Epistructural tension promotes protein associations

Epistructural tension is the reversible work per unit area required to span the aqueous interface of a soluble protein structure. The parameter accounts for the free-energy cost of imperfect hydration, involving water molecules with a shortage of hydrogen-bonding partnerships relative to bulk levels. The binding hot spots along protein-protein interfaces are identified with residues that contribute significantly to the epistructural tension in the free subunits. Upon association, such residues either displace or become deprived of low-coordination vicinal water molecules.     

A unifying definition of synchronization for dynamical systems

We propose a unifying definition for synchronization between stationary finite dimensional deterministic dynamical systems. By example, we show that the synchronization phenomena discussed in the dynamical systems literature fits within the framework of this definition, and discuss problems with previous definitions of synchronization. We conclude with a discussion of possible extensions of the definition to infinite dimensional systems described by partial differential equations and/or systems where noise is present. (c) 2000 American Institute of Physics.     

Dissipative hamiltonian systems: A unifying principle

The concept of hamiltonian sysem is generalized to include a wide class of dissipative processes. Evolution of any observable is generated jointly by a hamiltonian, with an entropy-conserving Poisson bracket, and an entropy, with an energy-conserving dissipative bracket. This approach yields many of the standard kinetic equations, such as those representing particle collisions, three-wave interactions, and wave-particle resonances.     

A generalized Hamiltonian formalism unifying classical and quantum mechanics

A Poisson bracket structure is defined on associative algebras which allows for a generalized Hamiltonian dynamics. Both classical and quantum mechanics are shown to be special cases of the general formalism.     

Substituent effects in cooperativity of chalcogen bonds

In the present work, substituent effects on cooperativity of S···N chalcogen bonds are studied in XHS···NCHS···4-Z–Py (X = F, Cl; Z = H, F, OH, CH₃, NH₂, NO₂, and CN; and Py = pyridine) complexes using ab initio calculations. An increased attraction or a positive cooperativity is observed on introduction of a third molecule to the XHS···NCHS and NCHS···4-Z–Py binary systems. The shortening of each chalcogen bond distance in the ternary systems is dependent on the substituent Z and is increased in the order Z = NH₂ > OH > CH₃ > H > F > CN > NO₂. The electronic aspects of the complexes are analysed using molecular electrostatic potential, and the parameters derived from the atoms in molecules and natural bond orbital methodologies. According to interaction energy decomposition analysis, the electrostatic energies are important in the interaction energy of S···N bonds and may be regarded as being responsible for the stability of these complexes.     

Bubble nucleation and cooperativity in DNA melting

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied.     

Fragility and cooperativity concepts in hydrogen-bonded organic glasses

Molecular dynamics at the glass transition of three lactose/oil glassy systems have been investigated according to the cooperativity and fragility approaches. From Donth's approach, the cooperativity length is estimated by modulated temperature calorimetric measurements. Results reveal that modification of the disaccharide by oil leads to increase the disorder degree in the lactose, the size of the cooperative domains and the fragility index. These particular hydrogen-bonded organic glasses follow the general tendency observed on organic and inorganic polymers: the higher the cooperativity length, the higher the value of the fragility index at T_g.     

Pressure-induced intermolecular interactions in crystalline silane-hydrogen

The structure and dynamics of a recently discovered solid silane-hydrogen complex under high pressure are elucidated with first-principles molecular dynamics calculations. A structure with orientationally disordered silane and hydrogen with their centers of mass arranged in a distinctive manner are found. Natural bond orbital analysis reveals that perturbative donor-acceptor interactions between the two molecular species are enhanced by pressure. The experimentally observed anticorrelated pressure-frequency dependency is a consequence of these novel interactions. Moreover, the experimentally observed multiple Raman peaks of H2 can be explained by temporal changes in the environment due to deviations of the lattice parameters from the ideal cubic lattice.     

Dynamics of cooperativity in chemical sensing among cell-surface receptors

Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to chemoeffector concentrations. However, cooperativity between receptors in large macromolecular complexes is necessarily based on local interactions and consequently is fundamentally connected to slowing of receptor-conformational dynamics, which increases intrinsic noise. Therefore, it is not clear whether or under what conditions cooperativity actually increases the precision of the concentration measurement. We explicitly calculate the signal-to-noise ratio (SNR) for sensing a concentration change using a simple, Ising-type model of receptor-receptor interactions, generalized via scaling arguments, and find that the optimal SNR is always achieved by independent receptors.     

The intermolecular potential of HF

The functional form of separate contributions to the intermolecular potential between small dipolar molecules has been analysed using the HF intermolecular potential as an example. The SCF energy was partitioned into first order electrostatic and exchange terms and higher order terms, called the polarization energy, which can be obtained by iterating the wavefunction to self consistency. A comparison was made for each term between a bipolar expansion about a single centre in each molecule and spherically symmetric site-site models. The overlap dependent part of the electrostatic energy could be combined with the exchange energy to give a single term which we call the repulsion energy and this was most accurately represented by a six term bipolar expansion. The polarization energy has a long range (R ^-6) component and an overlap dependent component and both could be separately represented by a two-term bipolar expansion. A semiempirical estimate was made of the dispersion energy and the total potential predicts a geometry of the HF dimer in good agreement with experiment. The predicted binding energy of the dimer is 17 kJ mol^-1 which is slightly smaller than a previous empirical estimate (23 kJ mol^-1).     

Role of fluctuations in ligand binding cooperativity of membrane receptors

Signal transduction upon binding of a ligand to a membrane protein can occur not only via allosteric conformational changes but also through fluctuations. We report a numerical study on the influence of conformational fluctuations on the cooperativity of a binding reaction in a simple model of an integral membrane receptor consisting of transmembrane helices. We find that small fluctuations lateral as well as perpendicular to the membrane can increase the cooperativity, with the former more dominant. Moreover, too much fluctuation induces negative cooperativity. Proteins with fewer than four helices do not show positive cooperativity under any circumstances. This behavior is rather robust, and independent of the receptor topology or ligand size. Fluctuations measured in all-atom molecular dynamics simulations of a G-protein coupled receptor fall within the predicted region of maximum cooperativity.     

First passage and cooperativity of queuing kinetics

We model the kinetics of ligand-receptor systems, where multiple ligands may bind and unbind to the receptor, either randomly or in a specific order. Equilibrium occupation and first occurrence of complete filling of the receptor are determined and compared. At equilibrium, receptors that bind ligands sequentially are more likely to be saturated than those that bind in random order. Surprisingly however, for low cooperativity, the random process first reaches full occupancy faster than the sequential one. This is true except near a critical binding energy where a "kinetic trap" arises and the random process dramatically slows down when the number of binding sites N > or = 8. These results demonstrate the subtle interplay between cooperativity and sequentiality for a wide class of kinetic phenomena, including chemical binding, nucleation, and assembly line strategies.     

A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging

A unifying theoretical and algorithmic framework for diffusion tensor estimation is presented. Theoretical connections among the least squares (LS) methods, (linear least squares (LLS), weighted linear least squares (WLLS), nonlinear least squares (NLS) and their constrained counterparts), are established through their respective objective functions, and higher order derivatives of these objective functions, i.e., Hessian matrices. These theoretical connections provide new insights in designing efficient algorithms for NLS and constrained NLS (CNLS) estimation. Here, we propose novel algorithms of full Newton-type for the NLS and CNLS estimations, which are evaluated with Monte Carlo simulations and compared with the commonly used Levenberg-Marquardt method. The proposed methods have a lower percent of relative error in estimating the trace and lower reduced chi2 value than those of the Levenberg-Marquardt method. These results also demonstrate that the accuracy of an estimate, particularly in a nonlinear estimation problem, is greatly affected by the Hessian matrix. In other words, the accuracy of a nonlinear estimation is algorithm-dependent. Further, this study shows that the noise variance in diffusion weighted signals is orientation dependent when signal-to-noise ratio (SNR) is low (相似文献