PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “conformational ensemble”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41Linked to original sources
PubMed2006

Destruction or potentiation of different prions catalyzed by similar Hsp104 remodeling activities.

Yeast prions are protein-based genetic elements that self-perpetuate changes in protein conformation and function. A protein-remodeling factor, Hsp104, controls the inheritance of several yeast prions, including those formed by Sup35 and Ure2. Perplexingly, deletion of Hsp104 eliminates Sup35 and Ure2 prions, whereas overexpression of Hsp104 purges cells of Sup35 prions, but not Ure2 prions. Here, we used pure components to dissect how Hsp104 regulates prion formation, growth, and division. For both Sup35 and Ure2, Hsp104 catalyzes de novo prion nucleation from soluble, native protein. Using a distinct mechanism, Hsp104 fragments both prions to generate new prion assembly surfaces. For Sup35, the fragmentation endpoint is an ensemble of noninfectious, amyloid-like aggregates and soluble protein that cannot replicate conformation. In vivid distinction, the endpoint of Ure2 fragmentation is short prion fibers with enhanced infectivity and self-replicating ability. These advances explain the distinct effects of Hsp104 on the inheritance of the two prions.

Adenosine Diphosphate↗
PubMed2003

Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy.

Complex conformational changes influence and regulate the dynamics of ion channels. Such conformational changes are stochastic and often inhomogeneous, which makes it extremely difficult, if not impossible, to characterize them by ensemble-averaged experiments or by single-channel recordings of the electric current that report the open-closed events but do not specifically probe the associated conformational changes. Here, we report our studies on ion channel conformational changes using a new approach, patch-clamp fluorescence microscopy, which simultaneously combines single-molecule fluorescence spectroscopy and single-channel current recordings to probe the open-closed transitions and the conformational dynamics of individual ion channels. We demonstrate patch-clamp fluorescence microscopy by measuring gramicidin ion channel conformational changes in a lipid bilayer formed at a patch-clamp micropipette tip under a buffer solution. By measuring single-pair fluorescence resonance energy transfer and fluorescence self-quenching from dye-labeled gramicidin channels, we observed that the efficiency of single-pair fluorescence resonance energy transfer and self-quenching is widely distributed, which reflects a broad distribution of conformations. Our results strongly suggest a hitherto undetectable correlation between the multiple conformational states of the gramicidin channel and its closed and open states in a lipid bilayer.

Anti-Bacterial Agents↗
PubMed2006

Effect of DNA supercoiling on the geometry of holliday junctions.

Unusual DNA conformations including cruciforms play an important role in gene regulation and various DNA transactions. Cruciforms are also the models for Holliday junctions, the transient DNA conformations critically involved in DNA homologous and site-specific recombination, repair, and replication. Although the conformations of immobile Holliday junctions in linear DNA molecules have been analyzed with the use of various techniques, the role of DNA supercoiling has not been studied systematically. We utilized atomic force microscopy (AFM) to visualize cruciform geometry in plasmid DNA with different superhelical densities at various ionic conditions. Both folded and unfolded conformations of the cruciform were identified, and the data showed that DNA supercoiling shifts the equilibrium between folded and unfolded conformations of the cruciform toward the folded one. In topoisomers with low superhelical density, the population of the folded conformation is 50-80%, depending upon the ionic strength of the buffer and a type of cation added, whereas in the sample with high superhelical density, this population is as high as 98-100%. The time-lapse studies in aqueous solutions allowed us to observe the conformational transition of the cruciform directly. The time-dependent dynamics of the cruciform correlates with the structural changes revealed by the ensemble-averaged analysis of dry samples. Altogether, the data obtained show directly that DNA supercoiling is the major factor determining the Holliday junction conformation.

DNA↗
PubMed2005

Ensemble versus single-molecule protein unfolding.

Molecular dynamics (MD) simulations are the classic single-molecule "experiments," providing atomic-resolution structural and dynamic information. However, the single-molecule nature of the technique has also been its shortcoming, with frequent criticisms of sampling inadequacies and questions regarding the ensemble behavior of large numbers of molecules. Given the increase in computer power, we now address this issue by performing a large number of simulations and comparing individual and ensemble properties. One hundred independent MD simulations of the protein chymotrypsin inhibitor 2 were carried out for 20 ns each at 498 K in water to more fully describe the potentially diverse routes of protein unfolding and investigate how representative a single trajectory can be. Rapid unfolding was observed in all cases with the trajectories distributed about an average "ensemble" path in which secondary and tertiary structure was lost concomitantly, with tertiary structure loss occurring slightly faster. Individual trajectories did, however, sample conformations far from the average path with very heterogeneous time-dependent properties. Nevertheless, all of the simulations but one followed the average ensemble pathway, such that a small number of simulations (5-10) are sufficient to capture the average properties of these states and the unfolding pathway.

Hydrogen Bonding↗
PubMed2006

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.

We report unrestrained, all-atom molecular dynamics simulations of HIV-1 protease that sample large conformational changes of the active site flaps. In particular, the unliganded protease undergoes multiple conversions between the "closed" and "semiopen" forms observed in crystal structures of inhibitor-bound and unliganded protease, respectively, including reversal of flap "handedness." Simulations in the presence of a cyclic urea inhibitor yield stable closed flaps. Furthermore, we observe several events in which the flaps of the unliganded protease open to a much greater degree than observed in crystal structures and subsequently return to the semiopen state. Our data strongly support the hypothesis that the unliganded protease predominantly populates the semiopen conformation, with closed and fully open structures being a minor component of the overall ensemble. The results also provide a model for the flap opening and closing that is considered to be essential to enzyme function.

Acquired Immunodeficiency Syndrome↗
PubMed1988

The nature of conformational correlations in alpha- and beta-anomers of nucleic acid components in aqueous solution by nuclear magnetic resonance.

The solution distribution of combinations of the sugar ring puckering domains, C2'endo(S), C3'endo(N), and C4'-C5' rotamers, +sc(g+), ap(t), -sc(g-), in alpha and beta-anomers in ribo- and deoxyribo- pyrimidine nucleic acid components can be determined from vicinal coupling constants (M. Remin, J. Biomol. Str. Dyn. 2, 211 (1984). A general correlation pattern with a conformational constant lambda reflecting an intrinsic physical property of the sugar-side chain ensemble, is developed and expressed in terms of four principles: I) The +sc rotamer contributes to the C3'endo population to a higher extent (1-Yt) than to C2'endo, (1-Yt-Yg-/Xs). II) The ap rotamer contributes to both C2'endo and C3'endo populations to the same extent (Yt). III) The -sc rotamer contributes only to the C2'endo population, (Yg-/Xs). IV) The molar fractions Xs, Yt and Yg- of conformations C2'endo, ap and -sc, respectively, are strongly correlated, lambda = (Yg-/Xs)/Yt approximately 0.5, and therefore Yt is a basic variable parameter which determines all others in the correlation pattern. In alpha-anomers, regardless of the type and conformation of the sugar ring and base, the molar fraction Yt = 0.37 +/- 0.02. This finding means that different alpha-anomers show one correlation pattern free of the influence of the base. In beta-anomers, structure and conformation of the base are important factors which modulate (through Yt) the correlation pattern, conserving its fundamental features. Yt is considerably increased by a syn-oriented pyrimidine base, but decreases when the base is anti. The transition from anti to syn orientation of the base is followed by destabilization of (C2'endo, +sc) in favor of (C3'endo, ap). The principles of conformational correlations rationalize a variety of correlations observed in the past.

Chemical Phenomena↗
PubMed2005

Fast collapse but slow formation of secondary structure elements in the refolding transition of E. coli adenylate kinase.

The various models proposed for protein folding transition differ in their order of appearance of the basic steps during this process. In this study, steady state and time-resolved dynamic non-radiative excitation energy transfer (FRET and trFRET) combined with site specific labeling experiments were applied in order to characterize the initial transient ensemble of Escherichia coli adenylate kinase (AK) molecules upon shifting conditions from those favoring denaturation to refolding and from folding to denaturing. Three sets of labeled AK mutants were prepared, which were designed to probe the equilibrium and transient distributions of intramolecular segmental end-to-end distances. A 176 residue section (residues 28-203), which spans most of the 214 residue molecule, and two short secondary structure chain segments including an alpha-helix (residues 169-188) and a predominantly beta-strand region (residues 188-203), were labeled. Upon fast change of conditions from denaturing to folding, the end-to-end distance of the 176 residue chain section showed an immediate collapse to a mean value of 26 A. Under the same conditions, the two short secondary structure elements did not respond to this shift within the first ten milliseconds, and retained the characteristics of a fully unfolded state. Within the first 10 ms after changes of the solvent from folding to denaturing, only minor changes were observed at the local environments of residues 203 and 169. The response of these same local environments to the shift of conditions from denaturing to folding occurred within the dead time of the mixing device. Thus, the response of the CORE domain of AK to fast transfer from folding to unfolding conditions is slow at all three conformational levels that were probed, and for at least a few milliseconds the ensemble of folded molecules is maintained under unfolding conditions. A different order of the changes was observed upon initiation of refolding. The AK molecules undergo fast collapse to an ensemble of compact structures where the local environment of surface probes seems to be native-like but the two labeled secondary structure elements remain unfolded.

Adenylate Kinase↗
PubMed2003

Significant kinetic solvent isotope effects in folding of the catalytic RNA from the hepatitis delta virus.

The exchange of deuterium for hydrogen in water often produces solvent kinetic isotope effects (KSIEs) on the rate constants associated with enzyme reactions, including those catalyzed by RNA. Recently, KSIEs have been used to show that proton transfer occurs in the rate-limiting step of cleavage by the hepatitis delta virus (HDV) ribozyme and other catalytic RNAs. To test the underlying assumption that KSIEs are related to the chemistry step of ribozyme-mediated cleavage reactions, we developed fluorescence resonance energy transfer assays to measure KSIEs on the rate constants of conformational changes associated with substrate binding and dissociation by a trans-acting HDV ribozyme. We observe comparable KSIEs ( approximately 2-2.5-fold) of rate constants of conformational change and cleavage, while proton inventory experiments are consistent with a shift in the ensemble of transition states upon increase of D2O in the solvent. Taken together, these results challenge the common assumption that pL profiles of RNA-catalyzed reactions yielding a pKa and KSIE necessarily provide evidence for an ionization (chemistry) step to be rate-limiting. They also suggest that an unusual proton inventory may provide a signature for a conformational change contributing to the rate-limiting step.

Base Sequence↗
PubMed2004

Unusually slow denaturation and refolding processes of pyrrolidone carboxyl peptidase from a hyperthermophile are highly cooperative: real-time NMR studies.

The refolding rate of heat-denatured cysteine-free pyrrolidone carboxyl peptidase (PCP-0SH) from Pyrococcus furiosus has been reported to be unusually slow under some conditions. To elucidate the structural basis of the unusually slow kinetics of the protein, the denaturation and refolding processes of the PCP-0SH were investigated using a real-time 2D (1)H-(15)N HSQC and CD experiments. At 2 M urea denaturation of the PCP-0SH in the acidic region, all of the native peaks in the 2D HSQC spectrum completely disappeared. The conformation of the PCP-0SH just after removal of 6 M GuHCl could be observed as a stable intermediate (D(1) state) in 2D HSQC and CD experiments, which is similar to a molten globule structure. The D(1) state of the PCP-0SH, which is the initial state of refolding, corresponded to the state at 2 M urea and seemed to be the denatured state in equilibrium with the native state under the physiological conditions. The refolding of PCP-0SH from the D(1) state to the native state could be observed to be highly cooperative without any intermediates between them, even if the refolding rate was quite slow. In the higher concentration of denaturants, PCP-0SH showed HSQC and CD spectra characteristic of completely unfolded proteins called the D(2) state. The unusually slow refolding rate was discussed as originating in the conformations in the transition state and/or the retardation of reorganization in an ensemble of nonrandom denatured structures in the D(1) state.

Archaeal Proteins↗
PubMed1998

Experimentally determined chaotic phase synchronization in a neuronal system.

Mathematical analysis of the subthreshold oscillatory properties of inferior olivary neurons in vitro indicates that the oscillation is nonlinear and supports low dimensional chaotic dynamics. This property leads to the generation of complex functional states that can be attained rapidly via phase coherence that conform to the category of "generalized synchronization." Functionally, this translates into neuronal ensemble properties that can support maximum functional permissiveness and that rapidly can transform into robustly determined multicellular coherence.

Animals↗
PubMed2002

NMR evidence for different conformations of the bioactive region of rat CCK-8 and CCK-58.

Sulfated CCK-58 and CCK-8 have identical bioactive C-terminal primary sequences but distinct C-terminal solution structures and different bioactivities. To examine structural differences in greater detail, rat CCK-58 and -8 were synthesized with isotopic enrichment of C-terminal residues with (15)N at alpha-amino nitrogens. Proton and nitrogen chemical shift assignments of peptide solutions were obtained by homo- and heteronuclear NMR methods. These data show that the tertiary structure ensembles of C-terminal CCK-8 and CCK-58 differ significantly. Thus, distinct solution conformations may explain differences in CCK(A) and CCK(B) receptor interactions of large and small molecular forms of CCK.

Amino Acid Sequence↗
PubMed2004

Distributions in protein conformation space: implications for structure prediction and entropy.

By considering how polymer structures are distributed in conformation space, we show that it is possible to quantify the difficulty of structural prediction and to provide a measure of progress for prediction calculations. The critical issue is the probability that a conformation is found within a specified distance of another conformer. We address this question by constructing a cumulative distribution function (CDF) for the average probability from observations about its limiting behavior at small displacements and numerical simulations of polyalanine chains. We can use the CDF to estimate the likelihood that a structure prediction is better than random chance. For example, the chance of randomly predicting the native backbone structure of a 150-amino-acid protein to low resolution, say within 6 A, is 10(-14). A high-resolution structural prediction, say to 2 A, is immensely more difficult (10(-57)). With additional assumptions, the CDF yields the conformational entropy of protein folding from native-state coordinate variance. Or, using values of the conformational entropy change on folding, we can estimate the native state's conformational span. For example, for a 150-mer protein, equilibrium alpha-carbon displacements in the native ensemble would be 0.3-0.5 A based on T Delta S of 1.42 kcal/(mol residue).

Algorithms↗
PubMed1992

The ensemble reactions of hydroxyl radical exhibit no specificity for primary or secondary structure of DNA.

Hydroxyl radical reacts at numerous sites within nucleic acids to form a wide range of derivatives yet the conformational specificity of only one of these processes, direct strand fragmentation, has received much attention to date. Since the deleterious effects of this radical are not likely limited to strand fragmentation in vivo, this report examined the conformational specificity expressed in a more general manner. For this, modification of DNA was induced by the hydroxyl radical generating system of H2O2 and Fe-EDTA. The ensemble rate of oxidation (nucleobase + deoxyribose backbone) was determined from the overall consumption of a series of oligonucleotides that were designed to model random coils and double helixes containing complementary and noncomplementary base pairing. The resulting pseudo-first order rate constants derived from this model system were relatively unaffected by nucleotide sequence or secondary structure and varied from only 0.022 to 0.048 s-1. Consequently, the indiscriminant nature of hydroxyl radical appears to persist beyond strand fragmentation to include nucleobase oxidation as well.

Base Composition↗
PubMed2001

Conformational analysis of dehydrodidemnin B (aplidine) by NMR spectroscopy and molecular mechanics/dynamics calculations.

Dehydrodidemnin B (DDB or aplidine), a potent antitumoral natural product currently in phase II clinical trials, exists as an approximately 1:1 mixture of two slowly interconverting conformations. These are sufficiently long-lived so as to allow their resolution by HPLC. NMR spectroscopy shows that this phenomenon is a consequence of restricted rotation about the Pyr-Pro(8) terminal amide bond of the molecule's side chain. The same technique also indicates that the overall three-dimensional structures of both the cis and trans isomers of DDB are similar despite the conformational change. Molecular dynamics simulations with different implicit and explicit solvent models show that the ensembles of three-dimensional structures produced are indeed similar for both the cis and trans isomers. These studies also show that hydrogen bonding patterns in both isomers are alike and that each one is stabilized by a hydrogen bond between the pyruvyl unit at the terminus of the molecule's side chain and the Thr(6) residue situated at the junction betwen the macrocycle and the molecule's side chain. Nevertheless, each conformational isomer forms this hydrogen bond using a different pyruvyl carbonyl group: CO(2) in the case of the cis isomer and CO(1) in the case of the trans isomer.

Antineoplastic Agents↗
PubMed1991

Empirical solvation models can be used to differentiate native from near-native conformations of bovine pancreatic trypsin inhibitor.

Several hydration models for peptides and proteins based on solvent accessible surface area have been proposed previously. We have evaluated some of these models as well as four new ones in the context of near-native conformations of a protein. In addition, we propose an empirical site-site distance-dependent correction that can be used in conjunction with any of these models. The set of near-native structures consisted of 39 conformations of bovine pancreatic trypsin inhibitor (BPTI) each of which was a local minimum of an empirical energy function (ECEPP) in the absence of solvent. Root-mean-square (rms) deviations from the crystallographically determined structure were in the following ranges: 1.06-1.94 A for all heavy atoms, 0.77-1.36 A for all backbone heavy atoms, 0.68-1.33 A for all alpha-carbon atoms, and 1.41-2.72 A for all side-chain heavy atoms. We have found that there is considerable variation among the solvent models when evaluated in terms of concordance between the solvation free energy and the rms deviations from the crystallographically determined conformation. The solvation model for which the best concordance (0.939) with the rms deviations of the C alpha atoms was found was derived from NMR coupling constants of peptides in water combined with an exponential site-site distance dependence of the potential of mean force. Our results indicate that solvation free energy parameters derived from nonpeptide free energies of hydration may not be transferrable to peptides. Parameters derived from peptide and protein data may be more applicable to conformational analysis of proteins. A general approach to derive parameters for free energy of hydration from ensemble-averaged properties of peptides in solution is described.

Animals↗
PubMed2007

Negative compressibility and nonequivalence of two statistical ensembles in the escape transition of a polymer chain.

An end-tethered polymer chain compressed between two pistons undergoes an abrupt transition from a confined coil state to an inhomogeneous flowerlike conformation partially escaped from the gap. This phase transition is first order in the thermodynamic limit of infinitely long chains. A rigorous analytical theory is presented for a Gaussian chain in two ensembles: (a) the H-ensemble, in which the distance H between the pistons plays the role of the independent control parameter, and (b) the conjugate f-ensemble, in which the external compression force f is the independent parameter. Details about the metastable chain configurations are analyzed by introducing the Landau free energy as a function of the chain stretching order parameter. The binodal and spinodal lines, as well as the barrier heights between the stable and metastable states in the free energy landscape, are presented in both ensembles. In the loop region for the average force with dependence on the distance H (i.e., in the H-ensemble) a negative compressibility exists, whereas in the f-ensemble the average distance as a function of the force is strictly monotonic. The average fraction of imprisoned segments and the lateral force, taken as functions of the distance H or the average H, respectively, have different behaviors in the two ensembles. These results demonstrate a clear counterexample of a main principle of statistical mechanics, stating that all ensembles are equivalent in the thermodynamic limit. The authors show that the negative compressibility in the escape transition is a purely equilibrium result and analyze in detail the origin of the nonequivalence of the ensembles. It is argued that it should be possible to employ the escape transition and its anomalous behavior in macroscopically homogeneous, but microscopically inhomogeneous, materials.

Biopolymers↗
PubMed2004

Unfolded state of polyalanine is a segmented polyproline II helix.

Definition of the unfolded state of proteins is essential for understanding their stability and folding on biological timescales. Here, we find that under near physiological conditions the configurational ensemble of the unfolded state of the simplest protein structure, polyalanine alpha-helix, cannot be described by the commonly used Flory random coil model, in which configurational probabilities are derived from conformational preferences of individual residues. We utilize novel effectively ergodic sampling algorithms in the presence of explicit aqueous solvation, and observe water-mediated formation of polyproline II helical (P(II)) structure in the natively unfolded state of polyalanine, and its facilitation of alpha-helix formation in longer peptides. The segmented P(II) helical coil preorganizes the unfolded state ensemble for folding pathway entry by reducing the conformational space available to the diffusive search. Thus, as much as half of the folding search in polyalanine is accomplished by preorganization of the unfolded state.

Computer Simulation↗