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Biomedical subjects

P G Wolynes

Publications and source records attributed to P G Wolynes.

At least 19 recordsLinked to original sources
PubMed2005

Self-regulating gene: an exact solution.

An exact steady-state solution of the stochastic equations governing the behavior of a gene regulated by a self-generated proteomic atmosphere is presented. The solutions depend on an adiabaticity parameter measuring the relative rate of DNA-protein unbinding and protein degradation. The steady-state solution reveals deviations from the commonly used Ackers et al approximation based on the equilibrium law of mass action, allowing anticooperative behavior in the "nonadiabatic" limit of slow binding and unbinding rates. Noise from binding and unbinding events dominates the shot noise of protein synthesis and degradation up to quite high values of the adiabaticity parameter.

Animals↗
PubMed2005

Recent successes of the energy landscape theory of protein folding and function.

Protein folding and binding can be understood using energy landscape theory. When seeming deviations from the predictions of the funnel hypothesis are found, landscape theory helps us locate the cause. Sometimes the deviation reflects symmetry effects, allowing extra degeneracies to occur. Such effects seem to explain some kinetic anomalies in helical bundles. When binding processes were found to use apparently non-funneled landscapes this was traced to an inadequate understanding of biomolecular forces. The discrepancy allowed the discovery of new water-mediated forces - some of which act between hydrophilic residues. Introducing such forces into the algorithms greatly improves the quality of structure predictions.

Algorithms↗
PubMed2004

Vibrational energy flow and chemical reactions.

How vibrational energy flows in molecules has recently become much better understood through the joint efforts of theory, experiment, and computation. The phenomenology of energy flow is much richer than earlier thought. We now know energy flow depends on the local structure of molecular vibrational state space. The details of the theoretically predicted transition from localized vibrations to free flow, where the molecule can act as its own heat bath, are now well-established experimentally. Energy flow is a quantum diffusive process leading to nonexponential decays, also seen in experiment. The slowness of energy flow in activated molecules causes substantial deviation from statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theories for low barrier rate processes, such as isomerization. Quantitative calculations of rates in those cases are now possible.

Journal Article↗
PubMed2003

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins.

Large-scale motions of biomolecules involve linear elastic deformations along low-frequency normal modes, but for function nonlinearity is essential. In addition, unlike macroscopic machines, biological machines can locally break and then reassemble during function. We present a model for global structural transformations, such as allostery, that involve large-scale motion and possible partial unfolding, illustrating the method with the conformational transition of adenylate kinase. Structural deformation between open and closed states occurs via low-frequency modes on separate reactant and product surfaces, switching from one state to the other when energetically favorable. The switching model is the most straightforward anharmonic interpolation, which allows the barrier for a process to be estimated from a linear normal mode calculation, which by itself cannot be used for activated events. Local unfolding, or cracking, occurs in regions where the elastic stress becomes too high during the transition. Cracking leads to a counterintuitive catalytic effect of added denaturant on allosteric enzyme function. It also leads to unusual relationships between equilibrium constant and rate like those seen recently in single-molecule experiments of motor proteins.

Elasticity↗
PubMed2001

Intrinsic quantum excitations of low temperature glasses.

Several puzzling regularities concerning the low temperature excitations of glasses are quantitatively explained by quantizing domain wall motions of the random first order glass transition theory. The density of excitations agrees with experiment and scales with the size of a dynamically coherent region at T(g), being about 200 molecules. The phonon coupling depends on the Lindemann ratio for vitrification yielding the observed universal relation l/lambda approximately 150 between phonon wavelength lambda and mean free path l. Multilevel behavior is predicted to occur in the temperature range of the thermal conductivity plateau.

Journal Article↗
PubMed2001

Microscopic theory of heterogeneity and nonexponential relaxations in supercooled liquids.

Recent experiments show that supercooled liquids around the glass transition temperature are "dynamically heterogeneous" [H. Sillescu, J. Non-Cryst. Solids 243, 81 (1999)]. Such heterogeneity is expected from the random first order transition theory of the glass transition. Using a microscopic approach based on this theory, we derive a relation between the departure from Debye relaxation as characterized by the beta value of a stretched exponential response function, phi(t) = e(-(t/tau(KWW))beta), and the fragility of the liquid. The beta value is also predicted to depend on temperature and to vanish as the ideal glass transition is approached at the Kauzmann temperature.

Journal Article↗
PubMed2000

Associative memory hamiltonians for structure prediction without homology: alpha-helical proteins.

Energy landscape theory is used to obtain optimized energy functions for predicting protein structure, without using homology information. At short sequence separation the energy functions are associative memory Hamiltonians constructed from a database of folding patterns in nonhomologous proteins and at large separations they have the form of simple pair potentials. The lowest energy minima provide reasonably accurate tertiary structures even though no homologous proteins are included in the construction of the Hamiltonian. We also quantify the funnel-like nature of these energy functions by using free energy profiles obtained by the multiple histogram method.

Computer Simulation↗
PubMed2000

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism.

Protein folding and binding are kindred processes. Many proteins in the cell are unfolded, so folding and function are coupled. This paper investigates how binding kinetics is influenced by the folding of a protein. We find that a relatively unstructured protein molecule can have a greater capture radius for a specific binding site than the folded state with its restricted conformational freedom. In this scenario of binding, the unfolded state binds weakly at a relatively large distance followed by folding as the protein approaches the binding site: the "fly-casting mechanism." We illustrate this scenario with the hypothetical kinetics of binding a single repressor molecule to a DNA site and find that the binding rate can be significantly enhanced over the rate of binding of a fully folded protein.

Kinetics↗
PubMed2000

Fragilities of liquids predicted from the random first order transition theory of glasses.

A microscopically motivated theory of glassy dynamics based on an underlying random first order transition is developed to explain the magnitude of free energy barriers for glassy relaxation. A variety of empirical correlations embodied in the concept of liquid "fragility" are shown to be quantitatively explained by such a model. The near universality of a Lindemann ratio characterizing the maximal amplitude of thermal vibrations within an amorphous minimum explains the variation of fragility with a liquid's configurational heat capacity density. Furthermore, the numerical prefactor of this correlation is well approximated by the microscopic calculation. The size of heterogeneous reconfiguring regions in a viscous liquid is inferred and the correlation of nonexponentiality of relaxation with fragility is qualitatively explained. Thus the wide variety of kinetic behavior in liquids of quite disparate chemical nature reflects quantitative rather than qualitative differences in their energy landscapes.

Journal Article↗
PubMed1999

Single molecule physics and chemistry.

New experiments using scanning probe microcopies and advanced optical methods allow us to study molecules as individuals, not just as populations. The findings of these studies not only include the confirmation of results expected from studies of bulk matter, but also give substantially new information concerning the complexity of biomolecules or molecules in a structured environment. The technique lays the groundwork for achieving the control of an individual molecule's motion. Ultimately, this work may lead to such practical applications as miniaturized sensors.

Chemical Phenomena↗
PubMed1999

Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble.

We discuss the formulation of free energy functionals that describe the formation of structure in partially folded proteins. These free energy functionals take into account the inhomogeneous nature of contact energies, chain entropy and cooperative contributions reflecting the many body character of some folding forces like hydrophobicity, but do not directly account for non-native contacts because they assume the validity of the minimal frustration principle. We show how the free energy functionals can be used to interpret experiments on partially folded proteins that probe the fractional occupancy of specific local structures. In particular, we study the hydrogen protection factors in lysozyme studied in transient experiments by Gladwin and Evans and by Nash and Jonas using equilibrium pressure denaturation and the NMR order parameters measured by Dobson and Kim for the homologous protein alpha-lactalbumin.

Animals↗
PubMed1999

Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble.

We use free energy functionals that account for the partial ordering of residues in the transition state ensemble to characterize the free energy surfaces for fast folding proteins. We concentrate on chymotrypsin inhibitor and lambda-repressor. We show how the explicit cooperativity that can arise from many body forces, such as side-chain ordering or hydrophobic surface burial, determines the crossover from folding with a large delocalized nucleus and the specific small classical nucleus of the type envisioned in nucleation growth scenarios. We compare the structural correlations present in the transition state ensemble obtained from free energy functionals with those inferred from experiment using extrathermodynamic free energy relations for folding time obtained via protein engineering kinetics experiments. We also use the free energy functionals to examine both the size of barriers and multidimensional representations of the free energy profiles in order to address the question of appropriate reaction coordinates for folding.

DNA-Binding Proteins↗
PubMed1999

Stretching lattice models of protein folding.

A new class of experiments that probe folding of individual protein domains uses mechanical stretching to cause the transition. We show how stretching forces can be incorporated in lattice models of folding. For fast folding proteins, the analysis suggests a complex relation between the force dependence and the reaction coordinate for folding.

Amino Acid Sequence↗
PubMed1999

Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides.

We discuss the construction of a simple, off-lattice model protein with a comparatively detailed representation of the protein backbone, and use it to address some general aspects of the folding kinetics of a small helical protein and two peptide fragments. The model makes use of an associative memory hamiltonian to smoothly interpolate between the limits of a native contact only, or Go, potential and a statistical pair potential derived from a database of known structures. We have observed qualitatively different behavior in these two limits. In the Go limit, we see apparently barrier-less folding. As we increase the roughness of the model energy landscape, we can observe the emergence of the characteristic activated temperature dependence previously seen in lattice studies and analytical theories. We are also able to study the dependence of the folding kinetics on local interactions such as hydrogen bonds, and we discuss the implications of these results for the formation of secondary structure at intermediate stages of the folding reaction.

Bacterial Proteins↗
PubMed1998

Protein folding mechanisms and the multidimensional folding funnel.

An important idea that emerges from the energy landscape theory of protein folding is that subtle global features of the protein landscape can profoundly affect the apparent mechanism of folding. The relationship between various characteristic temperatures in the phase diagrams and landmarks in the folding funnel at fixed temperatures can be used to classify different folding behaviors. The one-dimensional picture of a folding funnel classifies folding kinetics into four basic scenarios, depending on the relative location of the thermodynamic barrier and the glass transition as a function of a single-order parameter. However, the folding mechanism may not always be quantitatively described by a single-order parameter. Several other order parameters, such as degree of secondary structure formation, collapse and topological order, are needed to establish the connection between minimalist models and proteins in the laboratory. In this article we describe a simple multidimensional funnel based on two-order parameters that measure the degree of collapse and topological order. The appearance of several different "mechanisms" is illustrated by analyzing lattice models with different potentials and sequences with different degrees of design. In most cases, the two-dimensional analysis leads to a classification of mechanisms totally in keeping with the one-dimensional scheme, but a topologically distinct scenario of fast folding with traps also emerges. The nature of traps depends on the relative location of the glass transition surface and the thermodynamic barrier in the multidimensional funnel.

Computer Simulation↗
PubMed1998

The vibrational energy flow transition in organic molecules: theory meets experiment.

Most large dynamical systems are thought to have ergodic dynamics, whereas small systems may not have free interchange of energy between degrees of freedom. This assumption is made in many areas of chemistry and physics, ranging from nuclei to reacting molecules and on to quantum dots. We examine the transition to facile vibrational energy flow in a large set of organic molecules as molecular size is increased. Both analytical and computational results based on local random matrix models describe the transition to unrestricted vibrational energy flow in these molecules. In particular, the models connect the number of states participating in intramolecular energy flow to simple molecular properties such as the molecular size and the distribution of vibrational frequencies. The transition itself is governed by a local anharmonic coupling strength and a local state density. The theoretical results for the transition characteristics compare well with those implied by experimental measurements using IR fluorescence spectroscopy of dilution factors reported by Stewart and McDonald [Stewart, G. M. & McDonald, J. D. (1983) J. Chem. Phys. 78, 3907-3915].

Journal Article↗