Average Rms Deviation Research Articles

Solution structure of reduced plastocyanin from the blue-green alga Anabaena variabilis.

The three-dimensional solution structure of plastocyanin from Anabaena variabilis (A.v.PCu) has been determined by nuclear magnetic resonance spectroscopy. Sixty structures were calculated by distance geometry from 1141 distance restraints and 46 dihedral angle restraints. The distance geometry structures were optimized by simulated annealing and restrained energy minimization. The average rms deviation from the mean structure for the 20 structures with the lowest total energy is 1.25 A for the backbone atoms and 1.75 A for all heavy atoms. Overall, the global tertiary fold of A.v.PCu resembles those of other plastocyanins which have been structurally characterized by X-ray diffraction and NMR methods. This holds even though A.v.PCu is longer than any other known plastocyanins, contains far less invariant amino acid residues, and has an overall charge that differs considerably from those of other plastocyanins (+1 vs -9 +/- 1 at pH > or = 7). The most striking feature of the A.v. PCu structure is the absence of the beta-turn, formed at the remote site by residues (58)-(61) in most higher plant plastocyanins. The displacement caused by the absence of this turn is compensated for by an extension of the small helix [from Ala53(51) to Ser60(58) in A.v.PCu] found in other plastocyanins. Moreover, the extra residues of A.v.PCu from Pro77 to Asp79 form an appended loop. These two features allow A.v.PCu to retain almost the same global fold as observed in other plastocyanins. From a comparison with the structures of other plastocyanins it is concluded that the lack of negatively charged residues at the remote site, rather than the specific structure of A.v.PCu, is the main reason for the failure of the remote site of this plastocyanin to function as a significant electron transfer site.

Solution structure of an oligodeoxynucleotide containing the human N-ras codon 12 sequence refined from 1H NMR using molecular dynamics restrained by nuclear Overhauser effects.

The structure of d(GGCAGGTGGTG).d(CACCACCTGCC), consisting of codons 11, 12 (underlined), and 13 of the human n-ras protooncogene, was refined from 1H NMR data. Patterns of internucleotide NOEs consistent with a B-form helix were observed for each strand. NOE intensities between purine H8 and H1' protons were small compared to intensities between cytosine H5 and H6 protons, indicative of glycosyl torsion angles in the anti range. Cross-peaks were observed between purine H8 and pyrimidine H5 and CH3 protons on adjacent bases in the direction of purine (5'-->3')pyrimidine, but not in the direction pyrimidine(5'-->3')purine. Watson-Crick hydrogen bonding between bases was intact. A total of 232 experimental distance restraints were obtained. Of these, 143 were intra-residue restraints and 89 were inter-residue restraints. A restrained molecular dynamics/simulated annealing approach yielded 6 MD structures calculated from a B-form starting structure and 6 MD structures from an A-form starting structure. These refined to an average pairwise rms difference of 0.92 angstrom, with maximum pairwise rmsd of 1.35 angstroms. Accuracy of emergent structures was assessed by relaxation matrix back-calculation. The sixth-root residual index of 7.0 x 10(-2) measured between the refined structures and the NOE intensity data suggested that the former were in reasonable agreement with the NOE data. The refined solution structures were in the B-family. Similar to the human n-ras codon 61 sequence [Feng, B., & Stone, M.P. (1995) Chem. Res. Toxicol. 8, 821-832], the ras12 sequence contained local variations in B-like conformation which did not confer large structural alterations upon the duplex, but perhaps modulated the reactivity of the first as compared to the second guanine in codon 12.

Falloff Behavior in the Thermal Dissociation Rate of N2O

The striking difference in falloff behavior (pressure dependence) observed between N{sub 2}O and Ar as collision partners in the thermal dissociation rate of N{sub 2}O is noted. A mechanism proposed by Lindars and Hinshelwood involves transitions, both unimolecular and collision-induced, from the ground singlet electronic state to a dissociating triplet state. The mechanism was fit to a wide range of experimental data for neat N{sub 2}O and N{sub 2}O-Ar mixtures (273 individual data points), accounting quantitatively for the observed behavior [0.006 average rms deviation in ln(k)]. Results derived for the limiting high- and low-pressure (M = Ar) rate constants exceed current recommended values by factors of approximately 1.4 and approximately 2, respectively, over the temperature range 925-2000 K. An alternative mechanistic interpretation involving a finite rate for intramolecular vibrational relaxation is discussed. 29 refs., 8 figs., 1 tab.

Monte Carlo Study of the Thermodynamic and Structural Properties of 1-Butanethiol + N-Heptane Mixtures

Abstract The ability to use computer simulations to predict mixture properties using potential models that have been optimized for the pure compounds is demonstrated. Since the potential models were optimized only for the pure compounds, there is no guarantee that they will describe the interactions between dissimilar molecules in the mixture correctly. In this study, Monte Carlo simulations have been carried out in the isothermal-isobaric (NPT) ensemble to calculate the density and excess enthalpy for 1-butanethiol + n-heptane mixtures at 298.15 K and 1 atm. The OPLS potential-parameters developed by Jorgensen were used to describe the n-heptane molecule. Two models for the butanethiol molecule were employed: PES1 used the OPLS potential-parameters unaltered, while PES2 used the OPLS parameters with slightly modified partial charges. Simulations were performed on mixtures with butyl mercaptan mole fractions of 0.0, 0.23, 0.42, 0.62, 0.83, and 1.0. The average rms deviation between the calculated densities for PES1 and PES2 and the experimental results is 0.021 g/cc and 0.015 g/cc, respectively, while the average rms deviation for the excess enthalpies for PES1 and PES2 is 0.058 kcal/mol and 0.027 kcal/mol, respectively. We also compared our calculated densities with the COSTALD correlation. The extent of self-association of the butanethiol molecules was found it to be small for all of the mixtures for the PES2 model.

Structure of the Oct-3 POU-homeodomain in solution, as determined by triple resonance heteronuclear multidimensional NMR spectroscopy.

The POU-homeodomain (POUH) forms the bipartite DNA-binding POU domain in association with the POU-specific domain. The 1H, 15N, and 13C magnetic resonances of the 67-amino acid long POUH of mouse Oct-3 have almost completely been assigned, mainly through the combined use of three-dimensional triple resonance NMR methods. Based on the distance and dihedral angle constraints derived from the NMR data, the solution structure of the POUH domain has been calculated by the ab initio simulated annealing method. The average RMS deviation for all backbone heavy atoms of the 20 best calculated structures for residues 9-53 of the total 67 amino acid residues is 0.44 A. The POUH domain consists of three alpha-helices (helix-I, 10-20; helix-II, 28-38; and helix-III, 42-53), and helices-II and -III form a helix-turn-helix motif. In comparison with other classical homeodomains, the folding of the three helices is quite similar. However, the length of helix-III is fairly short. In the complex of the Oct-1 POU domain with an octamer site (Klemm JD, et al., 1994, Cell 77:21-32), the corresponding region is involved in helix-III. The structural difference between these two cases will be discussed.

Structure of a Duplex Oligodeoxynucleotide Containing Propanodeoxyguanosine Opposite a Two-Base Deletion in the (CpG)3 Frame-Shift Hotspot of Salmonella typhimurium hisD3052 Determined by 1H NMR and Restrained Molecular Dynamics

Structural refinement from solution 1H NMR data was performed on the 5'-d[ATCGC(PdG)-CGGCATG]-3'.5'-d[CATGCCGCGAT]-3' duplex, in which the adducted oligodeoxynucleotide containing the exocyclic lesion 1,N2-propano-2'-deoxyguanosine (PdG) was annealed with the complementary strand which contained a CpG deletion. The resulting duplex required PdG and one adjacent cytosine to be unpaired. A total of 352 distances were utilized to restrain molecular dynamics calculations, of which 264 were NOE-derived. These distances were calculated using complete relaxation matrix methods from hybrid matrices, which were comprised of the experimentally determined distances and additional distances derived from either A-form or B-form DNA. A simulated annealing protocol combined with the distance restraints was able to refine a single structure with an average rms deviation of < 1.35 A. The accuracy of the refined structure was assessed using full relaxation matrix calculations, which gave good agreement with measured NOE intensities. PdG was found to be stacked into the helix below base pair C3.G18, whereas C5 was found to be unpaired and extruded toward the major groove and parallel to base pair G6.C17. This created a localized bend in the DNA helix of approximately 20-35 degrees at the junction between PdG and C5. The bending corroborated previous assays performed on this modified sequence [Moe, J. G., Reddy, G. R., Marnett, L. J., & Stone, M. P. (1994) Chem. Res. Toxicol. 7, 319-328].

The isomorphous structures of prethrombin2, hirugen–, and PPACK–thrombin: Changes accompanying activation and exosite binding to thrombin

The X-ray crystal structure of prethrombin2 (pre2), the immediate inactive precursor of alpha-thrombin, has been determined at 2.0 A resolution complexed with hirugen. The structure has been refined to a final R-value of 0.169 using 14,211 observed reflections in the resolution range 8.0-2.0 A. A total of 202 water molecules have also been located in the structure. Comparison with the hirugen-thrombin complex showed that, apart from the flexible beginning and terminal regions of the molecule, there are 4 polypeptide segments in pre2 differing in conformation from the active enzyme (Pro 186-Asp 194, Gly 216-Gly 223, Gly 142-Pro 152, and the Arg 15-Ile 16 cleavage region). The formation of the Ile 16-Asp 194 ion pair and the specificity pocket are characteristic of serine protease activation with the conformation of the catalytic triad being conserved. With the determination of isomorphous structures of hirugen-thrombin and D-Phe-Pro-Arg chloromethyl ketone (PPACK)-thrombin, the changes that occur in the active site that affect the kinetics of chromogenic substrate hydrolysis on binding to the fibrinogen recognition exosite have been determined. The backbone of the Ala 190-Gly 197 segment in the active site has an average RMS difference of 0.55 A between the 2 structures (about 3.7 sigma compared to the bulk structure). This segment has 2 type II beta-bends, the first bend showing the largest shift due to hirugen binding. Another important feature was the 2 different conformations of the side chain of Glu 192. The side chain extends to solvent in hirugen-thrombin, which is compatible with the binding of substrates having an acidic residue in the P3 position (protein-C, thrombin platelet receptor). In PPACK-thrombin, the side chain of Asp 189 and the segment Arg 221A-Gly 223 move to provide space for the inhibitor, whereas in hirugen-thrombin, the Ala 190-Gly 197 movement expands the active site region. Although 8 water molecules are expelled from the active site with PPACK binding, the inhibitor complex is resolvated with 5 other water molecules.

The NMR solution structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi

AbstractThe NMR structure of the pheromone Er‐2 from the ciliated protozoan Euplotes raikovi has been determined in aqueous solution. The structure of this 40‐residue protein was calculated with the distance geometry program DIANA from 621 distance constraints and 89 dihedral angle constraints; the program OPAL was employed for the energy minimization. For a group of 20 conformers used to characterize the solution structure, the average pairwise RMS deviation from the mean structure calculated for the backbone heavy atoms N, Cα, and C′ of residues 3–37 was 0.31 Å. The molecular architecture is dominated by an up‐down‐up bundle of 3 short helices of residues 5–11, 14–20, and 23–33, which is similar to the structures of the homologous pheromones Er‐1 and Er‐10. Novel structural features include a well‐defined N‐cap on the first helix, a 1‐residue deletion in the second helix resulting in the formation of a 310‐helix rather than an α‐helix as found in Er‐1 and Er‐10, and the simultaneous presence of 2 different conformations for the C‐terminal tetrapeptide segment, i.e., a major conformation with the Leu 39‐Pro 40 peptide bond in the trans form and a minor conformation with this peptide bond in the cis form.

Three-dimensional structure in solution of neurotoxin III from the sea anemone Anemonia sulcata.

The three-dimensional structure in aqueous solution of the 27-residue polypeptide neurotoxin Anemonia sulcata toxin III (ATX III) has been determined from 1H NMR data. As ATX III self-associates in the millimolar concentration range, causing a marked concentration dependence for the chemical shifts of several residues [Norton, R. S., Cross, K., Braach-Maksvytis, V., & Wachter, E. (1993) Biochem. J. 293, 545-551], it was necessary to record NOESY spectra over a range of concentrations in order to eliminate any intermolecular interactions from the NOE restraint set. The pairings of the six half-cystine residues were also unknown and had to be determined (as 3-17, 4-11, and 6-22) from preliminary structure calculations performed using both upper bound distance restraints from NOESY data and a substantial number of lower bound restraints inferred from the absence of NOESY cross-peaks. Final structures were determined, using the program X-PLOR, from interproton distance restraints inferred from NOEs, backbone and side chain dihedral angle restraints from spin-spin coupling measurements, and a smaller number of lower bound restraints. Stereospecific assignments for 11 beta-methylene pairs were also included. The final set of 28 structures had an average pairwise RMS difference of 1.32 A over the backbone heavy atoms (N, C alpha, and C) and 2.18 A over all heavy atoms. For the well-defined region encompassing residues 3-22, the corresponding values were 0.62 and 1.28 A, respectively. ATX III adopts a compact structure containing four reverse turns (a distorted type I beta-turn at residues 6-9, a type I beta-turn at residues 8-11, and inverse gamma-turns at residues 12-14 and 15-17) and two other chain reversals, but no regular alpha-helix or beta-sheet. Several of the residues most affected by aggregation are located on the surface of the molecule, forming a hydrophobic patch which may constitute part of the sodium channel binding surface. Possible relationships between the structure of ATX III and those of other sea anemone toxins that interact with the same site on the voltage-gated sodium channel are considered.

The NMR solution structure of the pheromone Er‐1 from the ciliated protozoan Euplotes raikovi—NMR structure of the pheromone Er‐I

AbstractThe 3‐dimensional structure of the pheromone Er‐1 isolated from the ciliated protozoan Euplotes raikovi has been determined in aqueous solution by 1H NMR spectroscopy. The structure of this 40‐residue protein was calculated with the distance geometry program DIANA on the basis of 503 upper distance constraints derived from nuclear Overhauser effects and 77 dihedral angle constraints derived from spin—spin coupling constants, and refined by restrained energy minimization with the program OPAL. The Er‐1 solution structure is represented by a group of 20 conformers with an average RMS deviation relative to the mean structure of 0.55 Å for the backbone atoms N, Cα, and C', and 0.93 Å for all heavy atoms of the complete polypeptide chain, residues 1–40. The molecular architecture is dominated by an up‐down‐up bundle of 3 α‐helices formed by residues 2–9, 12–19, and 24–33. Although this core part coincides closely with the previously determined structure of the homologous pheromone Er‐10, the C‐terminal peptide segment adopts a novel conformation. This is of interest in view of previous suggestions, based on sequence comparisons, that this molecular region may be important for the different specificity of receptor recognition by different pheromones.

Solution conformation of an atrial natriuretic peptide variant selective for the type A receptor.

Two-dimensional NMR spectroscopy has been used to characterize the solution conformation of an atrial natriuretic peptide (ANP) variant which is selective for the human natriuretic peptide receptor A (NPR-A) relative to receptor C (NPR-C). The ANP mutant, containing six substitutions, has reduced flexibility in aqueous solution relative to wild-type ANP and allows the observation of sufficient NOE connectivities for structure determination by distance geometry and restrained molecular dynamics calculations. The solution conformation is reasonably well defined, having an average backbone atom rms deviation from the average coordinates of approximately 1.1 A for residues 7-27. The structure is consistent with available functional data and shows a spatial separation between known receptor binding determinants and residues found to be outside the hormone-receptor interface.

High-resolution structure of an engineered biologically potent insulin monomer, B16 Tyr-->His, as determined by nuclear magnetic resonance spectroscopy.

Site-directed mutagenesis is used in conjunction with 1H nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy in order to find an insulin species amenable for structure determination in aqueous solution by NMR spectroscopy. A successful candidate in this respect, i.e., B16 Tyr-->His mutant insulin, is identified and selected for detailed characterization by two-dimensional 1H NMR. This mutant species retains 43% biological potency and native folding stability, but in contrast to human insulin it remains monomeric at millimolar concentration in aqueous solution at pH 2.4. The resulting homogeneous sample allows high-quality 2D NMR spectra to be recorded. The NMR studies result in an almost complete assignment of the 1H resonance signals as well as identification of NOE cross peaks. NOE-derived distance restraints in conjunction with torsion restraints based on measured coupling constants, 3JHNH alpha, are used for structure calculations using the hybrid method of distance geometry and simulated annealing. The calculated structures show that the major part of the insulin monomer is structurally well-defined with an average rms deviation between the 20 calculated structures and the mean coordinates of 0.89 A for all backbone atoms, 0.46 A for backbone atoms (A2-A19 and B4-B28), and 1.30 A for all heavy atoms. The structure of the A-chain is composed of two helices from A2 to A7 and from A12 to A19 connected by a short extended strand. The B-chain consists of a loop, B1-B8, an alpha-helix, B9-B19, a beta-turn, B20-B23, and an extended strand from B24 to B30.(ABSTRACT TRUNCATED AT 250 WORDS)

Three-dimensional solution structure of a curaremimetic toxin from Naja nigricollis venom: a proton NMR and molecular modeling study.

The solution conformation of toxin alpha from Naja nigricollis (61 amino acids and four disulfides), a snake toxin which specifically blocks the activity of the nicotinic acetylcholine receptor (AcChoR), has been determined using nuclear magnetic resonance spectroscopy and molecular modeling. The solution structures were calculated using 409 distance and 73 dihedral angle restraints. The average atomic rms deviation between the eight refined structures and the mean structure is approximately 0.5 A for the backbone atoms. The overall folding of toxin alpha consists of three major loops which are stabilized by three disulfide bridges and one short C terminal loop stabilized by a fourth disulfide bridge. All the disulfides are grouped in the same region of the molecule, forming a highly constrained structure from which the loops protrude. As predicted, this structure appears to be very similar to the 1.4-A resolution crystal structure of another snake neurotoxin, namely, erabutoxin b from Laticauda semifasciata. The atomic rms deviation for the backbone atoms between the solution and crystal structures is approximately 1.7 A. The minor differences which are observed between the two structures are partly related to the deletion of one residue from the chain of toxin alpha. It is notable that, although the two toxins differ from each other by 16 amino acid substitutions, their side chains have an essentially similar spatial organization. However, most of the side chains which constitute the presumed AcChoR binding site for the curaremimetic toxins are poorly resolved in toxin alpha.(ABSTRACT TRUNCATED AT 250 WORDS)

Three-dimensional structure in solution of barwin, a protein from barley seed.

The solution structure of a 125-residue basic protein, barwin, has been determined using 1H nuclear magnetic resonance spectroscopy. This protein is closely related to domains in proteins encoded by wound-induced genes in plants. Analysis of the 1H nuclear Overhauser spectrum revealed the assignment of more than 1400 nuclear Overhauser effects. Twenty structures were calculated based on 676 nontrivial distance restraints, 152 torsion angle restraints (92 phi, 56 chi 1, and 4 omega for proline), and stereospecific assignments of 38 chiral centers, using distance geometry, simulated annealing, and restrained energy minimization. None of the distance restraints was violated by more than 0.5 A in any of the 20 structures, and none of the torsion angle restraints was violated by more than 1 degree in any of the structures. The RMS difference between the calculated and target interproton distance restraints is 0.033 A, and the average atomic RMS differences between the 20 structures and their geometric average are 1.23 A for backbone atoms and 1.73 A for all heavy atoms. The dominating structural feature of the protein is a well-defined four-stranded antiparallel beta-sheet, two parallel beta-sheets packed antiparallel to each other and four short alpha-helices. The binding site of barwin to the tetramer N-acetylglucosamine has been qualitatively investigated, and the dissociation constant of the complex has been determined using one-dimensional 1H nuclear magnetic resonance spectroscopy.

Low resolution solution structure of the Bacillus subtilis glucose permease IIA domain derived from heteronuclear three-dimensional NMR spectroscopy

A low resolution solution structure of the IIA domain of the Bacillus subtilis phospho enolpyruvate-sugar phosphotransferase system (PTS) glucose permease has been determined using 945 inter-residue and 724 intra-residue distance constraints derived from three-dimensional 15N and 13C edited NOESY spectra. A total of 15 structures was generated using distance geometry calculations. The protein is comprised of 13 β-strands forming an antiparallel β-barrel, The average backbone atomic RMS deviation about the average distance geometry structure for the β-sheet residues is 1.1 Å. The conformations of the loop regions between the β-strands are less well determined. Backbone distance constraints obtained during the process of sequential assignment were insufficient to correctly calculate the polypeptide fold.

Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy

The solution conformation of the ribonuclease barnase has been determined by using 1H nuclear magnetic resonance (NMR) spectroscopy. The 20 structures were calculated by using 853 interproton distance restraints obtained from analyses of two-dimensional nuclear Overhauser spectra, 72 phi and 53 chi 1 torsion angle restraints, and 17 hydrogen-bond distance restraints. The calculated structures contain two alpha-helices (residues 6-18 and 26-34) and a five-stranded antiparallel beta-sheet (residues 50-55, 70-75, 85-91, 94-101, and 105-108). The core of the protein is formed by the packing of one of the alpha-helices (residues 6-18) onto the beta-sheet. The average RMS deviation between the calculated structures and the mean structure is 1.11 A for the backbone atoms and 1.75 A for all atoms. The protein is least well-defined in the N-terminal region and in three large loops. When these regions are excluded, the average RMS deviation between the calculated structures and the mean structure for residues 5-34, 50-56, 71-76, 85-109 is 0.62 A for the backbone atoms and 1.0 A for all atoms. The NMR-derived structure has been compared with the crystal structure of barnase [Mauguen et al. (1982) Nature (London) 297, 162-164].

Solution conformation of thymosin .beta.4: a nuclear magnetic resonance and simulated annealing study

The conformation of the polypeptide thymosin beta 4 in solutions of 60% (v/v) trifluoroethanol-d3 and 50% (v/v) hexafluoroisopropyl-d2 alcohol in water is investigated by nuclear magnetic resonance (NMR) spectroscopy. Under these conditions thymosin beta 4 adopts an ordered structure. By use of a combination of two-dimensional NMR techniques, the 1H NMR spectrum of thymosin beta 4 is assigned. A set of 180 approximate interproton distance constraints is derived from nuclear Overhauser enhancement (NOE) measurements. These, together with 33 phi constraints obtained for JNH alpha coupling data and the 23 psi dihedral angles identified on the basis of the pattern of short-range NOEs, form the basis of a three-dimensional structure determination by dynamical simulated annealing. The calculations are carried out starting from three initial structures, an alpha-helix, an extended beta-strand, and a mixed alpha/beta structure. Ten independent structures are computed from each starting structure by using different random number seeds for the assignments of the initial velocities. All 30 calculated structures satisfy the experimental constraints, display very small deviations from idealized covalent geometry, and possess good nonbonded contacts. Analysis of the 30 converged structures indicates that there are two helical regions extending from residues 4-16 and from residues 30-40, which are well defined both in terms of atomic root mean square differences and backbone torsion angles. For the two helical regions individually the average backbone rms difference between all pairs of structures is approximately 2 A. The two helices exhibit typical amino acid preferences for specific locations at the ends of helices.(ABSTRACT TRUNCATED AT 250 WORDS)

Overtone frequencies and intensities of bent XY 2 molecules in the vibron model

Calculations of overtone frequencies of five bent XY 2 molecules, H 2O 16, H 2O 18, D 2O 16, H 2S 32, and S 32O 2 16, with average rms deviations of 1–5 cm −1 are reported. The calculations are performed within the framework of the vibron model and sets of algebraic force field constants are presented. The corresponding wavefunctions are used to calculate intensities in the H 2O 16 molecule. The calculated intensities are compared with recent measurements of the ATMOS collaboration.

Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing

The solution structure of a synthetic 36-residue polypeptide comprising the C-terminal cellulose binding domain of cellobiohydrolase I (CT-CBH I) from Trichoderma reesei was investigated by nuclear magnetic resonance (NMR) spectroscopy. The 1H NMR spectrum was completely assigned in a sequential manner by two-dimensional NMR techniques. A large number of stereospecific assignments for beta-methylene protons, as well as ranges for the phi, psi, and chi 1 torsion angles, were obtained on the basis of sequential and intraresidue nuclear Overhauser enhancement (NOE) and coupling constant data in combination with a conformational data base search. The structure calculations were carried out in an iterative manner by using the hybrid distance geometry-dynamical simulated annealing method. This involved computing a series of initial structures from a subset of the experimental data in order to resolve ambiguities in the assignments of some NOE cross-peaks arising from chemical shift degeneracy. Additionally, this permitted us to extend the stereospecific assignments to the alpha-methylene protons of glycine using information on phi torsion angles derived from the initial structure calculations. The final experimental data set consisted of 554 interproton distance restraints, 24 restraints for 12 hydrogen bonds, and 33 phi, 24 psi, and 25 chi 1 torsion angle restraints. CT-CBH I has two disulfide bridges whose pairing was previously unknown. Analysis of structures calculated with all three possible combinations of disulfide bonds, as well as without disulfide bonds, indicated that the correct disulfide bridge pairing was 8-25 and 19-35. Forty-one structures were computed with the 8-25 and 19-35 disulfide bridges, and the average atomic rms difference between the individual structures and the mean structure obtained by averaging their coordinates was 0.33 +/- 0.04 A for the backbone atoms and 0.52 +/- 0.06 A for all atoms. The protein has a wedgelike shape with an amphiphilic character, one face being predominantly hydrophilic and the other mainly hydrophobic. The principal element of secondary structure is made up of an irregular triple-stranded antiparallel beta-sheet composed of residues 5-9 (beta 1), 24-28 (beta 2), and 33-36 (beta 3) in which strand beta 3 is hydrogen bonded to the other two strands.(ABSTRACT TRUNCATED AT 400 WORDS)

On Natural Convection Heat Transfer From Three-Dimensional Bodies of Arbitrary Shape

A simple expression is developed for the natural convection heat transfer from three-dimensional bodies of arbitrary shape immersed in an extensive fluid. The expression applies to both laminar and turbulent regimes and requires the calculation of purely geometric properties of the bodies. Experiments were performed with air, covering a Rayleigh number (Ra) range of from 10 to 108, on different body shapes oriented in various directions: for example, circular or square disks, a short circular cylinder of height equal to diameter and a similar cylinder but with hemispherical ends, prolate and oblate spheroids of various aspect ratio, and an “apple core” shape. Comparison between the predictions of the expression and the experimental results of this work and those gathered from several other sources ranging up to Ra = 1014 showed very good agreement, with an average rms difference of 3.5 percent for Ra &lt; 108 and 22 percent for 108 &lt; Ra &lt; 1014.