Jiri Vanicek

A KRAB/KAP1-miRNA Cascade Regulates Erythropoiesis Through Stage-Specific Control of Mitophagy

Red in Cell and Marrow About one hundred billion new red cells are released every day from the adult human bone marrow—the result of a complex differentiation pathway. Barde et al. (p. 350, published online 14 March) show that an essential step in this process, the elimination of mitochondria from maturing erythroblasts through mitophagy, is controlled through the timely induction of specific members of the large family of KRAB-containing zinc finger proteins (KRAB-ZFPs), which, together with their cofactor KAP1, repress the expression of micro-RNAs targeting the transcripts of mitophagy effector genes. This multilayered and combinatorial regulation system provides a level of modularity that may be shared by other physiological processes. Protein- and RNA-based transcriptional regulation governs the removal of mitochondria during red blood cell differentiation. During hematopoiesis, lineage- and stage-specific transcription factors work in concert with chromatin modifiers to direct the differentiation of all blood cells. We explored the role of KRAB-containing zinc finger proteins (KRAB-ZFPs) and their cofactor KAP1 in this process. In mice, hematopoietic-restricted deletion of Kap1 resulted in severe hypoproliferative anemia. Kap1-deleted erythroblasts failed to induce mitophagy-associated genes and retained mitochondria. This was due to persistent expression of microRNAs (miRNAs) targeting mitophagy transcripts, itself secondary to a lack of repression by stage-specific KRAB-ZFPs. The KRAB/KAP1-miRNA regulatory cascade is evolutionarily conserved, as it also controls mitophagy during human erythropoiesis. Thus, a multilayered transcription regulatory system is present, in which protein- and RNA-based repressors are superimposed in combinatorial fashion to govern the timely triggering of an important differentiation event.

Host MicroRNA Regulation of Human Cytomegalovirus Immediate Early Protein Translation Promotes Viral Latency

ABSTRACT Reactivation of human cytomegalovirus (HCMV) is a significant cause of disease and death in immunocompromised patients, underscoring the need to understand how latency is controlled. Here we demonstrate that HCMV has evolved to utilize cellular microRNAs (miRNAs) in cells that promote latency to regulate expression of a viral protein critical for viral reactivation. Our data reveal that hsa-miR-200 miRNA family members target the UL122 (immediate early protein 2) 3′ untranslated region, resulting in repression of this viral protein. Utilizing recombinant viruses that mutate the miRNA-binding site compared to the sequence of the wild-type virus results in lytic rather than latent infections in ex vivo infections of primary CD34+ cells. Cells permissive for lytic replication demonstrate low levels of these miRNAs. We propose that cellular miRNA regulation of HCMV is critical for maintenance of viral latency. IMPORTANCE Human cytomegalovirus (HCMV) is a herpesvirus that infects a majority of the population. Once acquired, individuals harbor the virus for life, where the virus remains, for the most part, in a quiet or latent state. Under weakened immune conditions, the virus can reactivate, which can cause severe disease and often death. We have found that members of a family of small RNAs, termed microRNAs, encoded by human myeloid progenitor cells are capable of repressing a key viral protein, thus enabling the virus to ensure a quiet/latent state. As these progenitor cells mature further down the myeloid lineage toward cells that support active viral replication, the levels of these microRNAs decrease. Together, our data suggest that host cell microRNA regulation of HCMV is important for the quiet/latent state of this pathogen.

Path integral evaluation of equilibrium isotope effects

A general and rigorous methodology to compute the quantum equilibrium isotope effect is described. Unlike standard approaches, ours does not assume separability of rotational and vibrational motions and does not make the harmonic approximation for vibrations or rigid rotor approximation for the rotations. In particular, zero point energy and anharmonicity effects are described correctly quantum mechanically. The approach is based on the thermodynamic integration with respect to the mass of isotopes and on the Feynman path integral representation of the partition function. An efficient estimator for the derivative of free energy is used whose statistical error is independent of the number of imaginary time slices in the path integral, speeding up calculations by a factor of approximately 60 at 500 K and more at room temperature. We describe the implementation of the methodology in the molecular dynamics package AMBER 10. The method is tested on three [1,5] sigmatropic hydrogen shift reactions. Because of the computational expense, we use ab initio potentials to evaluate the equilibrium isotope effects within the harmonic approximation and then the path integral method together with semiempirical potentials to evaluate the anharmonicity corrections. Our calculations show that the anharmonicity effects amount up to 30% of the symmetry reduced reaction free energy. The numerical results are compared with recent experiments of Doering et al., [J. Am. Chem. Soc. 128, 9080 (2006); J. Am. Chem. Soc.129, 2488 (2007)] confirming the accuracy of the most recent measurement on 2,4,6,7,9-pentamethyl-5-(5,5-(2)H(2))methylene-11,11a-dihydro-12H-naphthacene as well as concerns about compromised accuracy, due to side reactions, of another measurement on 2-methyl-10-(10,10-(2)H(2))methylenebicyclo[4.4.0]dec-1-ene.

Dephasing representation of quantum fidelity for general pure and mixed states

A general semiclassical expression for quantum fidelity (Loschmidt echo) of arbitrary pure and mixed states is derived. It expresses fidelity as an interference sum of dephasing trajectories weighed by the Wigner function of the initial state, and does not require that the initial state be localized in position or momentum. This general dephasing representation is special in that, counterintuitively, all of fidelity decay is due to dephasing and none is due to the decay of classical overlaps. Surprising accuracy of the approximation is justified by invoking the shadowing theorem: twice--both for physical perturbations and for numerical errors. Beyond justifying the approximation, the shadowing theorem makes the dephasing representation practical: without shadowing it would be impossible to find numerically the precise trajectories needed in a semiclassical approximation. It is shown how the general expression reduces to the previously known special forms for localized states. The superiority of the general over the specialized forms is explained and supported by numerical tests for wave packets, nonlocal pure states, and for simple and random mixed states. The tests are done in nonuniversal regimes in mixed phase space where detailed features of fidelity are important. Although semiclassically motivated, the present approach is valid for abstract systems with a finite Hilbert basis provided that the discrete Wigner transform is used. This makes the method applicable, via a phase-space approach, to problems of quantum computation.

Direct evaluation of the temperature dependence of the rate constant based on the quantum instanton approximation

A general method for the direct evaluation of the temperature dependence of the quantum-mechanical reaction rate constant in many-dimensional systems is described. The method is based on the quantum instanton approximation for the rate constant, thermodynamic integration with respect to the inverse temperature, and the path integral Monte Carlo evaluation. It can describe deviations from the Arrhenius law due to the coupling of rotations and vibrations, zero-point energy, tunneling, corner-cutting, and other nuclear quantum effects. The method is tested on the Eckart barrier and the full-dimensional H+H(2)-->H(2)+H reaction. In the temperature range from 300 to 1500 K, the error of the present method remains within 13% despite the very large deviations from the Arrhenius law. The direct approach makes the calculations much more efficient, and the efficiency is increased even further (by up to two orders of magnitude in the studied reactions) by using optimal estimators for reactant and transition state thermal energies. Which of the estimators is optimal, however, depends on the system and the strength of constraint in a constrained simulation.

Monte Carlo evaluation of the equilibrium isotope effects using the Takahashi–Imada factorization of the Feynman path integral

Abstract The Feynman path integral approach for computing equilibrium isotope effects and isotope fractionation corrects the approximations made in standard methods, although at significantly increased computational cost. We describe an accelerated path integral approach based on three ingredients: the fourth-order Takahashi–Imada factorization of the path integral, thermodynamic integration with respect to mass, and centroid virial estimators for relevant free energy derivatives. While the first ingredient speeds up convergence to the quantum limit, the second and third improve statistical convergence. The combined method is applied to compute the equilibrium constants for isotope exchange reactions H 2 + D ⇌ H + HD and H 2 + D 2 ⇌ 2 HD .

Beating the Efficiency of Both Quantum and Classical Simulations with a Semiclassical Method

While rigorous quantum dynamical simulations of many-body systems are extremely difficult (or impossible) due to exponential scaling with dimensionality, the corresponding classical simulations ignore quantum effects. Semiclassical methods are generally more efficient but less accurate than quantum methods and more accurate but less efficient than classical methods. We find a remarkable exception to this rule by showing that a semiclassical method can be both more accurate and faster than a classical simulation. Specifically, we prove that for the semiclassical dephasing representation the number of trajectories needed to simulate quantum fidelity is independent of dimensionality and also that this semiclassical method is even faster than the most efficient corresponding classical algorithm. Analytical results are confirmed with simulations of fidelity in up to 100 dimensions with 2(1700)-dimensional Hilbert space.

On-the-fly ab initio semiclassical dynamics: identifying degrees of freedom essential for emission spectra of oligothiophenes.

Vibrationally resolved spectra provide a stringent test of the accuracy of theoretical calculations. We combine the thawed Gaussian approximation (TGA) with an on-the-fly ab initio (OTF-AI) scheme to calculate the vibrationally resolved emission spectra of oligothiophenes with up to five rings. The efficiency of the OTF-AI-TGA permits treating all vibrational degrees of freedom on an equal footing even in pentathiophene with 105 vibrational degrees of freedom, thus obviating the need for the global harmonic approximation, popular for large systems. Besides reproducing almost perfectly the experimental emission spectra, in order to provide a deeper insight into the associated physical and chemical processes, we also develop a novel systematic approach to assess the importance and coupling between individual vibrational degrees of freedom during the dynamics. This allows us to explain how the vibrational line shapes of the oligothiophenes change with increasing number of rings. Furthermore, we observe the dynamical interplay between the quinoid and aromatic characters of individual rings in the oligothiophene chain during the dynamics and confirm that the quinoid character prevails in the center of the chain.

Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene

Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we explain how path integrals can be employed to evaluate the equilibrium (EIE) and kinetic (KIE) isotope effects, and the temperature dependence of the rate constant. The methodology is applied to the [1,5] sigmatropic hydrogen shift in pentadiene. Both the KIE and the temperature dependence of the rate constant confirm the importance of tunneling and other nuclear quantum effects as well as of the anharmonicity of the potential energy surface. Moreover, previous results on the KIE were improved by using a combination of a high level electronic structure calculation within the harmonic approximation with a path integral anharmonicity correction using a lower level method.

Communications: Evaluation of the nondiabaticity of quantum molecular dynamics with the dephasing representation of quantum fidelity.

We propose an approximate method for evaluating the importance of non-Born-Oppenheimer effects on the quantum dynamics of nuclei. The method uses a generalization of the dephasing representation (DR) of quantum fidelity to several diabatic potential energy surfaces and its computational cost is the cost of dynamics of a classical phase space distribution. It can be implemented easily into any molecular dynamics program and also can utilize on-the-fly ab initio electronic structure information. We test the methodology on three model problems introduced by Tully and on the photodissociation of NaI. The results show that for dynamics close to the diabatic limit, the decay of fidelity due to nondiabatic effects is described accurately by the DR. In this regime, unlike the mixed quantum-classical methods such as surface hopping or Ehrenfest dynamics, the DR can capture more subtle quantum effects than the population transfer between potential energy surfaces. Hence we propose using the DR to estimate the dynamical importance of diabatic, spin-orbit, or other couplings between potential energy surfaces. The acquired information can help reduce the complexity of a studied system without affecting the accuracy of the quantum simulation.