Cysteine *OPLS-AA K Cys Methionine OPLS-AA *2000 K Met Asparagine OPLS-AA 2 N O OPLS-AA/L 2 N O *2000 K Asn 2 N O Aspartate OPLS-AA *2000 K Asp Glutamine OPLS-AA K Gln *2000 K Gln Emp Glutamate OPLS-AA K Glu *2000 K Glu Emp Phenylalanine *OPLS-AA K Phe Tyrosine *OPLS-AA K Tyr Tryptophan *OPLS-AA K Trp Histidine-ε OPLS-AA OPLS-AA/L K Hie *2000 K Hie/Hid a Both the parameters and the Error values have units of kcal/mol 9
10 Table S3 Continued Parameters a Average Boltzmann Weighted Error Per Scan a V1 V2 V3 500 K 1000 K 2000 K Unweighted Histidine-δ OPLS-AA OPLS-AA/L K Hid *2000 K Hie/Hid Protonated His OPLS-AA OPLS-AA/L *2000 K Hip K Hie/Hid a Both the parameters and the Error values have units of kcal/mol Table S4. Summary of the Results of the Molecular Dynamics Simulations of Blocked Dipeptides Performed in this Work with all Force Fields. Valine 2000K 2000K Library b OPLS-AA OPLS-AA/L Val/Ile/Leu Val/Ile 3 J(H NH α) (Hz) ± ± ± ± 0.01 %m 8.1 ± ± ± ± ± 1.2 %p 39.2 ± ± ± ± ± 0.9 %t 52.8 ± ± ± ± ± 0.3 Isoleucine Library b OPLS-AA OPLS-AA/L 2000K Val/Ile/Leu 2000K Val/Ile 3 J(H NH α) (Hz) ± ± ± ± 2.3 %m 63.1 ± ± ± ± ± 6.3 %p 28.3 ± ± ± ± ± 10.2 %t 8.6 ± ± ± ± ± 4.1 Leucine Library b OPLS-AA OPLS-AA/L 2000K Val/Ile/Leu 2000 K Leu 3 J(H NH α) (Hz) ± ± ± ± 0.01 %m 73.6 ± ± ± ± ± 1.7 %p 7.0 ± ± ± ± ± 0.1 %t 19.6 ± ± ± ± ± 1.8 Serine Library b OPLS-AA OPLS-AA/L 2000 K Ser 2000 K Ser Reweighted 3 J(H NH α) (Hz) ± ± ± ± 0.01 %m 33.1 ± ± ± ± ± 2.9 %p 29.4 ± ± ± ± ± 4.4 %t 37.5 ± ± ± ± ± 3.7 Threonine Library b OPLS-AA OPLS-AA/L 2000 K Ser 2000 K Ser Reweighted 3 J(H NH α) (Hz) ± ± ± ± 0.04 %m 39.3 ± ± ± ± ± 11.6 %p 46.6 ± ± ± ± ± 11.6 %t 14.1 ± ± ± ± ± 0.4 J couplings for dipeptides given in reference 48. Rotamer populations and errors given are the averages and standard deviations over all residues in denatured ubiquitin and protein G from reference reference 42 b library data from reference 43 10
11 Table S4 Continued Cysteine Library b OPLS-AA OPLS-AA/L 2000 K Cys 2000 K Cys Reweighted 3 J(H NH α) (Hz) ± ± ± ± 0.01 %m ± ± ± ± 0.9 %p ± ± ± ± 1.6 %t ± ± ± ± 0.0 Methionine Library b OPLS-AA OPLS-AA/L 2000 K Met 3 J(H NH α) (Hz) ± ± ± 0.02 %m ± ± ± 0.9 %p ± ± ± 0.2 %t ± ± ± 1.0 Asparagine Library b OPLS-AA OPLS-AA/L 2000 K Asn 3 J(H NH α) (Hz) ± ± ± 0.00 %m 46.1 ± ± ± ± 2.9 %p 27.1 ± ± ± ± 1.8 %t 26.5 ± ± ± ± K Aspartate Library b OPLS-AA OPLS-AA/L 2000 K Asp Asp/Asn 2000 K Asp Reweighted 3 J(H NH α) (Hz) ± ± ± ± ± 0.02 %m 44.9 ± ± ± ± ± ± 5.2 %p 30.3 ± ± ± ± ± ± 4.6 %t 24.8 ± ± ± ± ± ± 2.7 Glutamine Library b OPLS-AA OPLS-AA/L 2000K Gln/Lys 3 J(H NH α) (Hz) ± ± ± 0.02 %m 61.4 ± ± ± ± 3.5 %p 15.7 ± ± ± ± 0.8 %t 22.9 ± ± ± ± K Glu Glutamate Library b OPLS-AA OPLS-AA/L 2000 K Glu Reweighted 3 J(H NH α) (Hz) ± ± ± ± 0.04 %m 60.8 ± ± ± ± ± 5.5 %p 16.4 ± ± ± ± ± 3.6 %t 22.7 ± ± ± ± ± 4.6 Lysine Library b OPLS-AA OPLS-AA/L 2000K Gln/Lys 3 J(H NH α) (Hz) ± ± ± 0.02 %m 60.7 ± ± ± ± 2.7 %p 15.3 ± ± ± ± 1.9 %t 24.0 ± ± ± ± 4.3 Arginine Library b OPLS-AA OPLS-AA/L 2000 K Arg 3 J(H NH α) (Hz) ± ± ± 0.02 %m 59.5 ± ± ± ± 4.0 %p 16.1 ± ± ± ± 0.7 %t 24.4 ± ± ± ± 3.7 J couplings for dipeptides given in reference 48. Rotamer populations and errors given are the averages and standard deviations over all residues in denatured ubiquitin and protein G from reference reference 42 b library data from reference 43 11
12 Table S4 Continued Phenylalanine Library b OPLS-AA OPLS-AA/L 2000 K Phe 3 J(H NH α) (Hz) ± ± ± 0.02 %m 60.7 ± ± ± %p 12.2 ± ± ± %t 27.2 ± ± ± Tyrosine Library b OPLS-AA OPLS-AA/L 2000 K Tyr 3 J(H NH α) (Hz) ± ± ± 0.05 %m 59.4 ± ± ± ± 4.4 %p 14.1 ± ± ± ± 0.3 %t 26.5 ± ± ± ± 4.2 Tryptophan Library b OPLS-AA OPLS-AA/L 2000 K Trp 2000 K Trp Reweighted 3 J(H NH α) (Hz) ± ± ± ± 2.8 %m ± ± ± ± 2.7 %p ± ± ± ± 0.8 %t ± ± ± ± 1.9 (NMR) Library b OPLS-AA OPLS-AA/L 2000 K Hid Histidine-δ 3 J(H NH α) (Hz) 7.94 ± ± ± 0.02 %m ± ± ± 3.7 %p ± ± ± 0.7 %t ± ± ± 3.5 (NMR) Library b OPLS-AA OPLS-AA/L 2000 K Hie Histidine-ε 3 J(H NH α) (Hz) 7.88 ± ± ± 0.01 %m ± ± ± 1.9 %p ± ± ± 1.1 %t ± ± ± 1.0 Histidine Protonated (NMR) Library b OPLS-AA OPLS-AA/L 2000 K Hip 3 J(H NH α) (Hz) %m %p %t J couplings for dipeptides given in reference 48. Rotamer populations and errors given are the averages and standard deviations over all residues in denatured ubiquitin and protein G from reference reference 42 b library data from reference 43 12
13 Table S5. Relative Conformer Energies (in kcal/mol) for the Blocked Alanine Dipeptide Calculated with Various Ab Initio Methods and Molecular Mechanics Force Fields CCSD(T)/ CBS a DF- LCCSD(T0) b OPLS- AA OPLS- AA/L 500K 1000K 2000K Unweighted C7-eq C C7-ax B2 c Alpha L c Alpha Prime RMSD Minima RMSD All a Reference 16 b Reference 15 c Not true minima with the force fields, phi and psi were fixed at their values from the B97X-D/ G(d,p) calculations 13
14 Table S6. Relative Conformer Energies (in kcal/mol) for the Blocked Alanine Tetrapeptide Calculated with Various ab initio and DFT Methods Conformer Number RI- MP2(CBS)// HF/6-31G** Energy a ωb97x-d/ g(p,d) Optimized Geometry ωb97x-d/ g(p,d) Energy ωb97x-d/augcc-pvtz Energy ωb97x-d/ jun-cc-pvqz Energy M06-2X/6-31+g(d) Optimized Geometry M06-2X/ 6-31+g(d) Energy a Reference 30 M06-2X/ aug-ccpvtz Energy M06-2X/juncc-pVQZ Energy 14
15 Table S7. Values of and ψ for the Alanine Tetrapeptides Calculated at the ωb97x-d/ g(p,d) Level of Theory Conformer Number ωb97x-d/ g(p,d) Optimized Geometry Ala1 Ala1 ψ Ala2 Ala2 ψ Ala3 Ala3 ψ
16 Table S8. Values of and ψ for the Alanine Tetrapeptides Calculated at the M06-2X/6-31+g(d) Level of Theory Conformer Number M06-2X/6-31+g(d) Optimized Geometry Ala1 Ala1 ψ Ala2 Ala2 ψ Ala3 Ala3 ψ
17 Table S9. Relative Conformer Energies (in kcal/mol) for the Blocked Proline Dipeptide Calculated with Various ab initio Methods and Molecular Mechanics Force Fields CCSD(T)/CBS a OPLS-AA OPLS-AA/L 2000 K tcd tcu cad cau tau 4.95 cfd cfu RMSD a Reference 16 Table S10. Summary of the Force Field Parameters Developed and Tested in this Work for Proline and their Average per Scan Boltzmann-Weighted Errors Compared to the B2PLYP-D3BJ/aug-cc-pVTZ// B97X-D/ G(d,p) Energies for the Two Proline Scans. Parameters Noted with a * are those Selected for the OPLS-AA/M Force Field. Parameters a Atoms Boltzmann Weighted Error a V1 V2 V3 500 K 1000 K 2000 K Unweighted OPLS-AA N-Cα-C-N N-C-Cα-Cβ N-Cα-Cβ-Cγ C-Cα-Cβ-Cγ Cδ-N-Cα-C Cδ-N-Cα-Cβ Cγ-Cδ-N-Cα OPLS-AA/L N-Cα-C-N N-C-Cα-Cβ N-Cα-Cβ-Cγ C-Cα-Cβ-Cγ Cδ-N-Cα-C Cδ-N-Cα-Cβ Cγ-Cδ-N-Cα *2000 K Pro N-Cα-C-N N-C-Cα-Cβ N-Cα-Cβ-Cγ C-Cα-Cβ-Cγ Cδ-N-Cα-C Cδ-N-Cα-Cβ Cγ-Cδ-N-Cα a Both the parameters and the RMSD values have units of kcal/mol 17
18 Figure SI2. The populations of each rotamer as a percentage from molecular dynamics simulations of blocked dipeptides versus the average populations from a coil library. Results are given for the OPLS-AA (A), OPLS-AA/L (B), and OPLS-AA/M (C). Dashed lines delineate the 18
19 region of populations that fall within +/- 20% of the experimental result. Error bars from simulation represent the standard deviation in the populations from triplicate 200 ns simulations. Figure SI3. The RMSD between the coordinates of the backbone atoms in the MD simulations compared to the starting experimental structure over the course of the trajectory for the first run. 19
20 The first, second, and third rows correspond to trajectories with OPLS-AA, OPLS-AA/L, and OPLS-AA/M, while the first and second columns correspond to ubiquitin residues 1-72 and GB3 respectively. 20
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