How Accurately do Current Force Fields Predict. Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study:
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1 How Accurately do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Dynamics Study: Supplementary Information (SI) Alexandar T. Tzanov, Michel A. Cuendet,, and Mark E. Tuckerman,, Department of Chemistry, New York University, New York, NY 13, USA, Swiss Institute of Bioinformatics, UNIL Sorge, 115 Lausanne, Switzerland, and Courant Institute of Mathematical Sciences, New York University, New York, New York 13, USA 1 Supplementary Information As Supplementary Information, we provide additional tables and figures with information that is not necessary to point of the main text. Supplementary tables include quantitative information about the position and height of FES minima for each of the system considered in this study. We also provide numerical values for the macrostate populations obtained from the clustering approach and Eq. () and represented in Figures 5 and. In addition, the statistical uncertainty related to both FES minima and macrostate populations are given for each system. To whom correspondence should be addressed Department of Chemistry, New York University, New York, NY 13, USA Swiss Institute of Bioinformatics, UNIL Sorge, 115 Lausanne, Switzerland Courant Institute of Mathematical Sciences, New York University, New York, New York 13, USA 1
2 Supplementary figures show the FES and clusters obtained for all systems and force fields, as represented in the middle and lower panels of Figure 3.
3 1.1 Supplementary Tables NAAMA in Solution Table S1: Calculated coordinates in degrees, free energy values and barriers in between conformers for NA-A-MA in solution. FE FE CHARMM3 CHARMM7 α R C P II C7 eq C7 ax α L C5->P II P II ->α L 7..5 C7 ax ->α 5.3. α R ->α L AMBER99SB FUJI α R C P II C7 eq C7 ax α L C5->P II.9. P II ->α L C7 ax ->α. 5. α R ->α L OPLS AA/L GROMOS 5a7 α R C P II C7 eq C7 ax α L C5->P II P II ->α L C7 ax ->α R.7.3 α R ->α L α R ->α
4 Table S: Calculated fractional populations vs. average experimental populations from Ref. 3 per conformer for NA-A-MA in solution. An asterisk (*) denotes deviation from averaged experimental data. C5 P II α R C5 PII αr Experimental CHARMM CHARMM AMBER FUJI FF OPLS-AA/L GROMOS
5 1.1. NATMA in Solution Table S3: Calculated macrostates and conformers for NA-T-MA in solution with CHARMM7 Macrostate Conformer χ 1 χ FE [] C5 (AP) C5 (AP) P II (AΦ) C7 eq (ΦP) α R (ΦA) C7 ax (AA) C7 ax (PA) α L Table S: Calculated macrostates and conformers for NA-T-MA in solution with CHARMM3 Macrostate Conformer χ 1 χ FE [] C5 (AP) C5 (AP) P II (AΦ) C7 eq (ΦP) α R (ΦA) C7 ax (PA) α L Table S5: Calculated macrostates and conformers for NA-T-MA in solution with AMB99SB Macrostates Conformer χ 1 χ FE [] C5 (AP) C5 (AΦ) P II (AΦ) C7 eq (ΦP) α R (AP) α R (ΦA) C7 ax (AP) C7 ax (PA) α L
6 Table S: Calculated macrostates and conformers for NA-T-MA in solution with FUJI FF Macrostate Conformer χ 1 χ FE [] C5 (AP) C5 (AP) PII (AΦ) C7 eq (ΦP) α R (AP) C7 ax (AP) α L Table S7: Calculated macrostates and conformers for NA-T-MA in solution with OPLS-AA/L Macrostates Conformer χ 1 χ FE [] C5 (AP) C5 (AP) P II (AΦ) C7 eq (ΦP) C7 eq (ΦP) α R (ΦA) C7 ax (AP) C7 ax (PA) α L Table S: Calculated macrostates and conformers for NA-T-MA in solution with GROMOS Macrostates Conformer χ 1 χ FE [] C5 (AP) P II (AΦ) C7 eq (ΦP) α R (ΦA) C7 ax (PAP) α L Table S9: Calculated fractional populations of NA-T-MA macrostates in solution vs. experimental data. An asterisk (*) denotes deviation from experimental results. C5 P II α R C5 PII αr Experimental 5 CHARMM CHARMM AMB99SB FUJI FF OPLS-AA/L GROMOS
7 1.1.3 NATMA in the Gas Phase Table S1: Calculated conformers of NA-T-MA in gas phase with the CHARMM7 force field vs. data from Ref.. In Ref., relative free energies of the 1 lowest-energy minima are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C7 eq (AP) C7 eq (AΦ) C5 (ΦP) C5 (AΦ) A C7 eq (ΦP) C α R C7 ax Table S11: Calculated conformers of NA-T-MA in gas phase with CHARM3 force field vs. data from Ref. and their relation to Macrostates. In Ref., relative free energies are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C7 eq (AP) C5 (AΦ) A C5 (ΦP) C7 eq (ΦP) C C7 eq (AΦ) α R C7 ax Table S1: Calculated conformers of NA-T-MA in gas phase with AMBER99SB force field vs. data from Ref. and their relation to macrostates. In Ref., relative free energies of the 1 lowestenergy minima are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C7 eq (AP) C5 (AΦ) A C7 eq (ΦP) C α R C7 ax
8 Table S13: Calculated conformers of NA-T-MA in gas phase with FUJI force field vs. data from Ref. and their relation to Macrostates. In Ref., relative free energies of the 1 lowest-energy minima are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C7 eq (AP) C5 (AΦ) A C5 (ΦP) C7 eq (ΦP) C α R C7 eq (AΦ) C7 ax Table S1: Calculated conformers of NA-T-MA in gas phase with OPLS-AA/L force field vs. data from Ref.. In Ref., relative free energies of the 1 lowest-energy minima are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C5 (AΦ) A C7 eq (ΦP) C C7 ax α R Table S15: Calculated conformers of NA-T-MA in gas phase with GROMOS 5a7 force field vs. data from Ref. and their relation to Macrostates. In Ref., relative free energies are calculated at the DFT Becke3LYP/-31+GG* level of theory. Structure Conformer χ 1 χ FE [] Ref. Macrostate C5 (AP) B C5 (ΦP) C7 eq (AP) C5 (AΦ) A C7 eq (ΦP) C α R C7 eq (AΦ) C7 ax
9 Table S1: Calculated fractional populations vs experimental data for NATMA in gas phase. * denotes difference to experimental findings. A B C A B C Experimental 5 3 CHARMM CHARMM3 5 - AMB99SB FUJI FF - - OPLS-AA/L GROMOS
10 1.1. Statistical Uncertainties on FES and Macrostate Populations Table S17: Variability of FES per FF for NAAMA in solution. SE and CI denote confidence interval of calculated free enrgy and confidence interval of this energy per macrostate. NAAMA in SOLUTION C5 PII α R C7 SE [] CI [] Population C3 SE [] CI [] Population AMB99 SE [] CI [] Poulation FUJI-FF SE [] CI [].9..1 Poulation OPLS SE [] CI [] Population GROMOS SE [] Population CI
11 Table S1: Variability of FES per FF for NATMA in solution. Popultation denotes confidence interval of populations per macrostate, SE and CI denote confidence interval of calculated free enrgy and confidence interval of this energy per macrostate. NATMA in SOLUTION C5 PII α R C7 SE [] CI [] Population C3 SE [] CI [] Population AMB99 SE [] CI [] Poulation FUJI-FF SE(cal/mol) CI [] Poulation OPLS SE [] CI [] Population GROMOS SE [] CI [] Population
12 Table S19: Variability of FES per FF for NATMA in gas phase. Popultation denotes confidence interval of populations per macrostate, SE and CI denote confidence interval of calculated free energy and confidence interval of this energy per macrostate. NATMA in GAS PHASE A B C C7 SE [] CI [] Population C3 SE [] CI [] Population AMB99 SE [] CI [] Poulation FUJI-FF SE [] CI [] Poulation OPLS SE [] CI [] Population GROMOS SE [] CI [] Population
13 1. Supplementary Figures (a) (b) (c) (d) (e) (f) Figure S1: FES of NA-A-MA in solution (a,b) with CHARMM7 (c,d) with CHARMM3 (e,f) with AMBER99SB (g,h) with FUJI FF (i,j) with OPLS-AA/L. (k,l) with GROMOS 5a7 13
14 (g) (h) (i) (j) (k) (l) Figure S1: (continued) 1
15 χ (a) (b) (c) χ (d) (e) χ χ (f) (g) (h) (i) Figure S: FES of NA-T-MA in solution with CV projected in the (Φ, Ψ) plane, clusters projected in the (Φ, Ψ) plane and FES projected in the (, χ ) plane, for: (a,b,c) with CHARMM7 (d,e,f) with CHARMM3 (g,h,i) with AMBER99SB (j,k,l) with FUJI FF (m,n,o) with OPLS-AA/L (p,q,r) with GROMOS 5a7 15
16 (j) (k) 1 (l) χ (m) (n) 1 15 (o) χ χ χ (p) 5 (q) Figure S: (continued) (r)
17 χ (a) (b) (c) χ (d) (e) χ (g) (f) (h) (i) Figure S3: FES of NA-T-MA in the gas phase with CV projected in the (Φ, Ψ) plane, clusters projected in the (Φ, Ψ) plane and FES projected in the (, χ ) plane, for: (a,b,c) with CHARMM7 (d,e,f) with CHARMM3 (g,h,i) with AMBER99SB (j,k,l) with FUJI FF (m,n,o) with OPLS-AA/L (p,q,r) with G5a7 17
18 (j) (k) 1 15 (l) χ (m) (n) 1 15 (o) χ (p) gas kcal/mol 1 χ (q) Figure S3: (continued) (r)
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