Biomedical subjects

Ursula Rothlisberger

Publications and source records attributed to Ursula Rothlisberger.

At least 19 recordsLinked to original sources

PubMed2006

Microsolvation effects on the excited-state dynamics of protonated tryptophan.

To better understand the complex photophysics of the amino acid tryptophan, which is widely used as a probe of protein structure and dynamics, we have measured electronic spectra of protonated, gas-phase tryptophan solvated with a controlled number of water molecules and cooled to approximately 10 K. We observe that, even at this temperature, the bare molecule exhibits a broad electronic spectrum, implying ultrafast, nonradiative decay of the excited state. Surprisingly, the addition of two water molecules sufficiently lengthens the excited-state lifetime that we obtain a fully vibrationally resolved electronic spectrum. Quantum chemical calculations at the RI-CC2/aug-cc-pVDZ level, together with TDDFT/pw based first-principles MD simulations of the excited-state dynamics, clearly demonstrate how interactions with water destabilize the photodissociative states and increase the excited-state lifetime.

Models, Molecular↗

PubMed2006

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa.

We have coupled hybrid quantum mechanics (density functional theory; Car-Parrinello)/molecular mechanics molecular dynamics simulations to a grand-canonical scheme, to calculate the in situ redox potential of the Cu(2+) + e(-) --> Cu(+) half reaction in azurin from Pseudomonas aeruginosa. An accurate description at atomistic level of the environment surrounding the metal-binding site and finite-temperature fluctuations of the protein structure are both essential for a correct quantitative description of the electronic properties of this system. We report a redox potential shift with respect to copper in water of 0.2 eV (experimental 0.16 eV) and a reorganization free energy lambda = 0.76 eV (experimental 0.6-0.8 eV). The electrostatic field of the protein plays a crucial role in fine tuning the redox potential and determining the structure of the solvent. The inner-sphere contribution to the reorganization energy is negligible. The overall small value is mainly due to solvent rearrangement at the protein surface.

Azurin↗

PubMed2006

Polarization effects and charge transfer in the KcsA potassium channel.

The electronic structure of the selectivity filter of KcsA K(+) channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].

Bacterial Proteins↗

PubMed2006

A comparative theoretical study of dipeptide solvation in water.

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).

Alanine↗

PubMed2006

Duocarmycins binding to DNA investigated by molecular simulation.

Duocarmycins are a potent class of antitumor agents, whose activity arises through their covalent binding to adenine nucleobases of DNA.(1-3) Here, we perform molecular dynamics (MD) and hybrid Car-Parinello QM/MM simulations to investigate aspects of duocarmycin binding to the d(pGpApCpTpApApTpTpGpApC) oligonucleotide. We focus on the derivatives (+)-duocarmycin SA (DSA) and (+)-duocarmycin SI (DSI), for which structural information of the covalent complex with the oligonucleotide is available, as well as on the related, but less reactive, NBOC-duocarmycin SA (NBOC-DSA), interacting with the same oligonucleotide. Comparison is made with adenine alkylation reaction in water performed by the smallest of these compounds (NBOC-DSA). The MD calculations suggest that, in noncovalent complexes, (i) drug binding causes a partial dehydration of the minor groove, without inducing a significant conformational changes, and (ii) DSA and DSI occupy a more favorable position for nucleophilic attack than NBOC-DSA, consistently with the lower reactivity of the latter. The QM/MM calculations, which are used to investigate the first step of the alkylation reaction, turn out to provide strongly underestimated free energy barriers. Within these approximations, our calculations suggest that an important ingredient for the experimentally observed DNA catalytic power is the polarization of the drug by the biomolecular scaffold.

Adenine↗

PubMed2005

Variational particle number approach for rational compound design.

Within density functional theory, a variational particle number approach for rational compound design (RCD) is presented. An expression for RCD is obtained in terms of minimization of a suitably defined energy penalty functional whose gradients are the nuclear and the electronic chemical potential. Using combined quantum and molecular mechanics, a nonpeptidic anticancer drug candidate is designed.

Journal Article↗

PubMed2005

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore.

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol solution, and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid quantum mechanics/molecular mechanics (QM/MM) descriptions). Finite temperature effects are taken into account by molecular dynamics simulations. The different components that determine the structure and dynamics of the chromophore in the protein are dissected, both in the dark state and in the early photointermediates. In vacuum and in solution the chromophore displays a very high flexibility, which is significantly reduced by the protein environment. In the 11-cis chromophore, the bond-length alternation, which is correlated with the dipole moment, is found to be similar in solution and in the protein, while it differs greatly with respect to minimum-energy vacuum structures. In the model of the earliest protein photointermediate, the highly twisted chromophore shows a very reduced bond-length alternation.

Molecular Structure↗

PubMed2005

Folding pathways for initiator and effector procaspases from computer simulations.

The folding pathways of procaspases 3, 7, and 8 have been studied using a Go-like Hamiltonian and molecular dynamics simulations coupled with a parallel tempering scheme. The folding pathways and the overall structures of procaspases 3 and 7 are similar, and are characterized by monomeric as well as dimeric folding intermediates in agreement with the available structural and thermochemical data. The folding pathway of procaspase 8, on the other hand, is characterized by a larger population of monomers and partially folded dimer intermediates, and only a relatively small population of folded dimer species. The most stable structure predicted for procaspase 8 is a dimer, in which the position of the linker is remarkably different from the one observed in procaspases 3 and 7, leading to the fact that all the contacts that stabilize the active site are essentially formed. This novel and unexpected structure provides a rationale for the observed activity of the procaspase 8 dimer, and thus could be highly relevant for the initiation of FAS-mediated apoptosis.

Caspase 3↗

PubMed2005

Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases.

The biological function of the aspartic protease from HIV-1 has recently been related to the conformational flexibility of its structural scaffold. Here, we use a multistep strategy to investigate whether the same mechanism affects the functionality in the pepsin-like fold. (i) We identify the set of conserved residues by using sequence-alignment techniques. These residues cluster in three distinct regions: near the cleavage-site cavity, in the four beta-sheets cross-linking the two lobes, and in a solvent-exposed region below the long beta-hairpin in the N-terminal lobe. (ii) We elucidate the role played by the conserved residues for the enzymatic functionality of one representative member of the fold family, the human beta-secretase, by means of classical molecular dynamics (MD). The conserved regions exhibit little overall mobility and yet are involved into the most important modes of structural fluctuations. These modes influence the substrate-catalytic aspartates distance through a relative rotation of the N- and C-terminal lobes. (iii) We investigate the effects of this modulation by estimating the reaction free energy at different representative substrate/enzyme conformations. The activation free energy is strongly affected by large-scale protein motions, similarly to what has been observed in the HIV-1 enzyme. (iv) We extend our findings to all other members of the two eukaryotic and retroviral fold families by recurring to a simple, topology-based, energy functional. This analysis reveals a sophisticated mechanism of enzymatic activity modulation common to all aspartic proteases. We suggest that aspartic proteases have been evolutionarily selected to possess similar functional motions despite the observed fold variations.

Amino Acid Sequence↗

PubMed2005

Variational optimization of effective atom centered potentials for molecular properties.

In plane wave based electronic structure calculations the interaction of core and valence electrons is usually represented by atomic effective core potentials. They are constructed in such a way that the shape of the atomic valence orbitals outside a certain core radius is reproduced correctly with respect to the corresponding all-electron calculations. Here we present a method which, in conjunction with density functional perturbation theory, allows to optimize effective core potentials in order to reproduce ground-state molecular properties from arbitrarily accurate reference calculations within standard density functional calculations. We demonstrate the wide range of possible applications in theoretical chemistry of such optimized effective core potentials (OECPs) by means of two examples. We first use OECPs to tackle the link atom problem in quantum mechanics/molecular mechanics (QM/MM) schemes proposing a fully automatized procedure for the design of link OECPs, which are designed in such a way that they minimally perturb the electronic structure in the QM region. In the second application, we use OECPs in two sample molecules (water and acetic acid) such as to reproduce electronic densities and derived molecular properties of hybrid (B3LYP) quality within general gradient approximated (BLYP) density functional calculations.

Journal Article↗

PubMed2004

A molecular spring for vision.

Light absorption by the visual pigment rhodopsin leads to vision via a complex signal transduction pathway that is initiated by the ultrafast and highly efficient photoreaction of its chromophore, the retinal protonated Schiff base (RPSB). Here, we investigate this reaction in real time by means of unrestrained molecular dynamics simulations of the protein in a membrane mimetic environment, treating the chromophore at the density functional theory level. We demonstrate that a highly strained all-trans RPSB is formed starting from the 11-cis configuration (dark state) within approximately 100 fs by a minor rearrangement of the nuclei under preservation of the saltbridge with Glu113 and virtually no deformation of the binding pocket. Hence, the initial step of vision can be understood as the compression of a molecular spring by a minor change of the nuclear coordinates. This spring can then release its strain by altering the protein environment.

Algorithms↗

PubMed2004

Optimization of effective atom centered potentials for london dispersion forces in density functional theory.

We add an effective atom-centered nonlocal term to the exchange-correlation potential in order to cure the lack of London dispersion forces in standard density functional theory. Calibration of this long-range correction is performed using density functional perturbation theory and an arbitrary reference. Without any prior assignment of types and structures of molecular fragments, our corrected generalized gradient approximation density functional theory calculations yield correct equilibrium geometries and dissociation energies of argon-argon, benzene-benzene, graphite-graphite, and argon-benzene complexes.

Biopolymers↗

PubMed2004

Unusual Ar-H/Rh-H J(HH) NMR coupling in complexes of rhodium(III): experimental evidence and theoretical support for an eta1-arene structure.

The synthesis and structural properties of three new hydridorhodium(III) complexes are reported. Hydrogenolysis of the cyclometalated rhodium dichloride complexes [RhCl(2)[(S,S)-benbox(Me(2))]] (2a-c) leads to formation of the new complexes [RhCl(2)(H)[(S,S)-ip-benbox(Me(2))H]] (3a-c) in 45% to 85% yield. Compounds 3a-c were found to have unusual features by NMR spectroscopy: in particular, downfield shifted aryl proton resonances (8.88-9.03 ppm) that were coupled to the rhodium hydride resonances. Using X-ray crystallographic studies, a variety of solid- and solution-state characterization techniques, and DFT calculations, these features were attributed to the presence of weak pi-type eta(1)-arene interactions in 3a-c.

Journal Article↗

PubMed2004

Water-assisted reaction mechanism of monozinc beta-lactamases.

Hybrid Car-Parrinello QM/MM calculations are used to investigate the reaction mechanism of hydrolysis of a common beta-lactam substrate (cefotaxime) by the monozinc beta-lactamase from Bacillus cereus (BcII). The calculations suggest a fundamental role for an active site water in the catalytic mechanism. This water molecule binds the zinc ion in the first step of the reaction, expanding the zinc coordination number and providing a proton donor adequately oriented for the second step. The free energy barriers of the two reaction steps are similar and consistent with the available experimental data. The conserved hydrogen bond network in the active site, defined by Asp120, Cys221, and His263, not only contributes to orient the nucleophile (as already proposed), but it also guides the second catalytic water molecule to the zinc ion after the substrate is bound. The hydrolysis reaction in water has a relatively high free energy barrier, which is consistent with the stability of cefotaxime in water solution. The modeled Michaelis complexes for other substrates are also characterized by the presence of an ordered water molecule in the same position, suggesting that this mechanism might be general for the hydrolysis of different beta-lactam substrates.

Bacillus cereus↗

PubMed2004

Molecular dynamics simulations of structural changes during procaspase 3 activation.

Molecular dynamics (MD) simulations of the structural rearrangements on the pathway leading to procaspase 3 activation are presented. A retrostructural approach is used to build procaspase 3 from mature caspase 3. The peptide bond that is cleaved during enzyme maturation is gradually reformed during the MD simulation and the most relevant structural changes that occur as a consequence are analyzed. The main structural features that characterize this procaspase 3 model are compared with the available X-ray structure of procaspase 7 as the only zymogen structure that has been crystallised so far. The MD simulations indicate that in the free caspase 3, the flexible selectivity loop is already preorganized to accomodate the substrate. Such a preorganization is not present in either monomeric caspase 3 or in the procaspase 3 dimer, indicating that the structure of the selectivity loop is highly sensitive to perturbations.

Caspase 3↗

PubMed2003

QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water.

We present a hybrid Car-Parrinello quantum mechanical/molecular mechanical (QM/MM) approach that is capable of treating the dynamics of molecular systems in electronically excited states in complex environments. The potential energy surface in the excited state is described either within the restricted open-shell Kohn-Sham (ROKS) formalism or within time-dependent density functional theory (TDDFT). As a test case, we apply this technique to the study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. Our results demonstrate that for this system a purely classical description of the solvent is sufficient, since inclusion of the first solvent shell of 12 water molecules into the quantum system does not show a significant effect on this transition. The excited-state energies calculated with ROKS are red shifted by a constant value compared to the TDDFT results, while the relative variations of the excitation energy for different configurations are in very good agreement. The experimentally observed blue shift of the excitation energy in going from gas phase to condensed phase is well reproduced. Excited-state dynamics carried out with ROKS yield the relaxation of the solute and the rearrangement of the solvent structure on a picosecond timescale. The calculated Stokes shift is in reasonable agreement with experimental data.

Journal Article↗

PubMed2003

Structure-based thermodynamic analysis of caspases reveals key residues for dimerization and activity.

Cysteine-dependent aspartic proteases (caspases) are a family of enzymes which play a crucial role in apoptosis. Caspases accumulate in eukaryotic cells in the form of low-activity proenzyme precursors. Proteolytic cleavage of specific sites triggers conformational changes that lead to full activation and thus to the initiation of the apoptotic cascade. Several experimental observations suggest that dimerization is crucial for activity and regulation, but the underlying molecular mechanisms have not yet been completely resolved. In this work, we have used a structure-based thermodynamic analysis method [Edgcomb, S. P., and Murphy, K. P. (2000) Curr. Opin. Biotechnol. 11, 62-66] to calculate the free energy of association and folding for all the caspases and procaspases whose structures are known at present. In all cases, analysis of the single-residue contributions to the dimerization energy shows that 30-50% of the dimer stability originates from the highly specific interaction of 12-14 residues located at the N- and C-termini of the large and small subunits, respectively. Moreover, our calculations indicate that these residues are also critical for stabilizing the conformation of the active site loops, which in turn is crucial for the binding of substrates and inhibitors. Thus, our results help to rationalize the relation between dimerization and activity in this important class of enzymes and can be used as a starting point for an active manipulation of the monomer-dimer equilibrium for preparatory and regulatory purposes.

Amino Acid Sequence↗

PubMed2002

Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations.

We present molecular dynamics simulations of bovine rhodopsin in a membrane mimetic environment based on the recently refined X-ray structure of the pigment. The interactions between the protonated Schiff base and the protein moiety are explored both with the chromophore in the dark-adapted 11-cis and in the photoisomerized all-trans form. Comparison of simulations with Glu181 in different protonation states strongly suggests that this loop residue located close to the 11-cis bond bears a negative charge. Restrained molecular dynamics simulations also provide evidence that the protein tightly confines the absolute conformation of the retinal around the C12-C13 bond to a positive helicity. 11-cis to all-trans isomerization leads to an internally strained chromophore, which relaxes after a few nanoseconds by a switching of the ionone ring to an essentially planar all-trans conformation. This structural transition of the retinal induces in turn significant conformational changes of the protein backbone, especially in helix VI. Our results suggest a possible molecular mechanism for the early steps of intramolecular signal transduction in a prototypical G-protein-coupled receptor.

Animals↗