Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins

Water and water-mediated interactions determine the thermodynamics and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we describe computer simulations of a few related model systems. The dynamics of collapse of eicosane shows that upon expulsion of water the linear hydrocarbon chain adopts an ordered helical hairpin structure with 1.5 turns. The structure of dimer of eicosane molecules has two well ordered helical hairpins that are stacked perpendicular to each other. As a prelude to studying folding in confined spaces we used simulations to understand changes in hydrophobic and ionic interactions in nano-sized water droplets. Solvation of hydrophobic and charged species change drastically in nano-scale water droplets. Hydrophobic species are localized at the boundary. The tendency of ions to be at the boundary where water density is low increases as the charge density decreases. The interactions between hydrophobic, polar, and charged residue are also profoundly altered in confined spaces. Using the results of computer simulations and accounting for loss of chain entropy upon confinement we argue and then demonstrate, using simulations in explicit water, that ordered states of generic amphiphilic peptide sequences should be stabilized in cylindrical nanopores.     

Folding of lattice protein chains with modified Gō potential

We propose a modified Gō model in which the pairwise interaction energies vary as local environment changes. The stability difference between the surface and the core is also well considered in this model. Thermodynamic and kinetic studies suggest that this model has improved folding cooperativity and foldability in contrast with the Gō model. The free energy landscape of this model has broad barriers and narrow denatured states, which is consistent with that of the two-state folding proteins and is lacked for the Gō model. The role of non-native interactions in protein folding is also studied. We find that appropriate consideration of the contribution of the non-native interactions may increase the folding rate around the transition temperature. Our results show that conformation-dependent interaction between the residues is a realistic representation of potential functions in protein folding. Received 10 April 2002 / Received in final form 20 August 2002 Published online 19 December 2002 RID="a" ID="a"e-mail: wangwei@nju.edu.cn     

Potts models and random-cluster processes with many-body interactions

Known differential inequalities for certain ferromagnetic Potts models with pair interactions may be extended to Potts models with many-body interactions. As a major application of such differential inequalities, we obtain necessary and sufficient conditions on the set of interactions of such a Potts model in order that its critical point be astrictly monotonic function of the strengths of interactions. The method yields some ancillary information concerning the equality of certain critical exponents for Potts models; this amounts to a small amount of rigorous universality. These results are achieved in the context of a Fortuin-Kasteleyn representation of Potts models with many-body interactions. For such a Potts model, the corresponding random-cluster process is a (random) hypergraph.     

Quantum spin dynamics of mode-squeezed Luttinger liquids in two-component atomic gases

We report on the observation of many-body spin dynamics of interacting, one-dimensional (1D) ultracold bosonic gases with two spin states. By controlling the nonlinear atomic interactions close to a Feshbach resonance we are able to induce a phase diffusive many-body spin dynamics of the relative phase between the two components. We monitor this dynamical evolution by Ramsey interferometry, supplemented by a novel, many-body echo technique, which unveils the role of quantum fluctuations in 1D. We find that the time evolution of the system is well described by a Luttinger liquid initially prepared in a multimode squeezed state. Our approach allows us to probe the nonequilibrium evolution of one-dimensional many-body quantum systems.     

Ab initio many-body perturbation theory and no-core shell model

In many-body perturbation theory(MBPT) we always introduce a parameter Nshellto measure the maximal allowed major harmonic-oscillator(HO) shells for the single-particle basis, while the no-core shell model(NCSM) uses N_(max)h? HO excitation truncation above the lowest HO configuration for the many-body basis. It is worth comparing the two different methods. Starting from "bare" and Okubo-Lee-Suzuki renormalized modern nucleon-nucleon interactions, NNLO_(opt) and JISP16, we show that MBPT within Hartree-Fock bases is in reasonable agreement with NCSM within harmonic oscillator bases for ~4He and ~(16)O in "close" model space. In addition, we compare the results using "bare" force with the Okubo-Lee-Suzuki renormalized force.     

Fermi gas on a lattice in the van Hove limit

We study a Fermi gas with general translation-invariant many-body interactions on a (v3)-dimensional lattice. A complete analysis is given of the perturbative terms up to second order and the program put forward by N. M. Hugenholtz for the derivative of the Boltzmann equation is verified to second order.     

Self-diffusion of spheres in a concentrated suspension

We calculate the concentration-dependence of the short-time self-diffusion coefficient D_s for spherical particles in suspension. Our analysis is valid up to high densities and fully takes into account the many-body hydrodynamic interactions between an arbitrary number of spheres. The importance of these many-body interactions can be inferred from our calculation of the second virial coefficient of D_s.     

Fast chain contraction during protein folding: "foldability" and collapse dynamics

Theory indicates that at least some proteins will undergo a rapid and unimpeded collapse, like a disorganized hydrophobic chain, prior to folding. Yet experiments continue to find signs of an organized, or barrier-limited, collapse in even the fastest (approximately mus) folding proteins. Does the kinetic barrier represent a signature of the equilibrium "foldability" of these molecules? We have measured the rate of chain contraction in two nonfolding analogs of a very fast-collapsing protein. We find that these chains contract on the same time scale (approximately 10(-5)s) as the natural protein, and both pass over an energetic barrier at least as large as that encountered by the protein. The equilibrium foldability of the native structure therefore does not alone determine the dynamics of collapse; even the disordered chains contract approximately 1000x slower than expected for an ideal chain.     

Simple off-lattice model to study the folding and aggregation of peptides

We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein (peptide): morphological analysis of the conformations at low temperature shows two well-known substructures α-helix and β-sheet depending on the chosen sequence. The folding pathway in the scope of this model is studied through a free-energy analysis. We then study the aggregation of proteins. Proteins in the aggregate are mainly bound via hydrogen bonds. Performing a free-energy analysis we show that the addition of a peptide to such an aggregate is not favourable. We qualitatively reproduce the abnormal aggregation of proteins in prion diseases.     

Stretch-induced hairpin-coil transitions in designed polynucleotide chains

The structural property of a poly( dG-dC) or poly( dA-dT) nucleotide is investigated. At low force and room temperatures, the polymer takes on compact hairpin structures. An abrupt transition from hairpin to random coil occurs at certain critical forces, its high cooperativity is related to the unfavorable formation of hairpin and other kinds of looped structures. It is hence necessary to consider the enthalpic effects of single-stranded loops in realistic models of RNA folding. A possible new way to obtain the statistical weights of elementary nucleotide arrangements is by single-macromolecular mechanical measurements on specifically designed polynucleotides.     

Description of the Superdeformed Bands of the Lutetium Isotopes

In the cases with and without a perturbation possessing the S0_sdg(5) (or SU_sdg(5)) symmetry in the supersymmetry scheme with many-body interactions, superdeformed bands in the odd-A Lu isotopes ^163,165,167Lu are investigated. Quantitatively good results of γ-ray energies and dynamical moments of inertia are obtained in both of the two cases. It shows that the supersymmetry scheme with many-body interactions has almost the same power to describe the triaxial superdeformed bands as to the other superdeformed bands.     

Colloid-polymer mixtures in the protein limit

We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit," where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal packing fraction tends to zero, whereas for interacting polymers in a good solvent the behavior is governed by a universal binodal, implying a constant critical colloid packing fraction. In both systems the depletion interaction is not well described by effective pair potentials but requires the incorporation of many-body contributions.     

From low-momentum interactions to nuclear structure

We present an overview of low-momentum two-nucleon and many-body interactions and their use in calculations of nuclei and infinite matter. The softening of phenomenological and effective field theory (EFT) potentials by renormalization group (RG) transformations that decouple low and high momenta leads to greatly enhanced convergence in few- and many-body systems, while maintaining a decreasing hierarchy of many-body forces. This review surveys the RG-based technology and results, discusses the connections to chiral EFT, and clarifies various misconceptions.     

Reconstructing the free-energy landscape of a mechanically unfolded model protein

The equilibrium free-energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the "folding transition" we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.     

The antikaon–nucleus interaction and alternative views to deeply bound antikaonic nuclear systems

We present an overview of the latest theoretical studies on the antikaon properties in the nuclear medium, in connection with the recent experimental claims of very deeply bound antikaon nuclear states. We argue that proper many-body formulations using modern realistic antikaon–nucleon interactions are not able to generate such systems. Instead, a simple two-nucleon antikaon absorption mechanism where the remaining nucleus acts as spectator explains the enhancement observed in semi-inclusive proton momentum spectra, seen as a bump in the KEK PS-E549 experiment on a ⁴He target or as a peak in the FINUDA experiment on a ⁶Li target. This signal is clearly visible in another FINUDA experiment measuring the invariant mass of Λ-proton pairs after two-nucleon kaon absorption. We also show that another peak of this experiment, seen at lower invariant masses and interpreted as a bound K⁻pp state, is simply generated by the same two-nucleon absorption mechanism followed by final-state interactions of the produced particles with the residual nucleus. Our conclusion is that all the experimental claims for the formation of very deeply bound antikaonic nuclear systems receive an alternative explanation in terms of conventional nuclear processes.     

The onset of disorder in Al(110) surfaces below the melting point

Molecular dynamics simulations of the disordering of Al(110) surfaces below the melting point are presented. Effective medium theory has been used to calculate the inter-atomic many-body interactions of the metallic system. The origin of the anisotropy of the disordering with respect to the direction along the surface deduced from LEED experiments is suggested to be mainly a consequence of the g² dependence of the Debye-Waller factor even for non-harmonic interactions. Further evidence is presented showing that the disordering of the first layers coincides with the onset of surface vacancy formation.     

The influence of many-body interactions on the de Haas-van Alphen effect

The de Haas-van Alphen (dHvA) effect, or Landau quantum oscillatory magnetization of metals, has been widely used to explore the single-particle aspects of electrons in metals with the aim of determining their Fermi surfaces. Its role in studying many-body effects in metals is less familiar, even though the influence of such interactions is well known. We present a general field-theoretic approach to this problem which shows that the paradigm for understanding the influence of many-body interactions in the dHvA effect should be shifted from the intuitively reasonable but potentially misleading arguments based on the electron self-energy on the real energy axis to an analysis of the self-energy along the imaginary energy axis. When viewed in this way, the dHvA effect assumes the role of a many-body self-energy filter in which the real part of the self-energy renormalizes the dHvA frequency while the imaginary part renormalizes independently the dHvA amplitude. We obtain a general theory for the dHvA effect in an interacting system which preserves the structure of the original non-interacting theory of Lifshitz and Kosevich. We then apply this extended Lifshitz-Kosevich theory to the analysis of several problems of interest, including electron-electron and electron-phonon interactions, heavy fermions and type II superconductors.