Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 21 What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary Information Zak E. Hughes, a and Tiffany R. Walsh a a Institute for Frontier Materials, Deakin University, Geelong, Australia. Fax: +61 ()3 227 113; Tel: +61 ()3 247 916; E-mail: zhughes@deakin.edu.au Contents REST Simulation Details: Further details of the REST simulation procedure. Table S1: The side-chain site used to determine whether a residue is in contact with the graphene surface. Table S2: Cluster populations for the REST simulations of the and peptides, in solution and adsorbed at the graphene interface. Table S3: Analysis of aromatic-aromatic residue interactions of in solution. Table S4: H-bonding analysis of and in solution. Figure S1: Exemplar metadynamics data for the adsorption of Ala. Evolution of the collective variable with simulation time, and population of the collective variable as a function of simulation time. Figure S2: Density profile of water and the adsorption freeenergy profiles for the amino acids; Ala, Arg, Asn, Asp, Cys, Glu, Gln and Gly to the graphene interface. Figure S3: Adsorption free energy profiles for the amino acids; HisA, HisH, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr and Val to the graphene interface. Figure S4: The adsorption enthalpy/free energy of amino acids to a graphene substrate reported in different studies. Figure S: Replica mobilities for the REST simulation of the peptide adsorbed on graphene. Figure S6: The number of clusters identified as a function of simulation time for the REST simulations of the peptides. Figure S7: The different secondary structure groups determined via analysis of the backbone dihedral angles for the peptides both in solution and when absorbed on graphene. Figure S8: The normalised probability distribution of the distance of the side-chain site to the graphene interface during the REST simulations for residues 1-6. Figure S9: The normalised probability distribution of the distance of the side-chain site to the graphene interface during the REST simulations for residues 7-12. REST simulation details The REST approach is a Hamilton replica exchange molecular dynamics (H-REMD) method, that provides advanced sampling of the conformational space of a system. 1 Previous studies of peptides adsorbed on inorganic substrates have shown that REST allows the efficient sampling of the conformational space of adsorbed peptides. 2 4 In the REST approach, only the peptide interactions are scaled between the replicas, giving the solute a different effective temperature in each replica. However, the non-peptide-non-peptide (graphene-graphene, graphene-water and water-water) interactions are not scaled, thus making the approach far more efficient that temperature replica exchange molecular dynamics. For a fuller outline of the REST approach and its implementation in GROMACS the authors refer readers to the previous studies of Terakawa et al. and Wright et al., 1,2 For these simulations 16 replicas with and effective temperature window spanning 3-43 K was used for the simulations of the peptides, both in the adsorbed states and when in solution. The l values were.,.7,.177,.24,.31,.48,.28,.97,.692,.83,.8,.93, 1.. These values were chosen on the basis that they have been optimised for previous simulations of similar materials binding peptides. 2,3 The initial peptide configuration differed for S1 S11 S1
reach replica, with a variety of different structure motifs selected, i.e. a-helix, b-sheet, polyproline II (PPII) and random coil. The placings of configurations in the different replicas was done randomly, with the exception that the single a-helix structure initial was placed in the top, 1th, replica. Fig. S shows the replica mobility of the th, th, 1 th and 1 th replicas for the peptide adsorbed on the graphene interface (data from the other replicas and other systems is not shown but is equivalent). The high degree of mobility indicates the excellent sampling efficiency of the REST simulations Table S1 The side-chain site of each residue used to determine whether a residue is in contact with the gaphene surface Residue Side-chain site Cutoff distance / Å Ala b-carbon. Asn side-chain N 4. HisH c.o.m. of ring heavy atoms 4. Lys side-chain N 6. Phe c.o.m. of ring heavy atoms 4. Ser side-chain O 4.2 Thr side-chain O 4.2 Trp mid-point of bond between two rings 3.7 Tyr c.o.m. of ring heavy atoms 4. Table S2 Percentages of top 1 clusters of and both adsorbed on graphene and in solution. Calculated over the full 2 ns of simulation. Percentages in bold indicate a helical cluster Solution Graphene Cluster No. 1 9.1 9.6 21.6 8.4 2 8.3 7.7 9.4 7. 3 4.9 6.3 6. 4. 4 4.7 4.2.7 4. 3. 3.7 4. 3.4 6 2.9 2.6 3.9 3. 7 2.6 2.1 2.7 2.9 8 2.6 1.8 2.4 2.9 9 2.4 1.8 2.2 2.6 1 2.3 1.8 2.1 2.6 Total No. of clusters 298 384 162 242 Table S3 Fraction of trajectory that the distance between the aromatic groups of are apple 6 Å, for both the REST simulation and the regular MD simulation of the helical configuration of in solution. The p p stacking interactions are marked in bold Groups REST Helix H1-Y4.. H1-W.21.99 H1-Y6.7.21 H1-F8.4. Y4-W.1. Y4-Y6.2. Y4-F8.18.7 W-Y6.3.79 W-F8.2. Y6-F8.. Table S4 Average number of H-bonds for and in solution, from the REST simulations and a regular MD simulation of the helical configuration of Groups REST helix REST Backbone - backbone 1. ±.2 3.7 ±.1.1 ±.1 Side-chain - side-chain.4 ±.1. ±.2 1. ±.1 Backbone - side-chain.9 ±.1.9 ±.1 1. ±.1 Protein - protein 2.3 ±.3.1 ±.1 2.2 ±.1 References 1 T. Terakawa, T. Kameda and S. Takada, J. Comput. Chem., 21, 32, 1228 1234. 2 L. B. Wright and T. R. Walsh, Phys. Chem. Chem. Phys., 213, 1, 471 4726. 3 Z. Tang, J. P. Palafox-Hernandez, W.-C. Law, Z. E. Hughes, M. T. Swihart, P. N. Prasad, M. R. Knecht and T. R. Walsh, ACS Nano, 213, 7, 9632 9646. 4 J. P. Palafox-Hernandez, Z. Tang, Z. E. Hughes, Y. Li, M. T. Swihart, P. N. Prasad, T. R. Walsh and M. R. Knecht, Chem. Mater., 214, 26, 496 4969. R. B. Pandey, Z. Kuang, B. L. Farmer, S. S. Kim and R. R. Naik, Soft Matter, 212, 8, 911 919. 6 A. N. Camden, S. A. Barr and R. J. Berry, J. Phys. Chem. B, 213, 117, 1691 1697. S2 S1 S11
Normalised population..4.4.3.3.2.2.1.1. 2 ns ns 7 ns 1 ns 12 ns 1 ns 1 1 2 2 3 3 4 4 Fig. S1 Exemplar metadynamics data for the adsorption of Ala. Evolution of the collective variable with simulation time; population of the collective variable as a function of simulation time. S1 S11 S3
4. 4 3. Water density Normalised density 3 2. 2 1. 1. Free energy of adsorption / kj mol -1 1 - -1-1 -2-2 Ala Arg Asn Asp -3 1 1 (d) Cys Glu (e) Gln Gly Free energy of adsorption / kj mol 1 1 2 2 3 1 1 2 1 1 2 Fig. S2 The density profile of water at the graphene interface, and the adsorption free energy profiles of Ala and Arg, Asn and Asp, (d) Cys and Glu and (e) Gln and Gly S4 S1 S11
1 1 HisA HisH Ile Leu Free energy of adsorption / kj mol 1 1 2 2 3 Free energy of adsorption / kj mol -1 1 - -1-1 -2-2 Lys Met (d) Phe Pro -3 1 1 (e) Ser Thr (f) Trp Tyr Val Free energy of adsorption / kj mol 1 1 2 2 3 1 1 2 1 1 2 Fig. S3 The adsorption free energy profiles of HisA and HisH, Ile and Leu, Lys and Met, (d) Phe and Pro, (e) Ser and Thr and (f) Trp, Tyr and Val S1 S11 S
Enthalpy of adsorption / kj mol -1-3 -4 - -6-7 -8-9 R K D N E Q H P Y S T G A M C F L V I -1 W - -4-3 -2-1 1 2 3 4 Hydropathy Index - V Enthalpy of adsorption / kj mol -1-1 -1-2 -2-3 -3-4 -4 R K E D H N Q P Y T S W G A M C F non-polar aromatic polar, neutral polar, acidic polar, basic L I Free energy of adsorption / kj mol -1 - - -4-3 -2-1 1 2 3 4 - -1-1 -2 R K D E N Q HA HH P Hydropathy Index non-polar aromatic polar, neutral polar, acidic polar, basic T S Y W G -2 - -4-3 -2-1 1 2 3 4 Hydropathy Index Fig. S4 The enthalpy of adsorption of amino acids as a function of their hydropathy index taken from Pandey et. al., Camden et al. 6 and the free energies of adsorption predicted in the present work. A M C F L V I S6 S1 S11
(d) Fig. S Replica mobilities for replica,, 1 and (d) 1 for the peptide adsorbed on graphene. S1 S11 S7
Number of clusters 4 3 3 2 2 1 1 2 2 Number of clusters 1 1 1 1 2 REST MD steps / 1 9 Fig. S6 The number of clusters identified as a function of simulation time for and, in solution and when adsorbed on graphene. S8 S1 S11
1 9 8 7 α i α oβ γ PPII Misc. Percentage 6 4 3 2 1 1 9 8 7 α i α oβ γ PPII Misc. Percentage 6 4 3 2 1 Fig. S7 The percentage of different secondary structure groups of the overall conformational ensemble of the peptides when in solution and adsorbed on graphene, determined via analysis of the backbone dihedral angles S1 S11 S9
.2.2.1.1..2 (d).2.1.1..2 (e) (f).2.1.1. 1 1 2 2 1 1 2 2 Fig. S8 The population distribution for the distance of the contact point of HisH1, Ser2, Ser3, (d) Tyr4/Ala4, (e) Trp/Ala and (f) Tyr6/Ala6 with the graphene interface. S1 S1 S11
.2.2.1.1..2 (d).2.1.1..2 (e) (f).2.1.1. 1 1 2 2 1 1 2 2 Fig. S9 The population distribution for the distance of the contact point of Ala7, Phe8, Asn9, (d) Asn1, (e) Lys11 and (f) Thr12 with the graphene interface. S1 S11 S11