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PubMed2002

Distance and exposure dependent effective dielectric function.

In an effort to develop a dielectric screening function for molecular dynamics simulations of biomolecules in implicit solvent, effective dielectric constants (D(eff)) for a large number of atom pairs in a typical globular protein are calculated by continuum electrostatics. Plots of D(eff) versus the intercharge distance are in general sigmoidal with the characteristics of the curve depending on the distance of the two charges from the dielectric boundary and, secondarily, on the extent to which the area surrounding each charge is occupied by solvent (the "exposure"). The D(eff) values were fitted to an empirical, analytical function of these parameters that reproduces the data reasonably well, although considerable scatter exists in the range of D(eff) from 30 to 80. In the system used for parameterization, the mean square deviation of electrostatic interaction energies with this function is 0.48 kcal/mol, compared to 1.45 for an analytical Generalized Born model and 1.52 for the linear distance-dependent dielectric model. When tested in other proteins of varying size and compactness, the present function is superior to both of the above models, except for a fully unfolded polypeptide chain, where the Generalized Born model is superior.

Journal Article↗
PubMed2003

Dynamic behavior of cryogen spray cooling: effects of spurt duration and spray distance.

BACKGROUND AND OBJECTIVES: Cryogen spray cooling (CSC) is used to minimize the risk of epidermal damage during laser dermatologic surgery. Since optimization of CSC permits the safe use of higher light doses, which improves therapeutic outcome in many patients with superficial skin lesions, studies have focused on understanding spray-surface interactions and cooling dynamics. The objective of this study is to measure accurately temperature variations at the sprayed surface and the effects of spurt duration (deltat) and nozzle-to-sprayed surface distance (L) on cooling dynamics during CSC. STUDY DESIGN/MATERIALS AND METHODS: A fast-response temperature measurement sensor is built using thin (20 microm) aluminum foil placed on top of a poly methyl-methacrylate resin (Plexiglass) with a 50 microm bead diameter thermocouple positioned in between. Liquid film residence time (t(r)) and minimum surface temperature (T(min)) are systematically measured as a function of deltat and L. RESULTS: Two distinct spray-surface interaction mechanisms are recognized. The transition between them occurs at a critical length L(c) approximately 25-30 mm. Noticeable characteristics include: (1) for spurts at L < L(c), shorter t(r), and lower T(min) are reached as compared to L > L(c), T(min) is dependent on deltat and L, while t(r) is a function of deltat only; (2) for spurts at L > L(c), T(min) still depends on L but not on deltat, while t(r) becomes a function of both deltat and L. Finally, for all deltat, t(r) reaches a maximum at L = 40 mm. CONCLUSIONS: Based on our results, a good choice to achieve low T(min) and t(r) for the treatment of superficial skin lesions may be met by using deltat of approximately 30-50 milliseconds and the shortest spray distance that is tolerable by the patient. Spurt durations (deltat) of more than 30-50 milliseconds at spray distances (L) greater than L(c) lead to higher T(min) and longer t(r). These parameters may be appropriate for laser therapy of deeper targets.

Cryotherapy↗
PubMed2001

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

A heavy atom distance-dependent knowledge-based pairwise potential has been developed. This statistical potential is first evaluated and optimized with the native structure z-scores from gapless threading. The potential is then used to recognize the native and near-native structures from both published decoy test sets, as well as decoys obtained from our group's protein structure prediction program. In the gapless threading test, there is an average z-score improvement of 4 units in the optimized atomic potential over the residue-based quasichemical potential. Examination of the z-scores for individual pairwise distance shells indicates that the specificity for the native protein structure is greatest at pairwise distances of 3.5-6.5 A, i.e., in the first solvation shell. On applying the current atomic potential to test sets obtained from the web, composed of native protein and decoy structures, the current generation of the potential performs better than residue-based potentials as well as the other published atomic potentials in the task of selecting native and near-native structures. This newly developed potential is also applied to structures of varying quality generated by our group's protein structure prediction program. The current atomic potential tends to pick lower RMSD structures than do residue-based contact potentials. In particular, this atomic pairwise interaction potential has better selectivity especially for near-native structures. As such, it can be used to select near-native folds generated by structure prediction algorithms as well as for protein structure refinement.

Computational Biology↗
PubMed2006

A topology-constrained distance network algorithm for protein structure determination from NOESY data.

This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality of input data and final 3D structures is evaluated using recall, precision, and F-measure (RPF) scores, a statistical measure of goodness of fit with the input data. AutoStructure has been tested on three protein NMR data sets for which high-quality structures have previously been solved by an expert, and yields comparable high-quality distance constraint lists and 3D protein structures in hours. We also compare several protein structures determined using AutoStructure with corresponding homologous proteins determined with other independent methods. The program has been used in more than two dozen protein structure determinations, several of which have already been published.

Algorithms↗
PubMed1997

Song transmission and auditory perception of distance in wood warblers (Parulinae)

The influence of breeding habitat on the evolution of song structure was examined in four wood warbler species of the sub-family Parulinae. The effects of song degradation on the ability of territorial paruline males to estimate distance by means of acoustic cues was also investigated. Song transmission characteristics of paruline breeding habitats were compared in southeastern Ontario, Canada; songs native to the habitat in which they were broadcast did not degrade less than foreign songs. The response of territorial paruline males to playback of 'near' (undegraded) and 'far' (degraded) conspecific songs broadcast from the same position within the territory at the same amplitude were then compared. Males responded to near songs as they would to a conspecific territorial intruder and with less intensity to far songs, suggesting that males may use cues from song degradation to estimate distance to vocal conspecifics. Our results from transmission and playback experiments are discussed with respect to the ranging hypothesis, which proposes that selection should favour males that structure songs to minimize their degradation, so that songs function to disrupt or intimidate rivals by providing unreliable distance cues.

Journal Article↗
PubMed1999

Optimal distances for squirrels to transport and hoard walnuts.

Walnuts, Juglans airanthifolia, are an important food item for Japanese squirrels, Sciurus lis, which hoard them for later use. We set up feeders in small walnut patches in secondary forest, mounted radiotransmitters on nuts, placed them on the feeders and tracked them when they were cached. Of 720 nuts placed on the feeders over a 3-year period, 32.6% were eaten immediately and 50.6% were scatter-hoarded 0-168 m from the feeders. With increasing distance to the cache site, the squirrels took longer to return to the feeders (range 0.35-35 min). However, the further away a cache was, the less likely it was to be stolen by conspecifics or other nut-eating animals: nuts we hoarded ourselves disappeared more quickly from near the source trees. Squirrels took nuts further away later in the season when caches were lost at a higher rate. Using a simple model maximizing the rate of energy gain per unit time taken to search for and hoard the nuts at different distances from the source, we discuss whether squirrels alter the transport distance of hoarding nuts according to cache survival rate and/or nut availability. Copyright 1999 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1993

Fluorescence energy transfer distance measurements. The hydrophobic helical hairpin of colicin A in the membrane bound state.

The ion-channel-forming C-terminal fragment of colicin A binds to negatively charged lipid vesicles and provides an example of the insertion of a soluble protein into a lipid bilayer. The soluble structure is known and consists of a ten-helix bundle containing a hydrophobic helical hairpin. In this study fluorescence resonance energy transfer spectroscopy was used to determine the position of this helical hairpin in the membrane bound state. An extrinsic probe, N'-(iodoacetyl)-N'-(5-sulpho-1-naphthyl)ethylenediamine (I-AEDANS) was attached to mutant proteins each of which bears a unique cysteine residue. Five mutants I26C (helix 1), F105C (between helices 4 and 5), G166CJ (helix 8), A169C (helix 8-9), G176C (helix 9) were used. All mutants show wild-type binding activity to phosphatidylglycerol vesicles as judged by fluorescence polarization anisotropy, emission wavelength changes and brominated lipid quenching. The three tryptophan residues were used as a compound donor to AEDANS in resonance energy transfer distance determinations. The distances obtained for the soluble form were equal to those found in the crystal structure. On adding vesicles under conditions where intermolecular transfer was avoided the indicated distances increased; I26(10.9 A) F105(3.4 A), G166(3.3 A), A169(1.9 A) and G176(2.9 A). This confirms that, in the absence of a membrane potential, helices 1 and 2 open out onto the membrane surface whilst the helical hairpin remains closely packed against the rest of the structure. The insertion of this hairpin is thus not the driving force behind colicin membrane binding.

Colicins↗
PubMed1993

Protein structure comparison by alignment of distance matrices.

With a rapidly growing pool of known tertiary structures, the importance of protein structure comparison parallels that of sequence alignment. We have developed a novel algorithm (DALI) for optimal pairwise alignment of protein structures. The three-dimensional co-ordinates of each protein are used to calculate residue-residue (C alpha-C alpha) distance matrices. The distance matrices are first decomposed into elementary contact patterns, e.g. hexapeptide-hexapeptide submatrices. Then, similar contact patterns in the two matrices are paired and combined into larger consistent sets of pairs. A Monte Carlo procedure is used to optimize a similarity score defined in terms of equivalent intramolecular distances. Several alignments are optimized in parallel, leading to simultaneous detection of the best, second-best and so on solutions. The method allows sequence gaps of any length, reversal of chain direction and free topological connectivity of aligned segments. Sequential connectivity can be imposed as an option. The method is fully automatic and identifies structural resemblances and common structural cores accurately and sensitively, even in the presence of geometrical distortions. An all-against-all alignment of over 200 representative protein structures results in an objective classification of known three-dimensional folds in agreement with visual classifications. Unexpected topological similarities of biological interest have been detected, e.g. between the bacterial toxin colicin A and globins, and between the eukaryotic POU-specific DNA-binding domain and the bacterial lambda repressor.

Actins↗
PubMed1994

Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints.

Solution NMR structures for sperm whale carbonmonoxy myoglobin have been calculated using 1301 distance restraints determined from nuclear Overhauser enhancement (NOE) measurements on 15N-labeled protein and chemical shift calculations for 385 protons. Starting structures included four crystal forms of myoglobin and 12 structures generated by metric matrix distance geometry. Refinements were also carried out using distance restraints alone. In general, the solution conformations are very close to the crystal structures, although the crystal structures are not consistent with some of the observed NOE connectivities. The solution structures are about as far apart from each other (as measured by backbone root-mean-square deviations) as they are from the crystal conformation. Inclusion of chemical shift restraints both tightened the spread of computed structures (especially in the heme pocket region) and led to structures that were closer to the X-ray conformation. The disposition of the side-chains near the heme group could in many cases be determined with considerable confidence, suggesting that a chemical shift analysis may be a useful adjunct to other sources of structural information available from NMR. In particular, this evidence suggests that the distal histidine residue is slightly displaced from the crystal conformation, but still inside the heme pocket at pH 5.6, that the side-chain of Leu89 is in contact with the heme ring but is probably disordered, and that the heme pocket where ligands bind is virtually identical in solution and in the crystal forms.

Carbon Monoxide↗
PubMed1997

Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin.

We have used a novel, largely automated, calculation method to refine the NMR solution structure of the pleckstrin homology domain of beta-spectrin. The method is called ARIA for Ambiguous Restraints for Iterative Assignment. The starting point for ARIA is an almost complete assignment of the proton chemical shifts, and a list of partially assigned NOEs, mostly sequential and secondary structure NOEs. The restraint list is then augmented by automatically interpreting peak lists generated by automated peak-picking. The central task of ARIA is the assignment of ambiguous NOEs during the structure calculation using a combination of ambiguous distance restraints and an iterative assignment strategy. In addition, ARIA calibrates ambiguous NOEs to derive distance restraints, merges overlapping data sets to remove duplicate information, and uses empirical rules to identify erroneous peaks. While the distance restraints for the structure calculations were exclusively extracted from homonuclear 2D experiments, ARIA is especially suited for the analysis of multidimensional spectra. Applied to the pleckstrin homology domain, ARIA generated structures of good quality, and of sufficiently high accuracy to solve the X-ray crystal structure of the same domain by molecular replacement. The comparison of the free NMR solution structure to the X-ray structure, which is complexed to D-myo-inositol-1,4,5-triphosphate, shows that the ligand primarily induces a disorder-order transition in the binding loops, which are disordered in the NMR ensemble but well ordered in the crystal. The structural core of the protein is unaffected, as evidenced by a backbone root-mean-square difference between the average NMR coordinates and the X-ray crystal structure for the secondary structure elements of less than 0.6 A.

Binding Sites↗
PubMed1998

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.

We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two virtual atom representations and one all-heavy atom representation. When applied to six different decoy sets containing a range of correct and incorrect conformations of amino acid sequences, the all-atom distance-dependent discriminatory function is able to identify correct from incorrect more often than the discriminatory functions using approximate representations. We illustrate the importance of using a detailed atomic description for obtaining the most accurate discrimination, and the necessity for testing discriminatory functions against a wide variety of decoys. The discriminatory function is also shown to be capable of capturing the fine details of atom-atom preferences. These results suggest that the all-atom distance-dependent discriminatory function will be useful for protein structure prediction and model refinement.

Models, Theoretical↗
PubMed1999

Domain motions accompanying Tet repressor induction defined by changes of interspin distances at selectively labeled sites.

To investigate internal movements in Tet repressor (TetR) during induction by tetracycline (tc) we determined the interspin distances between pairs of nitroxide spin labels attached to specific sites by electron paramagnetic resonance (EPR) spectroscopy. For this purpose, we constructed six TetR variants with engineered cysteine pairs located in regions with presumed conformational changes. These are I22C and N47C in the DNA reading head, T152C/Q175C, A161C/Q175C and R128C/D180C near the tc-binding pocket, and T202C in the dimerization surface. All TetR mutants show wild-type activities in vivo and in vitro. The binding of tc results in a considerable decrease of the distance between the nitroxide groups attached to both I22C residues in the TetR dimer and an increase of the distance between the N47C residues. These opposite effects are consistent with a twisting motion of the DNA reading heads. Changes of the spin-spin interactions between nitroxide groups attached to residues near the tc-binding pocket demonstrate that the C-terminal end of alpha-helix 9 moves away from the protein core upon DNA binding. Alterations of the dipolar interaction between nitroxide groups at T202C indicate different conformations for tc and DNA-bound repressor also in the dimerization area. These results are used to model structural changes of TetR upon induction.

Electron Spin Resonance Spectroscopy↗
PubMed2000

The transition between the open and closed states of rubisco is triggered by the inter-phosphate distance of the bound bisphosphate.

d-Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) catalyses the central CO(2)-fixing reaction of photosynthesis in a complex, multiple-step process. Several structures of rubisco complexed with substrate analogues, inhibitors and products have been determined by X-ray crystallography. The structures fall into two well-defined and distinct states. The active site is either "open" or "closed". The timing and mechanism of the transition between these two states have been uncertain. We solved the crystal structure of unactivated (metal-free) rubisco from tobacco with only inorganic phosphate bound and conclude that phosphate binding per se does not trigger closure, as it does in the similarly structured enzyme, triosephosphate isomerase. Comparison of all available rubisco structures suggests that, instead, the distance between the terminal phosphates (P1 and P2) of the bisphosphate ligand is the trigger: if that distance is less than 9.1 A, then the active site closes; if it is greater than 9.4 A then the enzyme remains open. Shortening of the inter-phosphate distance results from the ligand binding in a more curved conformation when O atoms of the ligand's sugar backbone interact either with the metal, if it is present, or with charged groups in the metal-binding site, if the metal is absent. This shortening brings the P1 phosphate into hydrogen bonding contact with Thr65. Thr65 exists in two discrete states related by a rotation of the backbone psi torsion angle. This rotation is coupled to domain rotation and hence to active site closure. Rotation of the side-chain of Thr65 also affects the C-terminal strand of large subunit which packs against Loop 6 after closure. The position of the C-terminal strand in the closed state is stabilised by multiple polar interactions with a distinctive highly-charged latch site involving the side-chain of Asp473. In the open state, this latch site may be occupied instead by phosphorylated anions.

Anions↗
PubMed2002

Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison.

The distribution of the C(alpha)-C(alpha) distances between residues separated by three to 30 amino acid residues is highly characteristic of protein folds and makes it possible to identify them from a straightforward comparison of the distance histograms. The comparison is carried out by contingency table analysis and yields a probability of identity (PRIDE score), with values between zero and 1. For closely related structures, PRIDE is highly correlated with the root-mean-square distance between C(alpha) atoms, but it provides a correct classification even for unrelated structures for which a structural alignment is not meaningful. For example, an analysis of the CATH database of fold structures showed that 98.8% of the folds fall into the correct CATH homologous superfamily category, based on the highest PRIDE score obtained. Structural alignment and secondary-structure assignment are not necessary for the calculation of PRIDE, which is fast enough to allow the scanning of large databases.

Animals↗
PubMed1995

The conformation of the monensin-A-sodium complex in solution determined from self-consistent NOE distance constraints.

The structure of the monensin-A-sodium complex in solution in chloroform is determined by means of NOESY experiments and distance-geometry calculations. The information extracted from the NOESY spectra is maximized by estimating errors on cross-peak intensities (D.L. Turner, J. Magn. Reson. A 107, 239 (1994)) which are used in defining upper and lower distance constraints and also for weighting when calculating distance scaling factors. The resulting structure is closely similar to that found in the crystal, with deviations which fall within the range found for different crystal forms.

Magnetic Resonance Spectroscopy↗
PubMed1998

Effect of deuteration on the accuracy of HN-HN distance constraints.

The effect of deuteration on the measurement of HN-HN distances in moderately sized (15 kDa) proteins is discussed. Data are presented for a 15 kDa protein which is 95% deuterated on the Halpha position, and partially (70%) deuterated at other aliphatic sites. Deuteration of the protein increases the signal intensity of HN-HN cross peaks in NOESY spectra such that dipolar couplings between protons 4-5 A apart are readily detected. Experimental data and computer simulations show that either perdeuteration or partial deuteration of the protein increases the accuracy of amide-amide distance constraints. Thus, partial deuteration can be used to obtain more accurate long-range distance constraints for structure determination by NMR.

Deuterium↗
PubMed1999

Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.

The NOAH/DIAMOD program suite was used to automatically assign an experimental 2D NOESY spectrum of the 46 residue protein crambin(S22/I25), using feedback filtering and self-correcting distance geometry (SECODG). Automatically picked NOESY cross peaks were combined with 157 manually assigned peaks to start NOAH/DIAMOD calculations. At each cycle, DIAMOD was used to calculate an ensemble of 40 structures from these NOE distance constraints and random starting structures. The 10 structures with smallest target function values were analyzed by the structure-based filter, NOAH, and a new set of possible assignments was automatically generated based on chemical shifts and distance constraints violations. After 60 iterations and final energy minimization, the 10 structures with smallest target functions converged to 1.48 A for backbone atoms. Despite several missing chemical shifts, 426 of 613 NOE peaks were unambiguously assigned; 59 peaks were ambiguously assigned. The remaining 128 peaks picked automatically by FELIX are probably primarily noise peaks, with a few real peaks that were not assigned by NOAH due to the incomplete proton chemical shifts list.

Amino Acids↗
PubMed1999

Deuterium REDOR: principles and applications for distance measurements

The application of short composite pulse schemes ( and ) to the rotational echo double-resonance (REDOR) spectroscopy of X-2H (X: spin 12, observed) systems with large deuterium quadrupolar interactions has been studied experimentally and theoretically and compared with simple 180 degrees pulse schemes. The basic properties of the composite pulses on the deuterium nuclei have been elucidated, using average Hamiltonian theory, and exact simulations of the experiments have been achieved by stepwise integration of the equation of motion of the density matrix. REDOR experiments were performed on 15N-2H in doubly labeled acetanilide and on 13C-2H in singly 2H-labeled acetanilide. The most efficient REDOR dephasing was observed when composite pulses were used. It is found that the dephasing due to simple 180 degrees deuterium pulses is about a factor of 2 less efficient than the dephasing due to the composite pulse sequences and thus the range of couplings observable by X-2H REDOR is enlarged toward weaker couplings, i.e., larger distances. From these experiments the 2H-15N dipolar coupling between the amino deuteron and the amino nitrogen and the 2H-13C dipolar couplings between the amino deuteron and the alpha and beta carbons have been elucidated and the corresponding distances have been determined. The distance data from REDOR are in good agreement with data from X-ray and neutron diffraction, showing the power of the method. Copyright 1999 Academic Press.

Journal Article↗