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A new model to study proteinic systems including a many-body polarization and a hydrogen bond energy contribution is presented. This model represents an extension of an earlier water many-body model [M. Masella and J.-P. Flament, J. Chem. Phys. 107 9105 (1997)]. As in this earlier model, the new model is developed to reproduce quantum computations on small molecular aggregates, and, in this first paper, we focus our efforts in developing an accurate potential to describe interactions among all nonbonded atoms occurring in proteins, and among those atoms and six cations of biological interest: Li[SUP+], Na[SUP+], K[SUP+], Mg[SUP2+], Ca[SUP2+], and Zn[SUP2+]. Intramolecular degrees of freedom are described as in classical two-body force fields. In the present paper, the new model is applied to investigate the properties of small ion-neutral [M,L[SUBn][SUPm+] complexes and of small hydrogen-bonded systems. The results showed that this model is able to reproduce most of the theoretical quantum predictions and experimental data published until now regarding those systems. [ABSTRACT FROM AUTHOR]

A number of experiments and experimentally based simulations showed that β-proteins are mechanically more stable than α-proteins. However, the theory that might explain this evidence is still lacking. In this paper we have developed a simple elastic theory, which allows to estimate critical forces for stretching both kinds of proteins. It has been shown that unfolding of β-proteins does really require notably higher forces as compared to the stretching of α-proteins. [ABSTRACT FROM AUTHOR]

S-layer proteins have a wide range of application potential due to their characteristic features concerning self-assembling, assembling on various surfaces, and forming of isoporous structures with functional groups located on the surface in an identical position and orientation. Although considerable knowledge has been experimentally accumulated on the structure, biochemistry, assemble characteristics, and genetics of S-layer proteins, no structural model at atomic resolution has been available so far. Therefore, neither the overall folding of the S-layer proteins—their tertiary structure—nor the exact amino acid or domain allocations in the lattices are known. In this paper, we describe the tertiary structure prediction for the S-layer protein SbsB from Geobacillus stearothermophilus PV72/p2. This calculation was based on its amino acid sequence using the mean force method (MF method) achieved by performing molecular dynamic simulations. This method includes mainly the thermodynamic aspects of protein folding as well as steric constraints of the amino acids and is therefore independent of experimental structure analysis problems resulting from biochemical properties of the S-layer proteins. Molecular dynamic simulations were performed in vacuum using the simulation software NAMD. The obtained tertiary structure of SbsB was systematically analyzed by using the mean force method, whereas the verification of the structure is based on calculating the global free energy minimum of the whole system. This corresponds to the potential of mean force, which is the thermodynamically most favorable conformation of the protein. Finally, an S-layer lattice was modeled graphically using CINEMA4D and compared with scanning force microscopy data down to a resolution of 1 nm. The results show that this approach leads to a thermodynamically favorable atomic model of the tertiary structure of the protein, which could be verified by both the MF Method and the lattice model. [ABSTRACT FROM AUTHOR]

An initial guess is one of the most important factors in solving self-consistent field (SCF) molecular orbital calculations for large molecules. Recently, the authors reported that the quasicanonical localized orbital (QCLO) method was useful to prove the initial guess for all-electron calculations for proteins. This paper describes a new QCLO method that takes into account protein information derived from protein structures such as salt bridges and the secondary structure of the molecule. In several test calculations using typical models, the difference between the initial guess and final atomic charges was markedly decreased, and the number of SCF iterations was reduced. We suggest that the structure-based QCLO method improves the precision of the initial guess and achievement of automatic all-electron calculations for proteins. [ABSTRACT FROM AUTHOR]

In order to probe the fundamental principles that govern protein evolution, we use a minimalist model of proteins to provide a mapping from genotype to phenotype. The model is based on physically realistic forces of protein folding and includes an explicit definition of protein function. Thus, we can find the fitness of a sequence from its ability to fold to a stable structure and perform a function. We study the fitness landscapes of these functional model proteins, that is, the set of all sequences mapped on to their corresponding fitnesses and connected to their one mutant neighbors. Through population dynamics simulations we directly study the influence of the nature of the fitness landscape on evolution. Populations are observed to move to a steady state, the distribution of which can often be predicted prior to the population dynamics simulations from the nature of the fitness landscape and a quantity analogous to a partition function. In this paper, we develop a scheme for predicting the steady-state population on a fitness landscape, based on the nature of the fitness landscape, thereby obviating the need for explicit population dynamics simulations and providing some insight into the impact on molecular evolution of the nature of fitness landscapes. Poor predictions are indicative of fitness landscapes that consist of a series of weakly connected sublandscapes. [ABSTRACT FROM AUTHOR]

Protein refolding to its native state in vitro is a challenging problem in biotechnology, i.e., in the biomedical, pharmaceutical, and food industry. Protein aggregation and misfolding usually inhibit the recovery of proteins with their native states. These problems can be partially solved by adding a surfactant into a suitable solution environment. However, the process of this surfactant-assisted protein refolding is not well understood. In this paper, we wish to report on the first-ever simulations of surfactant-assisted protein refolding. For these studies, we defined a simple model for the protein and the surfactant and investigated how a surfactant affected the folding behavior of a two-dimensional lattice protein molecule. The model protein and model surfactant were chosen such that we could capture the important features of the folding process and the interaction between the protein and the surfactant, namely, the hydrophobic interaction. It was shown that, in the absence of surfactants, a protein in an “energy trap” conformation, i.e., a local energy minima, could not fold into the native form, which was characterized by a global energy minimum. The addition of surfactants created folding pathways via the formation of protein-surfactant complexes and thus enabled the conformations that fell into energy trap states to escape from these traps and to form the native proteins. The simulation results also showed that it was necessary to match the hydrophobicity of surfactant to the concentration of denaturant, which was added to control the folding or unfolding of a protein. The surfactants with different hydrophobicity had their own concentration range on assisting protein refolding. All of these simulations agreed well with experimental results reported elsewhere, indicating both the validity of the simulations presented here and the potential application of the simulations for the design of a surfactant on assisting protein refolding. [ABSTRACT FROM AUTHOR]

Exploring the structures and spectral features of proteins with advanced quantum chemical methods is an uphill task. In this work, a fragment-based molecular tailoring approach (MTA) is appraised for the CAM-B3LYP/aug-cc-pVDZ-level geometry optimization and vibrational infrared (IR) spectra calculation of ten real proteins containing up to 407 atoms and 6617 basis functions. The use of MTA and the inherently parallel nature of the fragment calculations enables a rapid and accurate calculation of the IR spectrum. The applicability of MTA to optimize the protein geometry and evaluate its IR spectrum employing a polarizable continuum model with water as a solvent is also showcased. The typical errors in the total energy and IR frequencies computed by MTA vis-à-vis their full calculation (FC) counterparts for the studied protein are 5–10 millihartrees and 5 cm−1, respectively. Moreover, due to the independent execution of the fragments, large-scale parallelization can also be achieved. With increasing size and level of theory, MTA shows an appreciable advantage in computer time as well as memory and disk space requirement over the corresponding FCs. The present study suggests that the geometry optimization and IR computations on the biomolecules containing ∼1000 atoms and/or ∼15 000 basis functions using MTA and HPC facility can be clearly envisioned in the near future. [ABSTRACT FROM AUTHOR]

An efficient molecular dynamics (MD) algorithm is presented in this paper for biomolecular systems, which incorporates a novel variation on the fast multipole method (FMM) coupled to the reversible reference system propagator algorithm (r-RESPA). A top-down FMM is proposed which calculates multipoles recursively from the top of the box tree instead of from the bottom in Greengard’s original FMM, in an effort to be more efficient for noncubic or nonuniform systems. In addition, the use of noncubic box subdivisions of biomolecular systems is used and discussed. Reversible RESPA based on a Trotter factorization of the Liouville propagator in generating numerical integration schemes is coupled to the top-down FMM and applied to a MD study of proteins in vacuo, and is shown to be able to use a much larger time-step than the standard velocity Verlet method for a comparable level of accuracy. Furthermore, by using the FMM it becomes possible to perform MD simulations for very large biomolecules, since memory and CPU time requirements are now nearly of order of O(N) instead of O(N2). For a protein with 9513 atoms (the photosynthetic reaction center), the efficient MD algorithm leads to 20-fold reduction in CPU time for the Coulomb interaction and approximately 15-fold reduction in total CPU time over the standard velocity Verlet algorithm with a direct evaluation of Coulomb forces. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Many fundamental biological processes are regulated by protein-DNA complexes called synaptosomes, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation are not well understood. Because of the multisite nature of participating proteins, it is widely believed that their search for specific sites on DNA involves the formation and breaking of DNA loops and sliding in the looped configurations. In reality, DNA in live cells is densely covered by other biological molecules that might interfere with the formation of synaptosomes. In this work, we developed a theoretical approach to evaluate the role of obstacles in the target search of multisite proteins when the formation of DNA loops and the sliding in looped configurations are possible. Our theoretical method is based on analysis of a discrete-state stochastic model that uses a master equations approach and extensive computer simulations. It is found that the obstacle slows down the search dynamics in the system when DNA loops are long-lived, but the effect is minimal for short-lived DNA loops. In addition, the relative positions of the target and the obstacle strongly influence the target search kinetics. Furthermore, the presence of the obstacle might increase the noise in the system. These observations are discussed using physical-chemical arguments. Our theoretical approach clarifies the molecular mechanisms of formation of protein-DNA complexes with multiple interactions sites. [ABSTRACT FROM AUTHOR]

Recent single-molecule experiments probed transition paths of biomolecular folding and, in particular, measured the time biomolecules spend while crossing their free energy barriers. A surprising finding from these studies is that the transition barriers crossed by transition paths, as inferred from experimentally observed transition path times, are often lower than the independently determined free energy barriers. Here we explore memory effects leading to anomalous diffusion as a possible origin of this discrepancy. Our analysis of several molecular dynamics trajectories shows that the dynamics of common reaction coordinates used to describe protein folding is subdiffusive, at least at sufficiently short times. We capture this effect using a one-dimensional fractional Brownian motion (FBM) model, in which the system undergoes a subdiffusive process in the presence of a potential of mean force, and show that this model yields much broader distributions of transition path times with stretched exponential long-time tails. Without any adjustable parameters, these distributions agree well with the transition path times computed directly from protein trajectories. We further discuss how the FBM model can be tested experimentally. [ABSTRACT FROM AUTHOR]

The folding properties of a protein whose native structure contains a 52 knot are investigated by means of extensive Monte Carlo simulations of a simple lattice model and compared with those of a 31 knot. A 52 knot embedded in the native structure enhances the kinetic stability of the carrier lattice protein in a way that is clearly more pronounced than in the case of the 31 knot. However, this happens at the expense of a severe loss in folding efficiency, an observation that is consistent with the relative abundance of 31 and 52 knots in the Protein Data Bank. The folding mechanism of the 52 knot shares with that of the 31 knot the occurrence of a threading movement of the chain terminus that lays closer to the knotted core. However, co-concomitant knotting and folding in the 52 knot occurs with negligible probability, in sharp contrast to what is observed for the 31 knot. The study of several single point mutations highlights the importance in the folding of knotted proteins of the so-called structural mutations (i.e., energetic perturbations of native interactions between residues that are critical for knotting but not for folding). On the other hand, the present study predicts that mutations that perturb the folding transition state may significantly enhance the kinetic stability of knotted proteins provided they involve residues located within the knotted core. [ABSTRACT FROM AUTHOR]

Biomolecular polyanions mainly relax by electron emission after UV excitation. Here, we study photodetachment of protein polyanions in the 6-16 eV VUV range by coupling a linear quadrupole ion trap with a synchrotron beamline. Gas-phase VUV action spectra of electrospray-produced multiply deprotonated insulin (5.6 kDa) and myoglobin (16.7 kDa) proteins are reported, which significantly increases the amount of data available on the optical response of proteins in the VUV. The influence of the protein charge and oxidation state upon the electron detachment efficiency is discussed. For small protein such as insulin, it appears that higher charge states produce higher detachment yields. Investigations on oxidized species show that the nature of the groups bearing the negative charges has an influence on the yields. For larger proteins, comparison of two forms of myoglobin clearly indicate that the three-dimensional structure does not impact much on the shape and the magnitude of the photodetachment spectra, in spite of a slight shift for the first electronic excited states. [ABSTRACT FROM AUTHOR]

The hydrophobicity of surfaces has a strong influence on their interactions with biomolecules such as proteins. Therefore, for in vitro studies of bio-surface interactions model surfaces with tailored hydrophobicity are of utmost importance. Here, we present a method for tuning the hydrophobicity of atomically flat mica surfaces by hyperthermal Ar ion irradiation. Due to the sub-100 eV energies, only negligible roughening of the surface is observed at low ion fluences and also the chemical composition of the mica crystal remains almost undisturbed. However, the ion irradiation induces the preferential removal of the outermost layer of K+ ions from the surface, leading to the exposure of the underlying aluminosilicate sheets which feature a large number of centers for C adsorption. The irradiated surface thus exhibits an enhanced chemical reactivity toward hydrocarbons, resulting in the adsorption of a thin hydrocarbon film from the environment. Aging these surfaces under ambient conditions leads to a continuous increase of their contact angle until a fully hydrophobic surface with a contact angle >80° is obtained after a period of about 3 months. This method thus enables the fabrication of ultrasmooth biological model surfaces with precisely tailored hydrophobicity. [ABSTRACT FROM AUTHOR]

We discuss the use of velocity rescaling for generating rejection-free exchange moves in replica exchange molecular dynamics. We test the efficiency of this approach for a common test case, the trp-cage protein. Advantages and limitations of the approach are discussed and possible extensions outlined. [ABSTRACT FROM AUTHOR]

Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail. [ABSTRACT FROM AUTHOR]

We present design of novel low-power homonuclear dipolar recoupling experiments for magic-angle-spinning solid-state NMR studies of proteins. The pulse sequences are developed by combining principles of symmetry-based dipolar recoupling and optimal control-based pulse sequence design. The scaffold of the pulse sequences is formed by known CN-type recoupling sequences, while the intrinsic sequence elements are designed using optimal control. This procedure allows for the development of high-performance pulse sequences demanding significantly weaker rf fields than previous symmetry-based pulse sequences while compensating for rf inhomogeneity and providing excitation over relevant ranges of chemical shifts for biological applications. The new recoupling experiments, referred to as optimal control CN (OCCN), are demonstrated numerically and experimentally by two-dimensional (2D) 13C–13C and three-dimensional (3D) 15N–13C–13C chemical shift correlation experiments on uniformly 13C, 15N-labeled ubiquitin. Exploiting the double-quantum, band-selective dipolar recoupling properties of the OCCN experiments, we demonstrate significant sensitivity enhancement for 2D and 3D correlation spectra showing exclusively one- or two-bond correlations. [ABSTRACT FROM AUTHOR]

Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements based on nucleic magnetic resonance, disulfide linking, and electron paramagnetic resonance labeling studies can all provide useful partial distance constraint characteristic of the conformations of proteins. In this study, we describe a general approach for reconstructing conformations of biomolecules that are consistent with given distance constraints. Such constraints can be in the form of upper bounds and lower bounds of distances between residue pairs, contact maps based on specific contact distance cutoff values, or indirect distance constraints such as experimental [lowercase_phi_synonym]-value measurement. Our approach is based on the framework of sequential Monte Carlo method, a chain growth-based method. We have developed a novel growth potential function to guide the generation of conformations that satisfy given distance constraints. This potential function incorporates not only the distance information of current residue during growth but also the distance information of future residues by introducing global distance upper bounds between residue pairs and the placement of reference points. To obtain protein conformations from indirect distance constraints in the form of experimental [lowercase_phi_synonym]-values, we first generate properly weighted contact maps satisfying [lowercase_phi_synonym]-value constraints, we then generate conformations from these contact maps. We show that our approach can faithfully generate conformations that satisfy the given constraints, which approach the native structures when distance constraints for all residue pairs are given. [ABSTRACT FROM AUTHOR]

Lipid bilayers are essential structural component of biological membranes of all the living species: from viruses and bacteria to plants and humans. Biophysical and biochemical properties of such membranes are important for understanding physical mechanisms responsible for drug targeting. Binding events between proteins and the membrane may be ascertained by introducing fluorescence markers (chromophores) to the proteins. Here we describe a novel biosensing platform designed to enhance signals of these fluorescence markers. Nanoporous aluminum oxide membranes with and without gold (Au) surface coating have been employed for optical detection of bound conjugated streptavidin to biotinylated lipid bilayers—a model system that mimics protein docking to the membrane surface. Unexpectedly, it was found that fluorescence signals from such structures vary when pumped with E-polarized and H-polarized incident optical beams. The origin of the observed polarization-dependent effects and the implications for enhanced fluorescence detection in a biochip format are being discussed. [ABSTRACT FROM AUTHOR]

We present the results of several benchmarks comparing the relative efficiency of different coordinate systems in optimizing polypeptide geometries. Cartesian, natural internal, and primitive internal coordinates are employed in quasi-Newton minimization for a variety of biomolecules. The peptides and proteins used in these benchmarks range in size from 16 to 999 residues. They vary in complexity from polyalanine helices to a β-barrel enzyme. We find that the relative performance of the different coordinate systems depends on the parameters of the optimization method, the starting point for the optimization, and the size of the system studied. In general, internal coordinates were found to be advantageous for small peptides. For larger structures, Cartesians appear to be more efficient for empirical potentials where the energy and gradient can be evaluated relatively quickly compared to the cost of the coordinate transformations. [ABSTRACT FROM AUTHOR]

The possibility of downhill instead of two-state folding for proteins has been a very controversial topic which arose from recent experimental studies. From the theoretical side, this question has also been accomplished in different ways. Given the experimental observation that a relationship exists between the native structure topology of a protein and the kinetic and thermodynamic properties of its folding process, Gō-type potentials are an appropriate way to approach this problem. In this work, we employ an interaction potential from this family to get a better insight on the topological characteristics of the native state that may somehow determine the presence of a thermodynamic barrier in the folding pathway. The results presented here show that, indeed, the native topology of a small protein has a great influence on its folding behavior, mostly depending on the proportion of local and long range contacts the protein has in its native structure. Furthermore, when all the interactions present contribute in a balanced way, the transition results to be cooperative. Otherwise, the tendency to a downhill folding behavior increases. [ABSTRACT FROM AUTHOR]

Time series models, which are constructed from the projections of the molecular-dynamics (MD) runs on principal components (modes), are used to mimic the dynamics of two proteins: tendamistat and immunity protein of colicin E7 (ImmE7). Four independent MD runs of tendamistat and three independent runs of ImmE7 protein in vacuum are used to investigate the energy landscapes of these proteins. It is found that mean-square displacements of residues along the modes in different time scales can be mimicked by time series models, which are utilized in dividing protein dynamics into different regimes with respect to the dominating motion type. The first two regimes constitute the dominance of intraminimum motions during the first 5 ps and the random walk motion in a hierarchically higher-level energy minimum, which comprise the initial time period of the trajectories up to 20–40 ps for tendamistat and 80–120 ps for ImmE7. These are also the time ranges within which the linear nonstationary time series are completely satisfactory in explaining protein dynamics. Encountering energy barriers enclosing higher-level energy minima constrains the random walk motion of the proteins, and pseudorelaxation processes at different levels of minima are detected in tendamistat, depending on the sampling window size. Correlation (relaxation) times of 30–40 ps and 150–200 ps are detected for two energy envelopes of successive levels for tendamistat, which gives an overall idea about the hierarchical structure of the energy landscape. However, it should be stressed that correlation times of the modes are highly variable with respect to conformational subspaces and sampling window sizes, indicating the absence of an actual relaxation. The random-walk step sizes and the time length of the second regime are used to illuminate an important difference between the dynamics of the two proteins, which cannot be clarified by the investigation of relaxation times alone: ImmE7 has lower-energy barriers enclosing the higher-level energy minimum, preventing the protein to relax and letting it move in a random-walk fashion for a longer period of time. [ABSTRACT FROM AUTHOR]

The networklike structure of actin bundles formed with the cross-linking protein α-actinin has been investigated via x-ray scattering and confocal fluorescence microscopy over a wide range of α-actinin/F-actin ratios. We describe the hierarchical structure of bundle gels formed at high ratios. Isotropic actin bundle gels form via cluster-cluster aggregation in the diffusion-limited aggregation regime at high α-actinin/actin ratios. This process is clearly observed by confocal fluorescence microscopy. Polylysine is investigated as an alternative bundling agent in the high-ratio regime and the effects of F-actin length are also discussed. One particularly fascinating aspect of this system is the presence of a structured skin layer at the gel/water interface. Confocal microscopy has elucidated the full three-dimensional structure of this layer and revealed several interesting morphologies. The protein skin layer is a micron-scale structure composed of a directed network of bundles and exhibits flat, crumpled, and tubelike shapes. We show that crumpling of the skin layer results from stresses due to the underlying gel. These biologically based geometric structures may detach from the gel, demonstrating potential for the generation of biological scaffolds with defined shapes for applications in cell encapsulation and tissue engineering. We demonstrate manipulation of the skin layer, producing hemispherical structures in solution. [ABSTRACT FROM AUTHOR]

Various aspects of the ab initio-based parametrization of an exciton model of amide I vibrations in peptides are discussed. Adopting “glycine dipeptide” (Ac-Gly-NHCH3) as a simple building-block model that describes the vibrational interaction between two peptide units, we perform comprehensive quantum-chemical calculations to investigate the effect and importance of the level of theory, the choice of local coordinates, and the localization method. A solvent continuum model description turns out important to obtain planar CONH peptide units when a full geometry optimization (which is necessary to obtain the correct frequencies) is performed. To study the conformational dependence of the amide I vibrations, we calculate ([lowercase_phi_synonym],ψ) maps of the local-mode frequencies and couplings. Performing conformational averages of the ([lowercase_phi_synonym],ψ) maps with respect to the most important peptide conformational states in solution (α, β, PII, and C5), we discuss the relation between these measurable quantities and the corresponding conformation of the peptide. Finally, the transferability of these maps to dipeptides with hydrophilic and hydrophobic side chains as well as to tripeptides with charged end groups is investigated. [ABSTRACT FROM AUTHOR]

A simple protein model of a four-helix bundle motif on a face-centered cubic lattice has been studied. Total energy of a conformation includes attractive interactions between hydrophobic residues, repulsive interactions between hydrophobic and polar residues, and a potential that favors helical turns. Using replica exchange Monte Carlo simulations we have estimated a set of parameters for which the native structure is a global minimum of conformational energy. Then we have shown that all the above types of interactions are necessary to guarantee the cooperativity of folding transition and to satisfy the thermodynamic hypothesis. [ABSTRACT FROM AUTHOR]

We evaluate the efficiency of multiple variants of energy landscape paving in all-atom simulations of the trp-cage protein using a recently developed new force field. Especially, we introduce a temperature-free variant of the method and demonstrate that it allows a fast scanning of the energy landscape. Nativelike structures are found in less time than by other techniques. The sampled low-energy configurations indicate a funnel-like energy landscape. [ABSTRACT FROM AUTHOR]

Using simulation to study the folding kinetics of 20-mer poly-phenylacetylene (pPA) oligomers, we find a long time scale trapped kinetic phase in the cumulative folding time distribution. This is demonstrated using molecular dynamics to simulate an ensemble of over 100 folding trajectories. The simulation data are fit to a four-state kinetic model which includes the typical folded and unfolded states, along with an intermediate state, and most surprisingly, a kinetically trapped state. Topologically diverse conformations reminiscent of α helices, β turns, and sheets in proteins are observed, along with unique structures in the form of knots. The nonhelical conformations are implicated, on the basis of structural correlations to kinetic parameters, to contribute to the trapped kinetic behavior. The strong solvophobic forces which mediate the folding process and produce a stable helical folded state also serve to overstabilize the nonhelical conformations, ultimately trapping them. From our simulations, the folding time is predicted to be on the order of 2.5–12.5 μs in the presence of the trapped kinetic phase. The folding mechanism for these 20-mer chains is compared with the previously reported folding mechanism for the pPA 12-mer chains. A linear scaling relationship between the chain length and the mean first passage time is predicted in the absence of the trapped kinetic phase. We discuss the major implications of this discovery in the design of self-assembling nanostructures. [ABSTRACT FROM AUTHOR]

We have exactly enumerated all sequences and conformations of hydrophobic-polar (HP) proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the HP model, where only two types of monomers are distinguished, we determined and statistically analyzed designing sequences, i.e., sequences that have a nondegenerate ground state. Furthermore we were interested in characteristic thermodynamic properties of HP proteins with designing sequences. In order to be able to perform these exact studies, we applied an efficient enumeration method based on contact sets. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

By using molecular dynamics simulation, the dynamic behaviors of particle permeation through a four-helix-bundle model channel are studied. The interior cavity of the four-helix-bundle provides the “routes” for particle permeation. The main structural properties of the model channel are similar to those that appear in natural four-helix-bundle proteins. It is found that the interior structure of the model channel may greatly influence the permeation process. At the narrow necks of the model channel, the particle would be trapped during the permeation. There is a threshold value for the driving force. When the driving force is larger than this threshold value, the mean first permeation time decreases sharply and tends to be saturated. Increasing the temperature of either the model channel or the particle reservoir can also facilitate the permeation. Enhancing the interaction strength between the particle and monomer on the four-helix-bundle model chain will hinder the permeation. Hence, the electrical current which is induced by the particle permeation is a function of the driving force and temperature. It is found that this current increases monotonically as the strength of the driving force or the temperature increases, but decreases as the interaction strength between the particle and monomer increases. It is also found that the larger the friction coefficient, the slower the permeation is. In addition, the multiparticle (or multi-ion) permeation process is also studied. The permeation of multiparticle is usually quicker than that of the single particle. The permeation of particle through a five-helix-bundle shows similar properties as that through a four-helix-bundle. [ABSTRACT FROM AUTHOR]

The rate of vibrational energy transfer and thermal transport coefficients are computed for two structurally distinct proteins, green fluorescent protein (GFP) and myoglobin. The computation of thermal transport coefficients exploits the scaling of the energy diffusion coefficient with the vibrational mode frequency of a protein. Near 300 K we find that vibrational energy transfer due to anharmonicity contributes substantially to thermal transport because of the localization of many thermally accessible normal modes. The thermal diffusivity for the β-barrel GFP is larger than that for myoglobin, particularly at low temperature due to a mean free path for vibrational energy propagation that is twice as large at low frequency. Vibrational energy transfer is also faster in GFP than in myoglobin for most vibrational modes. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called “collective coordinates.” We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fuctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-Cα distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein’s known active sites and experimentally determined mobile regions. © 2005 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We relate the condition for the elliptic shape of the phase diagram of proteins to the degree of correlation in the fluctuations of the changes of enthalpy and volume at the denaturing-refolding transition. Since this degree cannot be larger than 1, hyperbolically shaped diagrams are not likely to exist. Experiments show that the correlation factor is actually quite low for proteins implying that one-order parameter is not enough to describe the folding-denaturing transition. These findings seem to be the thermodynamic manifestation of the glasslike properties of proteins despite the fact that the transition itself is of first order.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Cosolvents added to aqueous solutions of biomolecules profoundly affect protein stability, as well as biochemical equilibria. Some cosolvents, such as urea and guanidine hydrochloride, denature proteins, whereas others, such as osmolytes and crowders, stabilize the native structures of proteins. The way cosolvents interact with biomolecules is crucial information required to understand the cosolvent effect at a molecular level. We present a statistical mechanical framework based upon Kirkwood–Buff theory, which enables one to extract this picture from experimental data. The combination of two experimental results, namely, the cosolvent-induced equilibrium shift and the partial molar volume change upon the reaction, supplimented by the structural change, is shown to yield the number of water and cosolvent molecules bound or released during a reaction. Previously, denaturation experiments (e.g., m-value analysis) were analyzed by empirical and stoichiometric solvent-binding models, while the effects of osmolytes and crowders were analyzed by the approximate molecular crowding approach for low cosolvent concentration. Here we synthesize these previous approaches in a rigorous statistical mechanical treatment, which is applicable at any cosolvent concentration. The usefulness and accuracy of previous approaches was also evaluated. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Explicit simulations of protein evolution, where protein chains are described at a molecular, although simplified, level provide important information to understand the similarities found to exist between known proteins. The results of such simulations suggest that a number of evolutionary-related quantities, such as the distribution of sequence similarity for structurally similar proteins, are controlled by evolutionary kinetics and do not reflect an equilibrium state. An important result for phylogeny is that a subset of the residues of each protein evolve on a much larger time scale than the other residues. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

The mapping of phenotype onto genotype for a set of functional model proteins is accomplished by exhaustive enumeration on a three-dimensional diamond lattice. Chains of up to 25 monomers are investigated and their evolution characterized. The model is used to investigate the origins of designability. Highly designable functional model protein structures possess contact maps that have a relatively little commonality with other physically allowed contact maps. Although the diamond lattice has the same coordination number as the square lattice, differences between three-dimensional and two-dimensional functional model proteins are observed. One difference is the lower frequency of structures of low designability on the three-dimensional lattice. In other respects, the conclusions drawn from previous studies using the square lattice remain valid in three dimensions. For example, we observe the tendency for longer chains to form larger networks of sequences with greater stability to mutation. We identify various topographical characteristics of the landscapes: evolutionary bottlenecks bridge otherwise unconnected networks, and hub sequences allow rapid movement between the different neutral networks. The diversity of landscapes that arises from even a minimalist model suggests that real proteins have a rich variety of evolutionary landscapes. [ABSTRACT FROM AUTHOR]

We present a numerical simulation of the phase behavior of a simple model for a protein solution. We find that this system can occur in three phases, namely a dilute liquid, a dense liquid and a crystal. The transition from dilute-liquid to dense-liquid takes place in the regime where the fluid phase is metastable with respect to the crystal. We have computed the relative stabilities of different crystal morphologies. In addition, we have analyzed the “nucleation” of the native state of an isolated lattice protein. Using a “Gō” model [N. Gō, J. Stat. Phys. 30, 413 (1983)] to describe the protein, we show that a first order transition exists between the native and the coil state. We show this by analyzing the free energy barrier for the coil-to-native transition. © 2003 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Motivated by the protein structure prediction problem, we develop two variants of the Hamiltonian replica exchange methods (REMs) for efficient configuration sampling, (1) the scaled hydrophobicity REM and (2) the phantom chain REM, and compare their performance with the ordinary REM. We first point out that the ordinary REM has a shortage for the application to large systems such as biomolecules and that the Hamiltonian REM, an alternative formulation of the REM, can give a remedy for it. We then propose two examples of the Hamiltonian REM that are suitable for a coarse-grained protein model. (1) The scaled hydrophobicity REM prepares replicas that are characterized by various strengths of hydrophobic interaction. The strongest interaction that mimics aqueous solution environment makes proteins folding, while weakened hydrophobicity unfolds proteins as in organic solvent. Exchange between these environments enables proteins to escape from misfolded traps and accelerate conformational search. This resembles the roles of molecular chaperone that assist proteins to fold in vivo. (2) The phantom chain REM uses replicas that allow various degrees of atomic overlaps. By allowing atomic overlap in some of replicas, the peptide chain can cross over itself, which can accelerate conformation sampling. Using a coarse-gained model we developed, we compute equilibrium probability distributions for poly-alanine 16-mer and for a small protein by these REMs and compare the accuracy of the results. We see that the scaled hydrophobicity REM is the most efficient method among the three REMs studied. © 2002 American Institute of Physics. [ABSTRACT FROM AUTHOR]