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  • 1
    Keywords: DENSITY-FUNCTIONAL-THEORY ; ENERGIES ; ENVIRONMENT ; MODEL ; MODELS ; SYSTEM ; SYSTEMS ; PROTEIN ; MECHANISM ; mechanisms ; NO ; ENERGY ; LENGTH ; FUTURE ; ORIENTATION ; STACKING INTERACTIONS ; BOND ; HARTREE-FOCK ; CHAIN ; BASE-PAIRS
    Abstract: Hartree-Fock calculations are first presented when a polyene is brought down parallel to the plane of some polyacenes and also, for one case, in a perpendicular orientation. Attention is given to the variation of (a) bond lengths and (b) the HOMO-LUMO energy gap. Following these numerical investigations on finite systems, some tight-binding models (Huckel-like) are worked out to illustrate the effects of different environments on the g-electron assembly in polyenes. Again the focal points are whether bond alternation is enhanced, or suppressed, and the consequences for the HOMO-LUMO energy gap. Some analytic progress proves possible for an infinite polyene chain interacting with (a) an infinite polyacene and (b) an infinite polyphenacene, when a "hopping" energy is used to couple the polyene with its "environment". In the former model (a), with no HOMO-LUMO gap in the isolated infinite polyacene, a pi-electron polyene gap is opened up. In model (b), a similar variation of the energy gap is found. For future studies, reference is finally made to experiments on the (polyene) chromophore in the retinal protein bacteriorhodopsin. The observed red shift needs mechanisms additional to those considered in the present study, and some suggestions are made here
    Type of Publication: Journal article published
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  • 2
    Keywords: AB-INITIO ; ENERGIES ; OPTIMIZATION ; Germany ; MODEL ; DENSITY ; PROTEIN ; PROTEINS ; ACCURACY ; MECHANISM ; DYNAMICS ; SIMULATION ; ACID ; ENERGY ; STRESS ; sensitivity ; ANGSTROM RESOLUTION ; GAS-PHASE ; SINGLE ; molecular ; PROTON-TRANSFER ; SCHIFF-BASE ; AMINO-ACID ; interaction ; OPSIN SHIFT ; VISUAL PIGMENTS ; CHARGE ; bacteriorhodopsin ; QM/MM ; GROUND-STATE ; density functional theory ; FUNCTIONAL THEORY ; HIGH-SENSITIVITY ; CHROMOPHORE MODEL ; CONFIGURATION-INTERACTION PROCEDURE ; MOLECULAR ELECTRONIC-SPECTRA ; SENSORY RHODOPSIN-II/
    Abstract: Rhodopsins can modulate the optical properties of their chromophores over a wide range of wavelengths. The mechanism for this spectral tuning is based on the response of the retinal chromophore to external stress and the interaction with the charged, polar, and polarizable amino acids of the protein environment and is connected to its large change in dipole moment upon excitation, its large electronic polarizability, and its structural flexibility. In this work, we investigate the accuracy of computational approaches for modeling changes in absorption energies with respect to changes in geometry and applied external electric fields. We illustrate the high sensitivity of absorption energies on the ground-state structure of retinal, which varies significantly with the computational method used for geometry optimization. The response to external fields, in particular to point charges which model the protein environment in combined quantum mechanical/molecular mechanical (QM/MM) applications, is a crucial feature, which is not properly represented by previously used methods, such as time-dependent density functional theory (TDDFT), complete active space self-consistent field (CASSCF), and Hartree-Fock (HF) or semiempirical configuration interaction singles (CIS). This is discussed in detail for bacteriorhodopsin (bR), a protein which blue-shifts retinal gas-phase excitation energy by about 0.5 eV. As a result of this study, we propose a procedure which combines structure optimization or molecular dynamics simulation using DFT methods with a semiempirical or ab initio multireference configuration interaction treatment of the excitation energies. Using a conventional QM/MM point charge representation of the protein environment, we obtain an absorption energy for bR of 2.34 eV. This result is already close to the experimental value of 2.18 eV, even without considering the effects of protein polarization, differential dispersion, and conformational sampling
    Type of Publication: Journal article published
    PubMed ID: 16851399
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  • 3
    Keywords: ENERGIES ; ENVIRONMENT ; Germany ; COMPLEX ; DNA ; MECHANISM ; CONTRAST ; DYNAMICS ; SIMULATION ; NUCLEIC-ACID ; TRANSPORT ; ENERGY ; REPAIR ; DAMAGE ; PARAMETERS ; DUPLEX DNA ; MOLECULAR-DYNAMICS ; molecular ; CHEMISTRY ; DEPENDENCE ; USA ; AQUEOUS-SOLUTION ; modeling ; molecular dynamics ; LONG-RANGE ; dynamic ; HOLE TRANSFER ; HOPPING MECHANISM ; MEDIATED ELECTRON-TRANSFER ; RADICAL-CATION MIGRATION ; RESP MODEL ; STRUCTURAL FLUCTUATIONS
    Abstract: Charge transfer in DNA has received much attention in the last few years due to its role in oxidative damage and repair in DNA and also due to possible applications of DNA in nanoelectronics. Despite intense experimental and theoretical efforts, the mechanism underlying long-range hole transport is still unresolved. This is in particular due to the sensitive dependence of charge transfer on the complex structure and dynamics of DNA and the interaction with the solvent, which could not be addressed adequately in the modeling approaches up to now. In this work, we study the factors governing hole transfer in detail, using a DFT-based fragment-orbital method, which allows to compute the charge transfer parameters along multinanosecond molecular dynamics simulations. Environmental effects are captured using a hybrid quantum mechanics-molecular mechanics (QM/MM) coupling scheme. This methodology allows to analyze several factors responsible for charge transfer in DNA in detail. The fluctuation of counterions, strongly counterbalanced by the surrounding water, leads to large oscillations of onsite energies, which govern the energetics of hole propagation along the DNA strand. In contrast, the electronic couplings depend only on DNA conformation and are not affected by the solvent. In particular, the onsite energies are strongly correlated between neighboring nucleobases, indicating that a conformational-gating type of mechanism may be induced by the collective environmental degrees of freedom
    Type of Publication: Journal article published
    PubMed ID: 18582109
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  • 4
    Keywords: AB-INITIO ; ENERGIES ; ENVIRONMENT ; Germany ; MODEL ; MODELS ; MOLECULES ; ACCURACY ; MECHANISM ; BASE ; BINDING ; FIELD ; DIFFERENCE ; ENERGY ; MUTATION ; EVOLUTION ; molecular ; CHEMISTRY ; ELECTRONIC POLARIZATION ; PROTEIN ENVIRONMENT ; VISUAL PIGMENTS ; methods ; QM/MM ; USA ; CONFIGURATION-INTERACTION PROCEDURE ; EXCITATION ; PREDICT ; FIELDS ; OPSIN ; STATE ; mechanical ; ABSORPTION MAXIMUM ; COUNTERION
    Abstract: The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article
    Type of Publication: Journal article published
    PubMed ID: 18698712
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  • 5
    Keywords: SIMULATIONS ; Germany ; DNA ; DYNAMICS ; RATES ; OXIDATION ; ENERGETICS ; CHEMISTRY ; USA ; CHARGE-TRANSFER ; RESP MODEL ; WELL ; ELECTRON-TRANSFER REACTIONS ; GROMACS
    Abstract: We present an application of a molecular-dynamics-based scheme to evaluate the solvent reorganization energy of hole transfer in DNA. The obtained parameters can be used for simulations of hole transfer in DNA by means of Marcus' theory. Also, we perform an analysis of the reorganization energies, including the case of transfer of a delocalized hole
    Type of Publication: Journal article published
    PubMed ID: 19331336
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  • 6
    Keywords: Germany ; MODEL ; MODELS ; DISEASE ; DISEASES ; PROTEIN ; PROTEINS ; MOLECULES ; DNA ; MECHANISM ; ACID ; FORM ; DAMAGE ; DNA-DAMAGE ; AMINO-ACIDS ; CENTERS ; OXIDATION ; GAS-PHASE ; CHEMISTRY ; AMINO-ACID ; DNA damage ; PHASE ; proton transfer ; USA ; AQUEOUS-SOLUTION ; CROSS-LINKS ; STRAND BREAKS ; LOW-ENERGY ELECTRONS ; BASE RELEASE ; COUPLED ELECTRON-TRANSFER ; FLASH-QUENCH TECHNIQUE ; GUANINE RADICAL-CATION ; OH ADDUCTS
    Abstract: Direct and indirect radiation-induced DNA damage is associated with the formation of radical cations (G(center dot+)) and radical anions (G(center dot-)) of guanine, respectively. Deprotonation of G(center dot+) and dehydrogenation of G(center dot-) generate guanine neutral radical [G(-H)(center dot)] and guanine anion [G(-H)(-)], respectively. These products are of worrisome concern, as they are involved in reactions that are related to certain lethal diseases. It has been observed that guanyl radicals can be repaired by amino acids having strong reducing properties that are believed to be the residues of DNA-bound proteins such as histones. As a result, repair of G(-H)(center dot) and G(-H)(-) by the amino acids cysteine and tyrosine has been studied here in detail by density functional theory in both the gas phase and aqueous medium using the polarized continuum and Onsager solvation models of self-consistent reaction field theory: Solvation in aqueous medium using three explicit water molecules was also studied. Four equivalent tautomers of each the above radical and anion that will be formed through proton and hydrogen loss from all of the nitrogen centers of guanine radical cation and guanine radical anion, respectively, were considered in the present study. It was found that in both the gas phase and aqueous medium, normal guanine can be retrieved from its radical-damaged form by a hydrogen-atom-transfer (HT) mechanism. Normal guanine can also be retrieved from its anionic damaged form in both the gas phase and aqueous medium through a two-electron-coupled proton-transfer (TECPT) mechanism or a one-step hydrogen-atom- and electron-transfer (OSHET) mechanism. The present results are discussed in light of the experimental findings
    Type of Publication: Journal article published
    PubMed ID: 19334703
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  • 7
    Keywords: CELLS ; CELL ; Germany ; MODEL ; MODELS ; DNA ; MECHANISM ; DYNAMICS ; CHROMATIN ; DISRUPTION ; ADHESION ; REVEALS ; ANGSTROM RESOLUTION ; DIFFUSION ; CHEMISTRY ; SCALE ; CORE PARTICLE ; OCTAMER ; CIRCULAR-CYLINDERS ; HISTONE TAILS ; SYMMETRIC TOP MACROMOLECULES
    Abstract: Nucleosomes organize chromatin in eukaryotic cells at the lowest scale by wrapping the DNA double helix around a histone octamer. The mechanism by which this structure can be opened, giving access to DNA-processing enzymes, is of fundamental biological importance. Here we describe a new coarse-grained model based on the toroidal geometry of the nucleosome which allows the simulation of nucleosome stretching experiments with it Brownian dynamics algorithm including hydrodynamics. We obtain force-extension curves and calculate energy barriers and kinetic rate constants of the unrolling transition from rupture forces
    Type of Publication: Journal article published
    PubMed ID: 19061370
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  • 8
    Keywords: AB-INITIO ; PEPTIDE ; PATHWAY ; MECHANISM ; COLLISION-INDUCED DISSOCIATION ; TANDEM MASS-SPECTROMETRY ; INFRARED-SPECTROSCOPY ; AMINO-ACID-RESIDUES ; MOBILE PROTON ; TRYPTIC PEPTIDES ; OXAZOLONE STRUCTURES ; ION CHEMISTRY ; METASTABLE DECOMPOSITION
    Abstract: The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.
    Type of Publication: Journal article published
    PubMed ID: 20973555
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  • 9
    Keywords: ENERGIES ; Germany ; SITE ; PROTEIN ; RESOLUTION ; DYNAMICS ; PROTON ; ENERGY ; STRUCTURAL-CHANGES ; PROTON-TRANSFER ; SCHIFF-BASE ; INTERMEDIATE ; EVENTS ; bacteriorhodopsin ; proton transfer ; ENERGY-STORAGE ; PHOTOISOMERIZATION
    Abstract: Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back-isomerization. The question of how the protein controls these events in the active site is addressed here using quantum mechanical/molecular mechanical reaction-path calculations. The results indicate that, while retinal twisting, significantly contributes to lowering the barrier for the thermal cis-trans back-isomerization, the rate-limiting barrier for this isomerization is still 5-6 kcal/mol larger than that for the first proton-transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful back-isomerization
    Type of Publication: Journal article published
    PubMed ID: 16852870
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  • 10
    Keywords: DENSITY-FUNCTIONAL-THEORY ; PATHWAY ; PATHWAYS ; SYSTEM ; SYSTEMS ; SITE ; PROTEIN ; COMPLEX ; COMPLEXES ; IMPACT ; treatment ; TRANSPORT ; ENERGY ; NUMBER ; AFFINITY ; MOLECULAR-DYNAMICS SIMULATIONS ; PROTON-TRANSFER ; density functional theory ; SCC-DFTB METHOD ; CARBONIC-ANHYDRASE-II ; COMPUTER-SIMULATIONS ; FLUCTUATIONS ; FREE-ENERGY SIMULATIONS ; LINK-ATOM METHOD ; RANGE ELECTROSTATIC INTERACTIONS ; REDOX POTENTIAL CALCULATIONS ; TRIOSEPHOSPHATE ISOMERASE
    Abstract: Motivated by the long-term goal of understanding vectorial biological processes such as proton transport (PT) in biomolecular ion pumps, a number of developments were made to establish combined quantum mechanical/molecular mechanical (QM/MM) methods suitable for studying chemical reactions involving significant charge separation in the condensed phase. These developments were summarized and discussed with representative problems. Specifically, free energy perturbation and boundary potential methods for treating long-range electrostatics were implemented to test the robustness of QM/MM results for protein systems. It was shown that consistent models with sufficient sampling were able to produce quantitatively satisfactory results, such as pK(a) for titritable groups in the interior of T4-lysozyme, while an inconsistent treatment of electrostatics or lack of sufficient sampling may produce incorrect results. Modifications were made to an approximate density functional theory (SCC-DFTB) to improve the description of proton affinity and hydrogen-bonding, which are crucial for the treatment of PT in polar systems. Test calculations on water autoionization showed clearly that both improvements are necessary for quantitatively reliable results. Finally, the newly established SCC-DFTB/MM-GSBP protocol was used to explore mechanistic issues in carbonic anhydrase (CA). Preliminary results suggest that PT in CA occurs mainly through short water wires containing two water molecules in a thermally activated fashion. Although longer water wires occur with similar frequencies, PT along those pathways, on average, has substantially higher barriers, a result not expected based on previous studies. The fluctuations of water molecules peripheral to the water wire were found to make a larger impact on the PT energetics compared to polar protein residues in the active site, which are largely pre-organized and therefore have less tendency to reorganize during the reaction
    Type of Publication: Journal article published
    PubMed ID: 16570942
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