Ilya Chorny

De novo structure prediction and experimental characterization of folded peptoid oligomers

Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present blind-structure predictions for three peptoid sequences using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement. We correctly predicted the structure of a N-aryl peptoid trimer to within 0.2 Å rmsd-backbone and a cyclic peptoid nonamer to an accuracy of 1.0 Å rmsd-backbone. X-ray crystallographic structures are presented for a linear N-alkyl peptoid trimer and for the cyclic peptoid nonamer. The peptoid macrocycle structure features a combination of cis and trans backbone amides, significant nonplanarity of the amide bonds, and a unique “basket” arrangement of (S)-N(1-phenylethyl) side chains encompassing a bound ethanol molecule. REMD simulations of the peptoid trimers reveal that well folded peptoids can exhibit funnel-like conformational free energy landscapes similar to those for ordered polypeptides. These results indicate that physical modeling can successfully perform de novo structure prediction for small peptoid molecules.

In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability

Significance mAbs are increasingly being used for treatment of chronic diseases wherein the subcutaneous delivery route is preferred to enable self-administration and at-home use. To deliver high doses (several hundred milligrams) through a small volume (∼1 mL) into the subcutaneous space, mAb solutions need to have low viscosity. Concomitantly, acceptable chemical stability is required for adequate shelf life, and normal in vivo clearance is needed for less frequent dosing. We propose in silico tools that provide rapid assessment of atypical behavior of mAbs (high viscosity, chemical degradation, and fast plasma clearance), which are simply predicted from sequence and/or structure-derived parameters. Such analysis will greatly improve the probability of success to move mAb-based therapeutics efficiently into clinical development and ultimately benefit patients. For mAbs to be viable therapeutics, they must be formulated to have low viscosity, be chemically stable, and have normal in vivo clearance rates. We explored these properties by observing correlations of up to 60 different antibodies of the IgG1 isotype. Unexpectedly, we observe significant correlations with simple physical properties obtainable from antibody sequences and by molecular dynamics simulations of individual antibody molecules. mAbs viscosities increase strongly with hydrophobicity and charge dipole distribution and decrease with net charge. Fast clearance correlates with high hydrophobicities of certain complementarity determining regions and with high positive or high negative net charge. Chemical degradation from tryptophan oxidation correlates with the average solvent exposure time of tryptophan residues. Aspartic acid isomerization rates can be predicted from solvent exposure and flexibility as determined by molecular dynamics simulations. These studies should aid in more rapid screening and selection of mAb candidates during early discovery.

Molecular dynamics study of the vibrational relaxation of OClO in bulk liquids

The vibrational relaxation of OClO in bulk water, acetonitrile, and ethanol is studied using classical and semiclassical molecular dynamics computer simulations. Nonequilibrium classical trajectory calculations provide insight into the early stages of vibrational energy relaxation of highly excited states. Equilibrium force autocorrelation functions are used to determine the relaxation rate for the v=1→v=0 transition. Good agreement with experiments is found. The calculations suggest that the hydrogen bonding in water, as reflected by the high density of librational modes, is the reason for the fast relaxation in this liquid compared with that in ethanol and acetonitrile.

Molecular dynamics study of the photodissociation and photoisomerization of ICN in water

The photodissociation and photoisomerization of ICN in water is studied using molecular dynamics simulations. A water–ICN potential energy function that takes into account the different ground and excited state charges and their shift as a function of the reaction coordinate is developed. The calculations include nonadiabatic transitions between the different electronic states and allow for a complete description of the photodissociation leading to ground-state and excited-state iodine and to recombination producing ICN and INC. The calculated UV absorption spectrum, the cage escape probability, the quantum yield of ICN and INC, and the subsequent vibrational relaxation rate of ICN and INC are in reasonable agreement with recent experiments. The trajectories provide a detailed microscopic picture of the early events. For example, it is shown that most recombination events on the ground state involve nonadiabatic transitions before the molecule has a chance to completely dissociate on the excited state, an...

Vibrational relaxation at water surfaces

The vibrational relaxation of several diatomic molecules at the surface of liquid water is studied using classical molecular-dynamics computer simulations and compared with the same process in the bulk liquids. Both nonequilibrium classical trajectory calculations and equilibrium force autocorrleation functions are used to elucidate the factors that influence vibrational energy relaxation at the liquid surface region. We find that in general vibrational relaxation rates at interfaces are slower than in the bulk due to reduced friction. However, the degree of the slowing-down effect depends on the contribution of electrostatic forces and is correlated with the structure of the first solvation shell.

Photodissociation of ICN at the liquid/vapor interface of chloroform

The photodissociation of ICN initially adsorbed at the liquid/vapor interface of chloroform is studied using classical molecular dynamics computer simulations. The photodissociation and subsequent geminate recombination on the ground state of ICN is compared with the same reaction in the bulk liquid. We find that the probability for cage escape at the interface is significantly enhanced due to the possibility that one or both of the photodissociation fragments desorb into the gas phase. The desorption probability is sensitive to the initial location and orientation of the ICN. An examination of the energy disposal into these fragments provides additional information about the competition between geminate recombination and cage escape at the interface.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations

The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with Fab and Fc domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.

Molecular dynamics study of the photodissociation of OClO in bulk liquids

The electronic spectra and the photodissociation dynamics of OClO on the excited state in bulk water, acetonitrile, and ethanol are computed using classical molecular dynamics computer simulations. The trajectories are run on an ab initio potential energy surface of Peterson [J. Chem. Phys. 109, 8864 (1998)], which is fit to a global three-dimensional analytical surface. The calculated cage escape probability in these liquids seems to correlate with the vibrational relaxation rate of the parent molecule and is in reasonable agreement with experiments in water and acetonitrile, but somewhat overestimates the experimental probability in the case of ethanol.

Vibrational relaxation of ICN bulk and surface chloroform

The vibrational relaxation of ICN at the surface of chloroform is studied using classical molecular dynamics computer simulations and is compared with the same process in the bulk liquid. Non-equilibrium classical trajectory calculations and equilibrium force correlation functions are used to investigate the factors that control the vibrational energy relaxation rate. We find that the relaxation rate depends on the initial excitation energy and is a factor of three slower at the interface than in the bulk. In addition, the frequency dependent friction at the interface is found to be orientation dependent, reflecting strong inhomogeneity.