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PubMed2005

Molecular dynamics simulations of GlpF in a micelle vs in a bilayer: conformational dynamics of a membrane protein as a function of environment.

Octyl glucoside (OG) is a detergent widely employed in structural and functional studies of membrane proteins. To better understand the nature of protein-OG interactions, molecular dynamics simulations (duration 10 ns) have been used to explore an alpha-helical membrane protein, GlpF, in OG micelles and in DMPC bilayers. Greater conformational drift of the extramembraneous protein loops, from the initial X-ray structure, is seen for the GlpF-OG simulations than for the GlpF-DMPC simulation. The mobility of the transmembrane alpha-helices is approximately 1.3x higher in the GlpF-OG than the GlpF-DMPC simulations. The detergent is seen to form an irregular torus around the protein. The presence of the protein leads to a small perturbation in the behavior of the alkyl chains in the OG micelle, namely an approximately 15% increase in the trans-gauche(-)-gauche(+) transition time. Aromatic side chains (Trp, Tyr) and basic side chains (Arg, Lys) play an important role in both protein-detergent (OG) and protein-lipid (DMPC) interactions.

Aquaporins↗
PubMed2006

The conformational dynamics of a metastable serpin studied by hydrogen exchange and mass spectrometry.

Serpins are a class of protease inhibitors that initially fold to a metastable structure and subsequently undergo a large conformational change to a stable structure when they inhibit their target proteases. How serpins are able to achieve this remarkable conformational rearrangement is still not understood. To address the question of how the dynamic properties of the metastable form may facilitate the conformational change, hydrogen/deuterium exchange and mass spectrometry were employed to probe the conformational dynamics of the serpin human alpha(1)-antitrypsin (alpha(1)AT). It was found that the F helix, which in the crystal structure appears to physically block the conformational change, is highly dynamic in the metastable form. In particular, the C-terminal half of the F helix appears to spend a substantial fraction of time in a partially unfolded state. In contrast, beta-strands 3A and 5A, which must separate to accommodate insertion of the reactive center loop (RCL), are not conformationally flexible in the metastable state but are rigid and stable. The conformational lability required for loop insertion must therefore be triggered during the inhibition reaction. Beta-strand 1C, which anchors the distal end of the RCL and thus prevents transition to the so-called latent form, is also stable, consistent with the observation that alpha(1)AT does not spontaneously adopt the latent form. A surprising degree of flexibility is seen in beta-strand 6A, and it is speculated that this flexibility may deter the formation of edge-edge polymers.

Amino Acid Sequence↗
PubMed1986

Conformational dynamics of the anticodon loop in yeast tRNAPhe as sensed by the fluorescence of wybutine.

Conformational and dynamic properties of the anticodon loop of yeast tRNAPhe were investigated by analyzing the time resolved fluorescence of wybutine serving as a local structural probe adjacent to the anticodon GmAA on its 3' side. The influence of Mg2+, important for stabilizing the tertiary structure of tRNA, and of the complementary anticodon s2UUC of E. coli tRNA2Glu were investigated. Fluorescence lifetimes and anisotropies were measured with ps time resolution using time correlated single photon counting and a mode locked synchronously pumped and frequency doubled dye laser as excitation source. From the analysis of lifetimes (tau) and rotational relaxation times (tau R) we conclude that wybutine occurs in various structural states: one stacked conformation where the base has no free mobility and the only rotational motion reflects the mobility of the whole tRNA molecule (tau = 6 ns, tau R = 19 ns), an unstacked conformation where the base can freely rotate (tau = 100 ps, tau R = 370 ps) and an intermediary state (tau = 2 ns, tau R = 1.6 ns). Under biological conditions, i.e. in the presence of Mg2+ and neutral salts, wybutine is found in a stacked and immobile state which is consistent with the crystallographic picture. In the presence of the complementary codon however, as exemplified by the E. coli-tRNA2Glu anticodon, our analysis indicates that the codon-anticodon complex exists in an equilibrium of structural states with different rotational mobility of wybutine. The conformation with wybutine freely mobile is the predominant one and suggests that this conformation of the codon-anticodon structure differs from the canonical 3'-5' stack.

Anticodon↗
PubMed1998

Solution NMR structure and backbone dynamics of the major cold-shock protein (CspA) from Escherichia coli: evidence for conformational dynamics in the single-stranded RNA-binding site.

The major cold-shock protein (CspA) from Escherichia coli is a single-stranded nucleic acid-binding protein that is produced in response to cold stress. We have previously reported its overall chain fold as determined by NMR spectroscopy [Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D., Inouye, M., and Montelione, G. T. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 5114-5118]. Here we describe the complete analysis of 1H, 13C, and 15N resonance assignments for CspA, together with a refined solution NMR structure based on 699 conformational constraints and an analysis of backbone dynamics based on 15N relaxation rate measurements. An extensive set of triple-resonance NMR experiments for obtaining the backbone and side chain resonance assignments were carried out on uniformly 13C- and 15N-enriched CspA. Using a subset of these triple-resonance experiments, the computer program AUTOASSIGN provided automatic analysis of sequence-specific backbone N, Calpha, C', HN, Halpha, and side chain Cbeta resonance assignments. The remaining 1H, 13C, and 15N resonance assignments for CspA were then obtained by manual analysis of additional NMR spectra. Dihedral angle constraints and stereospecific methylene Hbeta resonance assignments were determined using a new conformational grid search program, HYPER, and used together with longer-range constraints as input for three-dimensional structure calculations. The resulting solution NMR structure of CspA is a well-defined five-stranded beta-barrel with surface-exposed aromatic groups that form a single-stranded nucleic acid-binding site. Backbone dynamics of CspA have also been characterized by 15N T1, T2, and heteronuclear 15N-1H NOE measurements and analyzed using the extended Lipari-Szabo formalism. These dynamic measurements indicate a molecular rotational correlation time taum of 4.88 +/- 0.04 ns and provide evidence for fast time scale (taue < 500 ps) dynamics in surface loops and motions on the microsecond to millisecond time scale within the proposed nucleic acid-binding epitope.

Amides↗
PubMed2000

Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.

Molecular modeling and molecular dynamics have been employed to study the conformation and flexibility of a 15-nucleotide fragment of the plant 5S rRNA containing loop D and a single uridine bulge. Two different model built initial structures were used: one with the bulge localized inside the helical stem and another with the bulge pointing out from the helix. Several independent 700-ps-long trajectories in aqueous solution with Na(+) conterions were produced for each starting structure. The bulge nucleotide inside the helix stayed in two main conformations, both of which affected the geometry of the stem part opposite the bulge. When the bulge nucleotide was located outside the helix, we found high base mobility and local backbone flexibility. The dynamics of the hydrogen bond network and conformational changes from a direct to a water mediated hydrogen bond in the sheared G-A basepair in the tetraloop was described. Our results correlate with lead ion induced cleavage patterns in 5S rRNA. Sites resistant to nonspecific lead cleavage appeared in all our simulations as the most rigid fragments independent of the localization of the bulge nucleotide.

Base Pairing↗
PubMed2005

Temperature-induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: a molecular simulation study.

Extensive molecular simulations are carried out as a function of temperature to understand and quantify the conformational disorder in molecular crystals of 4-vinyl benzoic acid. The conformational disorder is found to be dynamic and associated with a flip-flop motion of vinyl groups. The population of minor conformer is less than 3% up to 300 K and is 13.2% at 350 K and these results are consistent with the experimental observations. At still higher temperatures, the population of minor conformer increases up to 25%. The evolution of structure at both molecular and unit-cell level of the molecular crystal as a function of temperature has been characterized by various quantities such as radial distribution functions, average cell parameters, volume, and interaction energies. The van't Hoff plot shows a nonlinear behavior at lower temperatures as it has been reported recently by Ogawa and co-workers in the case of stilbene, azobenzene, and N-(4-methylbenzylidene)-4-methylaniline molecular crystals. A set of rigid body simulations were also carried out to quantify the effect of conformational disorder on structural quantities such as unit-cell volume and interaction energy. The anomalous shrinkage of vinyl C=C bond length as a function of temperature has been explained by combining the results of simulations and a set of constrained optimizations using ab initio electronic structure calculations for various molecular structures differing in torsional angle.

Journal Article↗
PubMed1999

DNA conformational dynamics in the presence of catanionic mixtures.

DNA conformational behavior in the presence of non-stoichiometric mixtures of two oppositely charged surfactants, cetyltrimethylammonium bromide and sodium octyl sulfate, was directly visualized in an aqueous solution with the use of a fluorescence microscopy technique. It was found that in the presence of cationic-rich catanionic mixtures, DNA molecules exhibit a conformational transition from elongated coil to compact globule states. Moreover, if the catanionic mixtures form positively charged vesicles, DNA is adsorbed onto the surface of the vesicles in a collapsed globular form. When anionic-rich catanionic mixtures are present in the solution, no change in the DNA conformational behavior was detected. Cryogenic transmission electron microscopy, as well as measurements of translational diffusion coefficients of individual DNA chains, supported our optical microscopy observations.

Anions↗
PubMed1980

Conformational dynamics of insulin in solution. Circular dichroic studies.

Conformational changes of bovine insulin in solution with concentration and pH detected by circular dichroic (CD) studies are reported. The change in the CD spectrum of insulin in the higher concentration range (from 100 microM down to 2 microM) is relatively small, but in the lower concentration range (from 2 microM down to 60 nM) the CD spectrum changes substantially with concentration. A detailed analysis of the data indicates that the hormone has two major conformational states: conformation I, a form which predominates in extremely dilute solutions and corresponds to the monomeric state, and conformation II, a form present in the crystalline state and also, with but minor changes, in all associated states in solution. The apparent conformation of insulin at various concentrations is computed by using a nonlinear least-squares iterative computer program. The mean residue ellipticities at 223 and 208 nm are extrapolated by using [theta] lambda VS. fmonomer plots to calculate the conformations of monomeric and dimeric insulin. These calculations indicate that conformation I of insulin has 21% less helix content than conformation II, the latter conformation being very similar to that found in the crystalline state. It is also evident from these calculations that the conformational transition is of the helix--coil type. Studies pertaining to the dependence of the CD spectrum of insulin on pH are also reported, and a comparison is made with earlier sedimentation coefficient studies. An analysis of the data indicates that changes in the sedimentation coefficient correspond quite closely to changes of CD spectra with pH. This paper is the first report known to us pertaining to conformational studies of insulin in the monomeric state; it presents evidence for conformational transitions of the protein hormone induced by concentration and pH. Since insulin is biologically active mainly in the monomeric state, a knowledge of its conformation in this state should be an important tool in deciphering the molecular basis of insulin action.

Animals↗
PubMed2002

Iterated conformal dynamics and Laplacian growth.

The method of iterated conformal maps for the study of diffusion limited aggregates (DLA) is generalized to the study of Laplacian growth patterns and related processes. We emphasize the fundamental difference between these processes: DLA is grown serially with constant size particles, while Laplacian patterns are grown by advancing each boundary point in parallel, proportional to the gradient of the Laplacian field. We introduce a two-parameter family of growth patterns that interpolates between DLA and a discrete version of Laplacian growth. The ultraviolet putative finite-time singularities are regularized here by a minimal tip size, equivalently for all the models in this family. With this we stress that the difference between DLA and Laplacian growth is not in the manner of ultraviolet regularization, but rather in their deeply different growth rules. The fractal dimensions of the asymptotic patterns depend continuously on the two parameters of the family, giving rise to a "phase diagram" in which DLA and discretized Laplacian growth are at the extreme ends. In particular, we show that the fractal dimension of Laplacian growth patterns is higher than the fractal dimension of DLA, with the possibility of dimension 2 for the former not excluded.

Journal Article↗
PubMed2006

Insights into allosteric control of vinculin function from its large scale conformational dynamics.

Vinculin is an important constituent of both cell-cell and cell-matrix junctions, where it plays crucial roles in the regulation of cell adhesion and migration. When activated, it mediates the linkage between cadherins (cell-cell) or integrins (cell-matrix) and the actin cytoskeleton through interactions with various proteins. The activation of vinculin requires structural conversions from an autoinhibited conformation to the "open" conformations in which the occluded binding sites of its different ligands become exposed, while the structural dynamics underlying the vinculin activation remains largely unknown. Here we report the first computational study of large scale conformational dynamics of full-length vinculin. We find that the "holding" and "releasing" motions between vinculin tail and pincer-like structure formed by first three domains of vinculin are the dominant motions near the native state of vinculin, indicating that an inherent flexibility of vinculin has a large influence on its allostery. We also find a cooperative dissociation between the head and tail domains of vinculin with increasing temperature in both thermodynamic and kinetic simulations, implying that vinculin may function as an allosteric switch in response to external signals. We show that the kinetics of vinculin unfolding exhibits specific sequential patterns, suggesting that a sophisticated interplay between domains may synergistically contribute to vinculin activation. We further find that the interaction between vinculin-binding site peptide from talin and vinculin significantly destabilizes the intramolecular head-tail interactions, suggesting a direct role of talin binding in vinculin activation.

Actins↗
PubMed1997

Quantitative determination of conformational, dynamic, and kinetic parameters of a ligand-protein/DNA complex from a complete relaxation and conformational exchange matrix analysis of intermolecular transferred NOESY.

We report a quantitative analysis of the 13C-edited intermolecular transferred NOESY (inter-TrNOESY) spectrum of the trp-repressor/operator complex (trp-rep/op) with [ul-13C/15N]-L-tryptophan corepressor using a computer program implementing complete relaxation and conformational exchange matrix (CORCEMA) methodology [Moseley et al. (1995) J. Magn. Reson. 108B, 243-261]. Using complete mixing time curves of three inter-TrNOESY peaks between the tryptophan and the Trp-rep/op, this self-consistent analysis determined the correlation time of the bound species (tauB = 13.5 ns) and the exchange off-rate (k(off) = 3.6 s(-1)) of the corepressor. In addition, the analysis estimated the correlation time of the free species (tauF approximately 0.15 ns). Also, we demonstrate the sensitivity of these inter-TrNOESY peaks to several factors including the k(off) and orientation of the tryptophan corepressor within the binding site. The analysis indicates that the crystal structure orientation for the corepressor is compatible with the solution NMR data.

Bacterial Proteins↗
PubMed1991

The solution structure and conformational dynamics of tumor necrosis factor-alpha and a (Cys69----Asp; Cys101----Arg) analog as examined by IR spectroscopy and hydrogen exchange.

An analog of human tumor necrosis factor-alpha (TNF-alpha) was created with Cys69 and Cys101 replaced with Asp and Arg respectively. We have undertaken a comparative study of the solution conformation and dynamics of the native and analog molecules using a combination of Fourier transform IR spectroscopy and hydrogen-deuterium (H-D) exchange kinetics. IR spectroscopic results indicate that the analog molecule adopts a gross structure similar to that of the native molecule but significant differences in the conformation of the beta-sheets are observed. Increased bandwidths observed for several of the amide I components also suggest a less rigid structure for the analog molecule. Further, by monitoring the frequency shifts of the individual amide I component bands as a function of hydrogen exchange, we have enhanced our ability to assign these components to individual protein secondary structures, particularly the high frequency beta-strand mode. Hydrogen exchange kinetic studies indicate that the Asp-Arg analog adopts a looser, more flexible solution structure relative to the natural sequence molecule.

Animals↗
PubMed2004

CBFbeta allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium.

Core binding factors (CBFs) are heterodimeric transcription factors consisting of a DNA-binding CBFalpha subunit and non-DNA-binding CBFbeta subunit. The CBFbeta subunit increases the affinity of the DNA-binding Runt domain of CBFalpha for DNA while making no direct contacts to the DNA. We present evidence for conformational exchange in the S-switch region in a Runt domain-DNA complex that is quenched upon CBFbeta binding. Analysis of (15)N backbone relaxation parameters shows that binding of CBFbeta reduces the backbone dynamics in the microsecond-to-millisecond time frame for several regions of the Runt domain that make energetically important contacts with the DNA. The DNA also undergoes conformational exchange in the Runt domain-DNA complex that is quenched in the presence of CBFbeta. Our results indicate that allosteric regulation by the CBFbeta subunit is mediated by a shift in an existing dynamic conformational equilibrium of both the Runt domain and DNA.

Allosteric Site↗
PubMed2003

Iron-sulfur cluster biosynthesis: biochemical characterization of the conformational dynamics of Thermotoga maritima IscU and the relevance for cellular cluster assembly.

Important for the understanding of the functional properties of the iron-sulfur scaffold IscU is knowledge of the structure and dynamics of this protein class. Structural characterization of Thermotoga maritima IscU by CD (Mansy, S. S., Wu, G., Surerus, K. K., and Cowan, J. A. (2002) J. Biol. Chem. 277, 21397-21404) and high resolution NMR (Bertini, I., Cowan, J. A., Del Bianco, C., Luchinat, C., and Mansy, S. S. (2003) J. Mol. Biol. 331, 907-924) yielded data indicating a high degree of secondary structure. However, the latter also revealed IscU to exist in a dynamic equilibrium between two or more distinct conformations, possibly existing in a molten globule state. Herein, we further characterize the molten globule characteristics of T. maritima IscU by near-ultraviolet circular dichroism, 1-anilino-8-naphthalenesulfonic acid binding, free energy of unfolding, hydrodynamic radius measurements, and limited tryptic digestion. The data suggest unusual dynamic behavior that is not fully consistent with typical protein states such as fully folded, fully unfolded, or molten globule. For instance, the existence of a stable tertiary fold is supported by near-UV CD spectra and hydrodynamic radius measurements, whereas other data are less clearly interpretable and may be viewed as consistent with either a molten globule or fully folded state. However, all of the data are consistent with our previous hypothesis of a protein sampling multiple discrete tertiary conformations in which these structural transitions occur on a "slow" time scale. To describe such proteins, we introduce the term multiple discrete conformers.

Amino Acid Sequence↗
PubMed2006

The receptor-bound "empty pocket" state of the heterotrimeric G-protein alpha-subunit is conformationally dynamic.

Heterotrimeric G-protein activation by a G-protein-coupled receptor (GPCR) requires the propagation of structural signals from the receptor-interacting surfaces to the guanine nucleotide-binding pocket. To probe conformational changes in the G-protein alpha-subunit (G(alpha)) associated with activated GPCR (R*) interactions and guanine nucleotide exchange, high-resolution solution NMR methods are being applied in studying signaling of the G-protein, transducin, by light-activated rhodopsin. Using these methods, we recently demonstrated that an isotope-labeled G(alpha) reconstituted heterotrimer forms functional complexes under NMR experimental conditions with light-activated, detergent-solubilized rhodopsin and a soluble mimic of R*, both of which trigger guanine nucleotide exchange [Ridge, K. D., et al. (2006) J. Biol. Chem. 281, 7635-7648]. Here, it is shown that both light-activated rhodopsin and the soluble mimic of R form trapped intermediate complexes with a GDP-released "empty pocket" state of the heterotrimer in the absence of GTP (or GTPgammaS). In contrast to guanine nucleotide-bound forms of G(alpha), the NMR spectra of the GDP-released, R-bound empty pocket state of G(alpha) display severe line broadening suggestive of a dynamic intermediate state. Interestingly, the conformation of a GDP-depleted, Mg(2+)-bound state of G(alpha) generated in a manner independent of R* does not exhibit a similar degree of line broadening but rather appears structurally similar to the GDP/Mg(2+)-bound form of the protein. Taken together, these results suggest that R*-mediated changes in the receptor-interacting regions of G(alpha), and not the absence of bound guanine nucleotide, are the predominant factors which dictate G(alpha) conformation and dynamics in this R*-bound state of the heterotrimer.

Animals↗
PubMed1994

Real-time beam monitoring in dynamic conformation therapy.

PURPOSE: Although portal imaging is a promising method of verification during static multiport irradiation, it cannot be applied directly to dynamic irradiation such as rotational conformation with multileaf collimator movement. A real-time beam monitoring system based on megavoltage computed tomography scanning has been developed to establish a verification method for the rotational conformation technique. METHODS AND MATERIALS: Exit beam through the patient is extracted by the same detector unit as used for megavoltage scanning during the actual treatment. Beam edge is defined as the 50% level of the maximum dose of the detector array. Megavoltage computed tomography is done after patient setup and just prior to the actual irradiation. Detected beam pathways are overlaid on this image approximately every 1 s. Therapists can monitor correlation between the target and actual beam pathways on a real-time computer display. RESULTS: The accuracy of field edge detection has been proven to be less than 2 mm from various measurements. Real-time monitoring is more useful in rotational conformation than in static multiport irradiation due to dynamic movement of the collimator. Field errors were identified in two of 54 sessions using this method. CONCLUSIONS: Although several limitations remain to be solved, the method presented is a useful tool for treatment verification of high accuracy radiation therapy, particularly rotational conformation irradiation.

Brain Neoplasms↗
PubMed2006

Design, synthesis, and conformational dynamics of a gated molecular basket.

We have developed a synthesis and examined the conformational behavior and recognition properties of dynamic molecular containers 1-3. As follows from the 1H NMR dilution, diffusion NMR, and vapor pressure osmometry measurements, compound 1 has a low affinity for intermolecular aggregation and is mostly present in monomeric form in dilute chloroform solutions. Inspecting the O-H chemical shift resonances of 1, 3, and model compound 4 as a function of temperature afforded the deltadelta/deltaT coefficients of 17.0, 17.3, and 4.7 ppb K(-1), respectively. In combination with the results from variable temperature 1H NMR and IR measurements, the existence of conformers of 1 and 3 in equilibrium, each having a different extent of hydrogen bonding, was confirmed. Molecular mechanics calculations suggested 1a as the most favorable conformation, with three additional conformers, 1b, 1c, and 1d, populating local energy minima. Further optimization of each of the four conformers using semiempirical PM3 and ab initio (HF/6-31G) methods allowed a determination of their relative free energies and the corresponding Boltzmann population distributions which were heavily weighted toward 1a. A computed composite IR spectrum of a fraction-weighted mixture of the conformers of 1 reproduced the experimentally observed IR spectrum in its structural features, leading to a conclusion that conformer 1a indeed dominates the equilibrium. The egg-shaped cavity of 1 (136.6 angstroms3) is complementary in size, shape, and electrostatic potential to chloroform (74.9 angstroms3). A single-crystal X-ray study of 2 revealed a disordered chloroform molecule positioned inside the cavitand along its C3 axis.

Journal Article↗
PubMed1999

[(Ethylenediamine)Pt(uracilate)](4), a Metal Analogue of Calix[4]arene. Coordination and Anion Host-Guest Chemistry Related to Its Conformational Dynamics.

The open "molecular box" [(en)Pt(UH-N(1),N(3))](4)(NO(3))(4) (with en = 1,2-diaminoethane, UH = uracil monoanion) resembles calix[4]arenes in its structure and solution dynamics. It adopts a 1,3-alternate conformation in the solid-state (1a), but in solution and after deprotonation to [(en)Pt(U-N(1),N(3))](4), a second major species (cone conformer (1b-4H(+))) occurs. 1b-4H(+) acts as an efficient ligand for additional metal ions through the oxo-surface formed by the four O(2) exocyclic atoms of the uracil nucleobases. As shown here, 1b-4H(+) can incorporate a single metal ion only, giving rise to the formation of species of type {[(en)PtU](4)M}(X)(n)() with M = Zn(II) (2a), Be(II) (3) (not isolated in the solid state), and La(III) (4); X = NO(3), SO(4)/2; n = 2, 3. In addition, both the protonated species of the cone conformer (1b, pH 2-4) and compounds 2a (at pH 3-8) and 3 (at pH 3-5) act as hosts for organic anions in water, as deduced from (1)H NMR studies. It is proposed that the cone conformers act as anion hosts due to a combination of positive charge as well as apolarity and size of the cavity. Host-guest complexes of type {[(en)PtU](4)Zn}(X)(NO(3),SO(4)/2) with X = p-toluenesulfonate (2b) and 3-(trismethylsilyl)-1-propanesulfonate (2c) included in the cone cavity have been prepared and association constants have been determined by (1)H NMR spectroscopy. The fact that 4 does not act as a host may be due to a possible tetradentate coordination of La to 1b-4H(+) which may result in a flatter cone cavity than in compounds 2 and 3.

Journal Article↗