Steven A. Corcelli

Self-assembly of hydrogen-bonded two-dimensional quasicrystals

The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

The Dynamics of Water at DNA Interfaces: Computational Studies of Hoechst 33258 Bound to DNA

Together, spectroscopy combined with computational studies that relate directly to the experimental measurements have the potential to provide unprecedented insight into the dynamics of important biological processes. Recent time-resolved fluorescence experiments have shown that the time scales for collective reorganization at the interface of proteins and DNA with water are more than an order of magnitude slower than in bulk aqueous solution. The molecular interpretation of this change in the collective response is somewhat controversial some attribute the slower reorganization to dramatically retarded water motion, while others describe rapid water dynamics combined with a slower biomolecular response. To connect directly to solvation dynamics experiments of the fluorescent probe Hoechst 33258 (H33258) bound to DNA, we have generated 770 ns of molecular dynamics (MD) simulations and calculated the equilibrium and nonequilibrium solvation response to excitation of the probe. The calculated time scales for the solvation response of H33258 free in solution (0.17 and 1.4 ps) and bound to DNA (1.5 and 20 ps) are highly consistent with experiment (0.2 and 1.2 ps, 1.4 and 19 ps, respectively). Decomposition of the calculated response revealed that water solvating the probe bound to DNA was still relatively mobile, only slowing by a factor of 2-3, while DNA motion was responsible for the long-time component (approximately 20 ps).

Nitrile Groups as Vibrational Probes: Calculations of the C≡N Infrared Absorption Line Shape of Acetonitrile in Water and Tetrahydrofuran

The C[TRIPLE BOND]N bond is a powerful probe of protein structure and dynamics because it absorbs in a region of the infrared spectrum apart from the other vibrations that occur naturally in proteins, and because its infrared absorption line shape is sensitive to specific characteristics of the local environment. Since the polarity experienced by the probe can differ dramatically within the protein, infrared spectroscopy of a C[TRIPLE BOND]N site-specifically labeled residue can be used to infer its local environment within the protein. It has been shown experimentally that the spectrum of acetonitrile in water is different in terms of peak position and width compared to acetonitrile in tetrahydrofuran (THF). An optimized quantum mechanics/molecular mechanics method for calculating accurate vibrational frequencies in condensed-phase was parametrized for acetonitrile in water. The transferability of the methodology to a different solvent was tested by computing the infrared line shapes of acetonitrile in both water and THF and comparing to experiment. The infrared absorption line shapes agree well with experiment in each case, and the trends observed experimentally are recovered. The accuracy of the methodology for two solvents of differing polarity indicates that this technique is suitable to study CN probes in proteins.

Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism.

αβ T-cell receptors (TCRs) recognize multiple antigenic peptides bound and presented by major histocompatibility complex molecules. TCR cross-reactivity has been attributed in part to the flexibility of TCR complementarity-determining region (CDR) loops, yet there have been limited direct studies of loop dynamics to determine the extent of its role. Here we studied the flexibility of the binding loops of the αβ TCR A6 using crystallographic, spectroscopic, and computational methods. A significant role for flexibility in binding and cross-reactivity was indicated only for the CDR3α and CDR3β hypervariable loops. Examination of the energy landscapes of these two loops indicated that CDR3β possesses a broad, smooth energy landscape, leading to rapid sampling in the free TCR of a range of conformations compatible with different ligands. The landscape for CDR3α is more rugged, resulting in more limited conformational sampling that leads to specificity for a reduced set of peptides as well as the major histocompatibility complex protein. In addition to informing on the mechanisms of cross-reactivity and specificity, the energy landscapes of the two loops indicate a complex mechanism for TCR binding, incorporating elements of both conformational selection and induced fit in a manner that blends features of popular models for TCR recognition.

Optimized quantum mechanics/molecular mechanics strategies for nitrile vibrational probes: acetonitrile and para-tolunitrile in water and tetrahydrofuran.

The nitrile (Ctriple bondN) group is a powerful probe of structure and dynamics because its vibrational frequency is extraordinarily sensitive to the electrostatic and chemical characteristics of its local environment. For example, site-specific nitrile labels are useful indicators of protein structure because their infrared (IR) absorption spectra can clearly distinguish between solvent-exposed residues and residues buried in the hydrophobic core of a protein. In this work, three variants of the optimized quantum mechanics/molecular mechanics (OQM/MM) technique for computing Ctriple bondN vibrational frequencies were developed and assessed for acetonitrile in water. For the most robust variant, the transferability of the OQM/MM methodology to different solutes and solvents was evaluated by simulating the IR absorption spectra of para-tolunitrile in water and tetrahydrofuran and comparing to experiment and density functional theory (DFT) calculations. The OQM/MM frequencies compared favorably to DFT for para-tolunitrile/water, and the calculated IR absorption spectra are in qualitative agreement with experiment. This suggests that a single parametrization of the OQM/MM technique is reasonable for the calculation of nitrile line shapes when the probe is attached to different chemical moieties and when the label experiences local environments of different polarity.

Phosphate vibrations probe local electric fields and hydration in biomolecules.

The role of electric fields in important biological processes such as binding and catalysis has been studied almost exclusively by computational methods. Experimental measurements of the local electric field in macromolecules are possible using suitably calibrated vibrational probes. Here we demonstrate that the vibrational transitions of phosphate groups are highly sensitive to an electric field and show how that sensitivity can be quantified, allowing electric field measurements to be made in phosphate-containing biological systems without chemical modification.

Dynamical Signature of Abasic Damage in DNA

Time-dependent Stokes shift (TDSS) responses in proteins and DNA exhibit a broad range of long time scales (>10 ps) that are not present in bulk aqueous solution. The physical interpretation of the long TDSS time scales in biomolecular systems is a matter of considerable debate because of the many different components present in the sample (water, biomolecule, counterions), which have highly correlated motions and intrinsically different abilities to adapt to local perturbations. Here we use molecular dynamics (MD) simulations to show that the surprisingly slow (∼10 ns) TDSS response of coumarin 102 (C102), a base pair replacement, reflects a distinct dynamical signature for DNA damage. When the C102 molecule is covalently incorporated into DNA, an abasic site is created on the strand opposite the C102 probe. The abasic sugar exhibits a reversible interchange between intra- and extrahelical conformations that are kinetically stable on a nanosecond time scale. This conformational change, only possible in damaged DNA, was found to be responsible for the long time scales in the measured TDSS response. For the first time, a TDSS measurement has been attributed to a specific biomolecular motion. This finding directly contradicts the prevailing notion that the TDSS response in biomolecular contexts is dominated by hydration dynamics. It also suggests that TDSS experiments can be used to study ultrafast biomolecular dynamics that are inaccessible to other techniques.

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study.

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.

Evidence of an unusual N-H···N hydrogen bond in proteins.

Many residues within proteins adopt conformations that appear to be stabilized by interactions between an amide N-H and the amide N of the previous residue. To explore whether these interactions constitute hydrogen bonds, we characterized the IR stretching frequencies of deuterated variants of proline and the corresponding carbamate, as well as the four proline residues of an Src homology 3 domain protein. The CδD2 stretching frequencies are shifted to lower energies due to hyperconjugation with Ni electron density, and engaging this density via protonation or the formation of the Ni+1-H···Ni interaction ablates this hyperconjugation and thus induces an otherwise difficult to explain blue shift in the C-D absorptions. Along with density functional theory calculations, the data reveal that the Ni+1-H···Ni interactions constitute H-bonds and suggest that they may play an important and previously underappreciated role in protein folding, structure, and function.

Carbon-deuterium vibrational probes of peptide conformation: alanine dipeptide and glycine dipeptide.

The utility of alpha-carbon deuterium-labeled bonds (C(alpha)-D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: C(alpha)-D labeled alanine dipeptide (Adp-d(1)) and C(alpha)-D(2) labeled glycine dipeptide (Gdp-d(2)). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d(1) and Gdp-d(2), we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of phi and psi, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5 degrees spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic C(alpha)-D and C(alpha)-D(2) stretch transition frequencies for each structure. For Adp-d(1) the C(alpha)-D stretch frequency exhibited a maximum variability of 39.4 cm(-1) between the six stable structures identified in the gas phase. The C(alpha)-D(2) frequencies of Gdp-d(2) show an even more substantial difference between its three stable conformations: there is a 40.7 cm(-1) maximum difference in the symmetric C(alpha)-D(2) stretch frequencies and an 81.3 cm(-1) maximum difference in the asymmetric C(alpha)-D(2) stretch frequencies. Moreover, the splitting between the symmetric and asymmetric C(alpha)-D(2) stretch frequencies of Gdp-d(2) is remarkably sensitive to its conformation.