Atomistic modeling of the low-frequency mechanical modes and Raman spectra of icosahedral virus capsids.

We describe a technique for calculating the low-frequency mechanical modes and frequencies of a large symmetric biological molecule where the eigenvectors of the Hessian matrix are determined with full atomic detail. The method, which follows order N methods used in electronic structure theory, determines the subset of lowest-frequency modes while using group theory to reduce the complexity of the problem. We apply the method to three icosahedral viruses of various T numbers and sizes; the human viruses polio and hepatitis B, and the cowpea chlorotic mottle virus, a plant virus. From the normal-mode eigenvectors, we use a bond polarizability model to predict a low-frequency Raman scattering profile for the viruses. The full atomic detail in the displacement patterns combined with an empirical potential-energy model allows a comparison of the fully atomic normal modes with elastic network models and normal-mode analysis with only dihedral degrees of freedom. We find that coarse-graining normal-mode analysis (particularly the elastic network model) can predict the displacement patterns for the first few (approximately 10) low-frequency modes that are global and cooperative.

Normal mode analysis and applications in biological physics.

Normal mode analysis has become a popular and often used theoretical tool in the study of functional motions in enzymes, viruses, and large protein assemblies. The use of normal modes in the study of these motions is often extremely fruitful since many of the functional motions of large proteins can be described using just a few normal modes which are intimately related to the overall structure of the protein. In this review, we present a broad overview of several popular methods used in the study of normal modes in biological physics including continuum elastic theory, the elastic network model, and a new all-atom method, recently developed, which is capable of computing a subset of the low frequency vibrational modes exactly. After a review of the various methods, we present several examples of applications of normal modes in the study of functional motions, with an emphasis on viral capsids.

Simulations of impulsive laser scattering of biological protein assemblies: application to M13 bacteriophage.

We develop a theoretical framework, based on a bond-polarizability model, for simulating the impulsive force experienced on a protein or an assembly of proteins from a pulsed light source by coupling the laser electric field to an atomic distortion. The mechanism is impulsive stimulated Raman scattering (ISRS) where mechanical distortions produce variation in the electronic polarization through atomic displacements similar to vibrational Raman scattering. The magnitude of the impulsive force is determined from the empirical two-body bond-polarizability model and the intensity of the incident light. We apply the method to the M13 bacteriophage protein capsid system by performing several classical molecular-dynamics simulations that include the additional impulsive laser scattering force at various light intensities and pulse widths. The results of the molecular-dynamics simulations are then qualitatively interpreted with a simple harmonic oscillator model driven by ISRS. The intensity of light required to produce damage to the capsid in the simulations was found to be far higher than what was found in recent pulsed laser scattering experiments of M13 phage, suggesting that the observed inactivation of viruses with ultrashort laser pulses involves processes and/or mechanisms not taken into account in the present simulations.

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing.

We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH(2))(2))-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

Structural and dynamic properties of BaInGeH: a rare solid-state indium hydride.

BaInGeH was synthesized by hydrogenating the intermetallic compound BaInGe. The crystal structure determination from the powder neutron diffraction data of BaInGeD [P3m1, Z = 1, a = 4.5354(3) A, c = 5.2795(6) A] reveals the presence of hydrogen in tetrahedral voids defined by three Ba atoms and one In atom.

Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing.

We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact's Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green's-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

Theory of the low frequency mechanical modes and Raman spectra of the M13 bacteriophage capsid with atomic detail.

We present a theoretical study of the low frequency vibrational modes of the M13 bacteriophage using a fully atomistic model. Using ideas from electronic structure theory, the few lowest vibrational modes of the M13 bacteriophage are determined using classical harmonic analysis. The relative Raman intensity is estimated for each of the mechanical modes using a bond polarizability model. Comparison of the atomic mechanical modes calculated here with modes derived from elastic continuum theory shows that a much richer spectrum emerges from an atomistic picture.

Vibrational energy funneling in viruses-simulations of impulsive stimulated Raman scattering in M13 bacteriophage.

The vibrational excitation of a tubular M13 bacteriophage capsid is simulated using classical molecular dynamics. The excitation occurs through impulsive stimulated Raman scattering by ultra-short laser pulses which ping the vibrational modes of the capsid. Tuning the laser pulse temporal width determines the frequency region of the capsid that is excited. The simulations reveal that electromagnetic energy transferred to the high frequency modes by ultra-short pulses is funneled via anharmonicity to just five low frequency modes which receive approximately 80% of the funneled energy. A single mode receives most of the funneled energy (3-4% of the total energy delivered) involves swelling and is effective in damaging the capsid. However, the laser intensity necessary to produce damage to the capsid from a single laser pulse is found to be extremely high for this mechanism to be effective.

Photonic approach to the selective inactivation of viruses with a near-infrared subpicosecond fiber laser.

We report a photonic approach for selective inactivation of viruses with a near-infrared subpicosecond laser. We demonstrate that this method can selectively inactivate viral particles ranging from nonpathogenic viruses such as the M13 bacteriophage and the tobacco mosaic virus to pathogenic viruses such as the human papillomavirus and the human immunodeficiency virus (HIV). At the same time, sensitive materials such as human Jurkat T cells, human red blood cells, and mouse dendritic cells remain unharmed. The laser technology targets the global mechanical properties of the viral protein shell, making it relatively insensitive to the local genetic mutation in the target viruses. As a result, the approach can inactivate both the wild and mutated strains of viruses. This intriguing advantage is particularly important in the treatment of diseases involving rapidly mutating viral species such as HIV. Our photonic approach could be used for the disinfection of viral pathogens in blood products and for the treatment of blood-borne viral diseases in the clinic.

Low frequency mechanical modes of viral capsids: an atomistic approach.

We present a method for the calculation of the low frequency vibrational modes and frequencies of viral capsids, or other large molecules, where the modes are modeled with atomic detail. Extending ideas from electronic structure theory, an energy functional is used to find modes of a classical dynamical matrix below a fixed (pseudo-Fermi) level. The icosahedral satellite tobacco necrosis virus is modeled as an example. We find that atoms around the C5 and C3 axis have small relative displacement while the beta sheet body shows gliding motion.

Vibrational property study of SrGa2H2 and BaGa2H2 by inelastic neutron scattering and first principles calculations.

Vibrational properties of the gallium hydrides SrGa2H2 and BaGa2H2 have been investigated by means of inelastic neutron scattering (INS) and first-principles calculations. The compounds contain Ga-H units being part of a two-dimensional polyanionic layer, [(GaH)(GaH)]2-. The INS spectra are composed of dispersed internal Ga-H bending and stretching modes at frequencies above 600 cm(-1) and external lattice modes at frequencies below 220 cm(-1). Frequencies of the internal modes are not susceptible to the metal countercation, indicating a strong integrity of the polyanionic layer as a building unit in the structures of SrGa2H2 and BaGa2H2. The Ga-H stretching modes have frequencies between 1200 and 1400 cm(-1), which is very low compared to molecular gallium hydrides. The weak Ga-H bond in SrGa2H2 and BaGa2H2 is balanced by Sr(Ba)-H interactions.

Raman intensity and spectra predictions for cylindrical viruses.

A theoretical framework for predicting low frequency Raman vibrational spectra of viral capsids is presented and applied to the M13 bacteriophage. The method uses a continuum elastic theory for the vibrational modes and a bond-charge polarizability model of an amorphous material to roughly predict the Raman intensities. Comparison is made to experimental results for the M13 bacteriophage virus.

Vibrational properties of polyanionic hydrides SrAl2H2 and SrAlSiH: new insights into Al-H bonding interactions.

The vibrational properties of the recently discovered aluminum hydrides SrAl2H2 and SrAlSiH have been investigated by means of inelastic neutron scattering (INS) and first-principles calculations. Both compounds contain Al-H units being part of a two-dimensional polyanionic layer, [(AlH)(AlH)]2- and [Si(AlH)]2-, respectively. The INS spectrum of SrAlSiH is characterized by very weakly dispersed Al-H modes with well-resolved overtones, while SrAl2H2 yields a solid-state dispersed phonon spectrum. The frequency of the stretching mode of the Al-H unit in SrAlSiH is the hitherto lowest observed for a terminal Al-H bond. At the same time, SrAlSiH displays the highest decomposition temperature known for an aluminum hydride compound. It is proposed that the stability of solid-state aluminum hydrides correlates inversely with the strength of Al-H bonding.

Probing the low-frequency vibrational modes of viruses with Raman scattering--bacteriophage M13 in water.

Raman spectroscopy is used to study low-wave-number (

Observation of the low frequency vibrational modes of bacteriophage M13 in water by Raman spectroscopy.

BACKGROUND: Recently, a technique which departs radically from conventional approaches has been proposed. This novel technique utilizes biological objects such as viruses as nano-templates for the fabrication of nanostructure elements. For example, rod-shaped viruses such as the M13 phage and tobacco mosaic virus have been successfully used as biological templates for the synthesis of semiconductor and metallic nanowires. RESULTS AND DISCUSSION: Low wave number (

Holliday junction dynamics and branch migration: single-molecule analysis.

The Holliday junction (HJ) is a central intermediate in various genetic processes including homologous and site-specific recombination and DNA replication. Branch migration allows the exchange between homologous DNA regions, but the detailed mechanism for this key step of DNA recombination is unidentified. Here, we report direct real-time detection of branch migration in individual molecules. Using appropriately designed HJ constructs we were able to follow junction branch migration at the single-molecule level. Branch migration is detected as a stepwise random process with the overall kinetics dependent on Mg2+ concentration. We developed a theoretical approach to analyze the mechanism of HJ branch migration. The data show steps in which the junction flips between conformations favorable to branch migration and conformations unfavorable to it. In the favorable conformation (the extended HJ geometry), the branch can migrate over several base pairs detected, usually as a single large step. Mg2+ cations stabilize folded conformations and stall branch migration for a period considerably longer than the hopping step. The conformational flip and the variable base pair hopping step provide insights into the regulatory mechanism of genetic processes involving HJs.

Electronic decay constant of carotenoid polyenes from single-molecule measurements.

The conductance of carotenoid polyenes chemically bound at each end to gold contacts has been measured for single molecules containing 5, 7, 9, and 11 carbon-carbon double bonds in conjugation. The electronic decay constant, beta, is determined to be 0.22 +/- 0.04 A-1, in close agreement with the value obtained from first principles simulations (0.22 +/- 0.01 A-1). The absolute values of the molecular conductance are within a factor of 3 of those calculated from first principles. The small value of beta demonstrates that conductivity drops off only slowly with chain length, confirming that carotenoid conjugated chains are relatively good molecular "wires".

Band-gap tunneling states in DNA.

An important issue regarding DNA electrical conductivity is the electron (hole) transfer rate. Experiments have found that this transfer rate involves quantum mechanical tunneling for short distances and thermally activated hopping over large distances. The electron (or hole) tunneling probability through a molecule depends on the length of molecule L, as e(-beta(E)L), where the tunneling betaE factor is strongly energy dependent. We have calculated betaE in DNA for poly(dA)-poly(dT) and poly(dG)-poly(dC) for the first time using a complex band structure approach. Although the DNA band gap is not exceptionally large, we find that the very large beta value near midgap makes DNA a poor tunneling conductor. The tunneling decay in DNA is more rapid than many other organic molecules, including those with a far wider gap.

Supercoiling-induced DNA bending.

Local DNA bending is a critical factor for numerous DNA functions including recognition of DNA by sequence-specific regulatory binding proteins. Negative DNA supercoiling increases both local and global DNA dynamics, and this dynamic flexibility can facilitate the formation of DNA-protein complexes. We have recently shown that apexes of supercoiled DNA molecules are sites that can promote the formation of an alternative DNA structure, a cruciform, suggesting that these positions in supercoiled DNA are under additional stress and perhaps have a distorted DNA geometry. To test this hypothesis, we used atomic force microscopy to directly measure the curvature of apical positions in supercoiled DNA. The measurements were performed for an inherently curved sequence formed by phased A tracts and a region of mixed sequence DNA. For this, we used plasmids in which an inverted repeat and A tract were placed at precise locations relative to each other. Under specific conditions, the inverted repeat formed a cruciform that was used as a marker for the unambiguous identification of the A tract location. When the A tract and cruciform were placed diametrically opposite, this yielded predominantly nonbranched plectonemic molecules with an extruded cruciform and A tract localized in the terminal loops. For both the curved A tract and mixed sequence nonbent DNA, their localization to an apex increased the angle of bending compared to that expected for DNA unconstrained in solution. This is consistent with increased helical distortion at an apical bend.

Theoretical analysis of electron transport through organic molecules.

We present a theoretical study of electron transport through a variety of organic molecules. The analysis uses the Landauer formalism in combination with complex bandstructure and projected densities of states calculations to reveal the main aspects of coherent electronic transport through alkanes, benzene-dithiol, and phenylene-ethynylene oligomers. We examine the dependence of the current on molecule length, the effects of molecule-molecule interactions from film packing, differences in contact geometry, and the influence of phenyl ring rotation on the conductances of phenylene-ethynylene oligomers such as 1,4-bis-phenylethynyl-benzene.