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The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this paper, we have studied nine structurally and spectroscopically well-characterised proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I band (by 30 to 50cm-1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations.

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted Keggin dimer [(PW11O39)2Ce]10- (CeK2) and the Zr(IV)-substituted Lindqvist anion [W5O18Zr(OH2)(OH)]3- (ZrL) in order to understand how POM features such as the shape, the size, the charge or the type of incorporated metal ion influence the POM···protein interactions. Simulations revealed two regions of the protein, in which the CeK anion interacts strongly: the cationic sites formed by Arg21 on one hand and by Arg45 and Arg68 on the other. The two sites can be related with the observed selectivity in the hydrolytic cleavage of HEWL. The POMs chiefly interact with the side chains of the positively charged (arginines and lysines) and the polar uncharged (tyrosines, serines and aspargines) residues via electrostatic attraction and hydrogen bonding with the oxygens of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for stablishing interactions with several residues simultaneously. The larger and more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and it cannot interact simultaneously with several residues so efficiently.

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides, and the hexapeptide Z-Aib L-Leu-(Aib)2-Gly- Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode ap- proach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parameterization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local mode approach provides a convenient platform for the development of site frequency and coupling maps.

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). Results: We compute a coefficient of dissimilarity (omega) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of omega in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of omega. The TPR for structures sharing a Superfamily is lower than in the first dataset, but omega performs slightly better than Z score. Overall, the sensitivity of omega in predicting common Fold level is higher than that of the DaliLite Z score. Conclusion: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of omega may be attractive to the curators and the end-users of SCOP. We suggest omega may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs.

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters for dehydroalanine and dehydrobutyrine, which are compatible with the CHARMM all-atom force field. The parameters reproduce the geometries and energy barriers from MP2/6-31G*//MP2/cc-pVTZ quantum chemistry calculations. Experimental, predicted and calculated NMR chemical shifts for the amino protons and alpha-, beta- and carbonyl carbon atoms of the dehydrated residues are consistent with a significant charge redistribution. The new parameters are used to perform the first molecular dynamics simulations of nisin, a widely used but poorly understood lantibiotic, in an aqueous environment and in a phospholipid bilayer. The simulations show surface association of the peptide with membranes in agreement with solid state NMR data and formation of beta-turns in agreement with solution NMR.

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results: We show the ETS dimerisation site undergoes conformational reorganisation at the a1b1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions: We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this paper, we have studied nine structurally and spectroscopically well-characterised proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I band (by 30 to 50cm-1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations.

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted Keggin dimer [(PW11O39)2Ce]10- (CeK2) and the Zr(IV)-substituted Lindqvist anion [W5O18Zr(OH2)(OH)]3- (ZrL) in order to understand how POM features such as the shape, the size, the charge or the type of incorporated metal ion influence the POM···protein interactions. Simulations revealed two regions of the protein, in which the CeK anion interacts strongly: the cationic sites formed by Arg21 on one hand and by Arg45 and Arg68 on the other. The two sites can be related with the observed selectivity in the hydrolytic cleavage of HEWL. The POMs chiefly interact with the side chains of the positively charged (arginines and lysines) and the polar uncharged (tyrosines, serines and aspargines) residues via electrostatic attraction and hydrogen bonding with the oxygens of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for stablishing interactions with several residues simultaneously. The larger and more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and it cannot interact simultaneously with several residues so efficiently.

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides, and the hexapeptide Z-Aib L-Leu-(Aib)2-Gly- Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode ap- proach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parameterization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local mode approach provides a convenient platform for the development of site frequency and coupling maps.

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). Results: We compute a coefficient of dissimilarity (omega) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of omega in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of omega. The TPR for structures sharing a Superfamily is lower than in the first dataset, but omega performs slightly better than Z score. Overall, the sensitivity of omega in predicting common Fold level is higher than that of the DaliLite Z score. Conclusion: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of omega may be attractive to the curators and the end-users of SCOP. We suggest omega may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs.

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters for dehydroalanine and dehydrobutyrine, which are compatible with the CHARMM all-atom force field. The parameters reproduce the geometries and energy barriers from MP2/6-31G*//MP2/cc-pVTZ quantum chemistry calculations. Experimental, predicted and calculated NMR chemical shifts for the amino protons and alpha-, beta- and carbonyl carbon atoms of the dehydrated residues are consistent with a significant charge redistribution. The new parameters are used to perform the first molecular dynamics simulations of nisin, a widely used but poorly understood lantibiotic, in an aqueous environment and in a phospholipid bilayer. The simulations show surface association of the peptide with membranes in agreement with solid state NMR data and formation of beta-turns in agreement with solution NMR.

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results: We show the ETS dimerisation site undergoes conformational reorganisation at the a1b1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions: We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this paper, we have studied nine structurally and spectroscopically well-characterised proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I band (by 30 to 50cm-1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations.

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted Keggin dimer [(PW11O39)2Ce]10- (CeK2) and the Zr(IV)-substituted Lindqvist anion [W5O18Zr(OH2)(OH)]3- (ZrL) in order to understand how POM features such as the shape, the size, the charge or the type of incorporated metal ion influence the POM···protein interactions. Simulations revealed two regions of the protein, in which the CeK anion interacts strongly: the cationic sites formed by Arg21 on one hand and by Arg45 and Arg68 on the other. The two sites can be related with the observed selectivity in the hydrolytic cleavage of HEWL. The POMs chiefly interact with the side chains of the positively charged (arginines and lysines) and the polar uncharged (tyrosines, serines and aspargines) residues via electrostatic attraction and hydrogen bonding with the oxygens of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for stablishing interactions with several residues simultaneously. The larger and more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and it cannot interact simultaneously with several residues so efficiently.

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides, and the hexapeptide Z-Aib L-Leu-(Aib)2-Gly- Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode ap- proach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parameterization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local mode approach provides a convenient platform for the development of site frequency and coupling maps.

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). Results: We compute a coefficient of dissimilarity (omega) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of omega in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of omega. The TPR for structures sharing a Superfamily is lower than in the first dataset, but omega performs slightly better than Z score. Overall, the sensitivity of omega in predicting common Fold level is higher than that of the DaliLite Z score. Conclusion: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of omega may be attractive to the curators and the end-users of SCOP. We suggest omega may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs.

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters for dehydroalanine and dehydrobutyrine, which are compatible with the CHARMM all-atom force field. The parameters reproduce the geometries and energy barriers from MP2/6-31G*//MP2/cc-pVTZ quantum chemistry calculations. Experimental, predicted and calculated NMR chemical shifts for the amino protons and alpha-, beta- and carbonyl carbon atoms of the dehydrated residues are consistent with a significant charge redistribution. The new parameters are used to perform the first molecular dynamics simulations of nisin, a widely used but poorly understood lantibiotic, in an aqueous environment and in a phospholipid bilayer. The simulations show surface association of the peptide with membranes in agreement with solid state NMR data and formation of beta-turns in agreement with solution NMR.

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.

The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this paper, we have studied nine structurally and spectroscopically well-characterised proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I band (by 30 to 50cm-1) is clearly evident. Similarly, the conformational dynamics contribute to the broadening of peaks in the spectrum. The inhomogeneous broadening in both the 1D and 2D spectra reflects the significant conformational diversity observed in the simulations. Through the computed 2D cross-peak spectra, we show how different pulse schemes can provide additional information on the coupled vibrations.

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results: We show the ETS dimerisation site undergoes conformational reorganisation at the a1b1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions: We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.

The molecular interactions between the Ce(IV)-substituted Keggin anion [PW11O39Ce(OH2)4]3- (CeK) and hen egg white lysozyme (HEWL), was investigated by molecular dynamics (MD) simulations. We compared the analysis of CeK with the Ce(IV)-substituted Keggin dimer [(PW11O39)2Ce]10- (CeK2) and the Zr(IV)-substituted Lindqvist anion [W5O18Zr(OH2)(OH)]3- (ZrL) in order to understand how POM features such as the shape, the size, the charge or the type of incorporated metal ion influence the POM···protein interactions. Simulations revealed two regions of the protein, in which the CeK anion interacts strongly: the cationic sites formed by Arg21 on one hand and by Arg45 and Arg68 on the other. The two sites can be related with the observed selectivity in the hydrolytic cleavage of HEWL. The POMs chiefly interact with the side chains of the positively charged (arginines and lysines) and the polar uncharged (tyrosines, serines and aspargines) residues via electrostatic attraction and hydrogen bonding with the oxygens of the POM framework. The CeK anion shows higher protein affinity than the CeK2 and ZrL anions, because it is less hydrophilic and it has the right size and shape for stablishing interactions with several residues simultaneously. The larger and more negatively charged CeK2 anion has a high solvent-accessible surface, which is sub-optimal for the interaction, while the smaller ZrL anion is highly hydrophilic and it cannot interact simultaneously with several residues so efficiently.

Non-linear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides, and the hexapeptide Z-Aib L-Leu-(Aib)2-Gly- Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode ap- proach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parameterization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local mode approach provides a convenient platform for the development of site frequency and coupling maps.

Lanthionine antibiotics are an important class of naturally-occurring antimicrobial peptides. The best-known, nisin, is a commercial food preservative. However, structural and mechanistic details on nisin/lipid II membrane complexes are currently lacking. Recently, we have developed empirical force-field parameters to model lantibiotics. Docking and molecular dynamics (MD) simulations have been used to study the nisin2:lipid II complex in bacterial membranes, which has been put forward as the building block of nisin/lipid II binary membrane pores. A Ile1Trp mutation of the N-terminus of nisin has been modelled and docked onto lipid II models; the computed binding affinity increased compared to wildtype. Wild-type nisin was also docked onto three different lipid II structures and a stable 2:1 nisin:lipid II complex formed. This complex was inserted into a membrane. Six independent MD simulations revealed key interactions in the complex, specifically the N terminal engagement of nisin with lipid II at the pyrophosphate and C-terminus of the pentapeptide chain. Nisin2 inserts into the membrane and we propose this is the first step in pore formation, mediated by the nisin N-terminus–lipid II pentapeptide hydrogen bond. The lipid II undecaprenyl chain adopted different conformations in the presence of nisin, which may also have implications for pore formation.

We present pair potentials for fluorinated methanes and their dimers with CO2 based on ab initio potential energy surfaces. These potentials reproduce the experimental second virial coefficients of the pure fluorinated methanes and their mixtures with CO2 without adjustment. Ab initio calculations on trimers are used to model the effects of nonadditive dispersion and induction. Simulations using these potentials reproduce the experimental phase-coexistence properties of CH3F within 10% over a wide range of temperatures. The phase coexistence curve of the mixture of CH2F2 and CO2 is reproduced with an error in the mole fractions of both phases of less than 0.1. The potentials described here are based entirely on ab initio calculations, with no empirical fits to improve the agreement with experiment.

Background: Classification of newly resolved protein structures is important in understanding their architectural, evolutionary and functional relatedness to known protein structures. Among various efforts to improve the database of Structural Classification of Proteins (SCOP), automation has received particular attention. Herein, we predict the deepest SCOP structural level that an unclassified protein shares with classified proteins with an equal number of secondary structure elements (SSEs). Results: We compute a coefficient of dissimilarity (omega) between proteins, based on structural and sequence-based descriptors characterising the respective constituent SSEs. For a set of 1,661 pairs of proteins with sequence identity up to 35%, the performance of omega in predicting shared Class, Fold and Super-family levels is comparable to that of DaliLite Z score and shows a greater than four-fold increase in the true positive rate (TPR) for proteins sharing the Family level. On a larger set of 600 domains representing 200 families, the performance of Z score improves in predicting a shared Family, but still only achieves about half of the TPR of omega. The TPR for structures sharing a Superfamily is lower than in the first dataset, but omega performs slightly better than Z score. Overall, the sensitivity of omega in predicting common Fold level is higher than that of the DaliLite Z score. Conclusion: Classification to a deeper level in the hierarchy is specific and difficult. So the efficiency of omega may be attractive to the curators and the end-users of SCOP. We suggest omega may be a better measure for structure classification than the DaliLite Z score, with the caveat that currently we are restricted to comparing structures with equal number of SSEs.

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters for dehydroalanine and dehydrobutyrine, which are compatible with the CHARMM all-atom force field. The parameters reproduce the geometries and energy barriers from MP2/6-31G*//MP2/cc-pVTZ quantum chemistry calculations. Experimental, predicted and calculated NMR chemical shifts for the amino protons and alpha-, beta- and carbonyl carbon atoms of the dehydrated residues are consistent with a significant charge redistribution. The new parameters are used to perform the first molecular dynamics simulations of nisin, a widely used but poorly understood lantibiotic, in an aqueous environment and in a phospholipid bilayer. The simulations show surface association of the peptide with membranes in agreement with solid state NMR data and formation of beta-turns in agreement with solution NMR.

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

It is increasingly easy to develop software that exploits Graphics Processing Units (GPUs). The molecular dynamics simulation community has embraced this recent opportunity. Herein, we outline the current approaches that exploit this technology. In the context of biomolecular simulations, we discuss some of the algorithms that have been implemented and some of the aspects that distinguish the GPU from previous parallel environments. The ubiquity of GPUs and the ingenuity of the simulation community augur well for the scale and scope of future computational studies of biomolecules.

Background: The Elk-1 transcription factor is a member of a group of proteins called ternary complex factors, which serve as a paradigm for gene regulation in response to extracellular signals. Its deregulation has been linked to multiple human diseases including the development of tumours. The work herein aims to inform the design of potential peptidomimetic compounds that can inhibit the formation of the Elk-1 dimer, which is key to Elk-1 stability. We have conducted molecular dynamics simulations of the Elk-1 ETS domain followed by virtual screening. Results: We show the ETS dimerisation site undergoes conformational reorganisation at the a1b1 loop. Through exhaustive screening of di- and tri-peptide libraries against a collection of ETS domain conformations representing the dynamics of the loop, we identified a series of potential binders for the Elk-1 dimer interface. The di-peptides showed no particular preference toward the binding site; however, the tri-peptides made specific interactions with residues: Glu17, Gln18 and Arg49 that are pivotal to the dimer interface. Conclusions: We have shown molecular dynamics simulations can be combined with virtual peptide screening to obtain an exhaustive docking protocol that incorporates dynamic fluctuations in a receptor. Based on our findings, we suggest experimental binding studies to be performed on the 12 SILE ranked tri-peptides as possible compounds for the design of inhibitors of Elk-1 dimerisation. It would also be reasonable to consider the score ranked tri-peptides as a comparative test to establish whether peptide size is a determinant factor of binding to the ETS domain.