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Topology and Parameter Data of Thirteen Non-Natural Amino Acids For Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎ 1 Contents lists available at ScienceDirect 2 3 4 Data in Brief 5 6 7 journal homepage: www.elsevier.com/locate/dib 8 9 Data Article 10 11 12 Topology and parameter data of thirteen 13 non-natural amino acids for molecular 14 15 Q5 simulations with CHARMM22 16 a,n,1 a,b 17 Q1 Olujide O. Olubiyi , Birgit Strodel 18 a Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 19 Jülich, Germany 20 b Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 21 40225 Düsseldorf, Germany 22 23 24 article info abstract 25 26 Article history: In this article we provide a data package containing the topology 27 Received 9 March 2016 files and parameters compatible with the CHARMM22 force field Received in revised form 28 for thirteen non-natural amino acids. The force field parameters 27 September 2016 were derived based on quantum mechanical (QM) calculations 29 Accepted 30 September 2016 30 involving geometry optimization and potential energy surface scanning at the HF 6-31G(d) and HF 6-311G(d,p) levels of theory. 31 Keywords: The resulting energy data points were fitted to mathematical 32 CHARMM functions representing each component of the CHARMM22 force Force field parameterization 33 field. Further fine-tuning of the parameters utilized molecular Quantum mechanics 34 mechanics energies, which were iteratively calculated and com- Molecular dynamics 35 Potential energy surface pared to the corresponding QM values until the latter were satis- 36Q3 Geometry optimization factorily reproduced. The final force field data were validated with 37 molecular dynamics simulations in explicit solvent conditions. 38 & 2016 Published by Elsevier Inc. This is an open access article 39 under the CC BY license 40 (http://creativecommons.org/licenses/by/4.0/). 41 42 43 44 45 46 47 48 Q2 n Corresponding author. 49 E-mail address: [email protected] (O.O. Olubiyi). 50 1 Author now works at Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences, Afe Babalola 51 University Nigeria. 52 http://dx.doi.org/10.1016/j.dib.2016.09.051 53 2352-3409/& 2016 Published by Elsevier Inc. This is an open access article under the CC BY license 54 (http://creativecommons.org/licenses/by/4.0/). Please cite this article as: O.O. Olubiyi, B. Strodel, Topology and parameter data of thirteen non- natural amino acids for molecular simulations with CHARMM22, Data in Brief (2016), http://dx. doi.org/10.1016/j.dib.2016.09.051i 2 O.O. Olubiyi, B. Strodel / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎ 55 Specifications Table 56 57 Subject area Chemistry, Biophysics 58 More specific Computational Biochemistry, Computational Biophysics 59 subject area 60 Type of data Figures, tables, text 61 How data was Quantum mechanics (QM) and all-atom molecular dynamics (MD) calculations 62 acquired 63 Data format Raw, analyzed 64 Experimental Software used: Spartan 10 for QM, NAMD for MD 65 factors 66 Experimental CHARMM22 force field 67 features 68 Data source Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum 69 location Jülich GmbH, 52425 Jülich, Germany 70 Data accessibility Data are supplied with this article 71 72 73 Value of the data 74 75 New parameters for MD simulations of thirteen non-natural amino acids are provided. 76 The parameters given here are compatible with the CHARMM22 force field, allowing to study the 77 biophysical properties of these non-natural amino acids alone or as part of proteins and their 78 interactions with other biomolecules and drugs. No further laborious parameterization is required. 79 The employed parameterization approach provides a template for future design of hybrid amino 80 acids, especially where it is desirable to combine small, drug-like organic molecular fragments with 81 amino acid backbones either in the L or D configuration. 82 83 84 85 1. Data 86 fi 87 In Supplementary material we provide the CHARMM22 topology and parameter les for following thirteen non-natural amino acids: D-4-fluo-rophenylalanine (FPA), D-4-benzoylphenylalanine (BPP), 88 γ β 89 D-3,5-diiodotyrosine (DIT), -aminobutyric acid (GAB), D-cyclohexyl- -alanine (CHA), D- β 90 phenylglycine (PGL), L- -homoarginine (LBH), L-homoarginine (LHR), L-homocitrulline (HCT),D-4- fl β 91 trans uoroproline (TFP), D-aminocyclobutyl-carboxylic acid (ABC), -alanine (BAL) and D-1- 92 naphthylalanine (NPA). The chemical structures of these amino acids are shown in Fig. 1. 93 94 95 2. Experimental design, materials and methods 96 97 2.1. Parameterization 98 99 In the present work, we provide the topologies and CHARMM22 force field [1] parameters for 100 thirteen non-natural amino acids to be used for molecular dynamics simulations. The para- 101 meterization process involved determining the equilibrium values for bond lengths, bond angles and 102 dihedral angles and the force constants or energy barriers for the respective motion in case that these 103 values were not already available in the CHARMM22 parameter set. To this end, QM calculations were 104 performed for the thirteen amino acids using the program Spartan 10 [2]. The QM calculations were 105 applied to the whole target molecules rather than to smaller representative submolecular systems as 106 this eliminates the need for an extrapolation of the physicochemical properties of the amino acids 107 from smaller model compounds. After generating structural models with the appropriate chirality, 108 geometry optimization was performed at the Hartree–Fock (HF) 6-31G(d) level of theory using an Please cite this article as: O.O. Olubiyi, B. Strodel, Topology and parameter data of thirteen non- natural amino acids for molecular simulations with CHARMM22, Data in Brief (2016), http://dx. doi.org/10.1016/j.dib.2016.09.051i O.O. Olubiyi, B. Strodel / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎ 3 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 Fig. 1. The chemical structures and atomic charges for the thirteen non-natural amino acids. Carbon atoms are shown in tan, nitrogen in blue, oxygen in red, hydrogen in white, fluorine in green and iodine in violet. See Fig. S1 in Supplementary Data for 160 the atom labels. 161 162 Please cite this article as: O.O. Olubiyi, B. Strodel, Topology and parameter data of thirteen non- natural amino acids for molecular simulations with CHARMM22, Data in Brief (2016), http://dx. doi.org/10.1016/j.dib.2016.09.051i 4 O.O. Olubiyi, B. Strodel / Data in Brief ∎ (∎∎∎∎) ∎∎∎–∎∎∎ 163 optimization scheme combining the Geometric Direct Minimization method [3] and the Pulay Direct 164 Inversion in the Iterative Subspace algorithm [4,5]. A 3.0 Â 10 À4 hartrees/Bohr force tolerance was 165 used. In the case of DIT, the HF 6-311G(d,p) basis set was employed as it allows higher flexibility for 166 treating period V elements like iodine. The decision to perform the QM calculations at the HF 6-31G 167 (d) level was based on the desire to stay close to the level of theory employed in parameterizing the 168 CHARMM22 force field for the standard amino acids and also nucleotides. 169 After geometry optimization, QM potential energy scans were performed along the various bond 170 stretching, angle bending and bond rotation coordinates. In the case of bond stretching, the potential 171 energy was computed for twenty configurations uniformly spread between b 70.25 Å with b as the 172 0 0 equilibrium bond length. Similarly, energy profiles for the valence angles within the range θ 75 173 0 were generated with θ as equilibrium bond angle. In the case of torsion, the full rotation 174 0 À180°rδo180° was considered and potential energies calculated every 18°. The force constants 175 fi 176 were then calculated for bond stretching and angle bending by tting the obtained potential energy 177 data to harmonic functions using bond length and valence angle with the lowest energy along the θ 178 potential energy curve as the equilibrium values, b0 and 0, respectively. The energy barriers for bond 179 torsions were determined by fitting the corresponding potential energy curve to a cosine function 180 using the multiplicity as obtained from the energy scan. 181 For determining partial charges, original CHARMM22 values were taken, whenever possible, from 182 similar atoms in a comparable local chemical environment. For instance, partial charges for the 183 aromatic side chain of phenylalanine were taken for the aromatic atoms of PGL. Also, no new van der 184 Waals (vdW) parameters had to be derived as for all atoms those already existing in the force field 185 were used as no new atom types had to be defined. This approach, while avoiding the duplication of 186 efforts ensures the new parameters to be close to—and thus compatible with— the existing 187 CHARMM22 force field parameters. Only for few atoms, such as for atoms C7 and O3 of HCT and I1 of 188 DIT (see Fig. S1 in Supplementary Data for the assignment of atom labels), charges had to be derived 189 for which a method similar to that reported in Ref. [1] was employed. With this approach charges 190 were taken from the Mulliken populations at the minimum of an interaction energy curve of a single 191 water molecule [HF 6-31G(d)-optimized] forming a supramolecular complex with HCT [HF 6-31G(d)- 192 193 optimized] via atom O3, and with DIT [HF 6-311G(d,p)-optimized] via atom I1.
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