摘要:

AbstractPyridoxylated adult human hemoglobin (HbAo) was prepared using a one molar equivalent of pyridoxal 5‐phosphate (PLP) per heme and reduced with either NaCNBH3or NaBH4. A separate sample was pyridoxylated and passed through a mixed‐bed ion exchange column without reduction. All three preparations had a P50of 29 ± 2 torr and a cooperativity ofn= 2.4 ± 0.1. These preparations, in both the oxy and deoxy forms, were then treated with 7 equivalents of glutaraldehyde per tetramer at pH 6.8 at 4°C and at room temperature. The polymerization invariably reduced the P50to 18 ± 2 torr with Hill coefficients of less than 2. These solutions, with or without further reduction using NaCNBH3, all retained the PLP in differing amounts (2–3 moles/tetramer). Methemoglobin concentrations were increased during the polymerization reaction. The normal pyridoxylation procedure, using sodium borohydride reduction, resulted in a number of different molecular species. Polymerization with glutaraldehyde caused a further proliferation of molecular species that could not be separated by anion exchange chromatography or by isoelectric focusing. The extent of polymerization, estimated by gel exclusion chromatography and SDS polyacrylamide gel electrophoresis, was from 40 to 50%. Analysis of the reverse phase chromatograms, which separate the heme and the α‐ and β‐chains, showed extensive polymerization and distribution of the radioactively labeled PLP on the protein for all preparations. All of the polymerized and pyridoxylated samples were unstable, and showed different chromatographic patterns after storage at 4°C for 1 month. Attempts to stabilize these preparations by further reduction with NaCNBH3gave products with a lower P50and lower cooperativity. When the reactions were conducted with a purified HbAo, heterogeneity was somewhat decreased compared to the normally used stroma‐free hemoglobin, but a large number of molecular species

ISSN:0006-3525    

DOI:10.1002/bip.360290602

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractThe translational and rotational diffusion coefficients and the intrinsic viscosity of semiflexible, randomly broken, and wormilike chains have been obtained by Monte Carlo simulation in the context of the rigid‐body treatment. Both approximate and rigorous rigid‐body hydrodynamics are used, so that the error introduced by the approximate methods can be evaluated. A randomly broken chain and a wormilike chain having the same contour length and persistence length have the same radius of gyration but different values for any of the hydrodynamic properties. The two types of chains are compared in this regard. Considering that the cross section of the chain is represented by a cylinder better than by a string of spheres, we devise a cylindrical correction to be applied to the results simulated for chains of beads. Application is made to the analysis of experimental data for the translational and rotational coefficients of DNA fragments with up to 103base pairs, obtaining the persistence length for each model. The values for the wormlike chain agree well with model‐independent values obtained from radii of gyration and with other literature data at varying ionic strength. The randomly broken chain is equally able to reproduce the experimental length dependence of the properties, but the resulting persistence length may be too

ISSN:0006-3525    

DOI:10.1002/bip.360290603

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractThe indirect solvent‐induced effect on the free energy of binding of biopolymers is examined within the framework of classical statistical mechanics. We focus specifically on the role of the solute–solvent hydrogen bonding. In particular, we have estimated the first order solvent effedt on the indirect interaction between two biopolymers. We find that the solvent‐induced interactios between two hydrophilic groups through water‐bridged hydrogen bonds could significantly enhance the binding free energy. Some preliminary estimates indicate that this effect is significant and perhaps could be crucial in molecular recognition processes. Furthermore, we have calculated, from crystal structure data, the distance distribution between all the oxygens and nitrogens on the surface of some proteins that do not belong to the binding domain. In most cases we found an enhanced peak in the range of 4–5 Å, which is where we expect to find strong solvent‐induced

ISSN:0006-3525    

DOI:10.1002/bip.360290604

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractQuaterpyridineiron(III) complex ions (FeT) anchored to ordered poly(L‐glutamate) or poly(D‐glutamate) were used as enantiomeric systems for stereoselective oxidation ofL‐cysteine, a widely encountered ligand in both heme and nonheme iron–sulfur proteins. Surprisingly, electron transfer from substrate to the central metal ion does not take place, despite the favorable thermodyamic driving force. Instead, a stable, polymer‐supported, Fe(III)T‐cysteinate complex forms, to which no stereoselectivity is associated. This finding contrasts the known lability of iron(III)–thiolate complexes, ultimately yielding disulfides and iron(II) species, and is relevant in view of the current interest in model compunds of cytochrome P‐450, where cysteine is axially bound to ferric prophyrin. The formation of this complex was studied by kinetics and low‐temperature electron paramagnetic resonance spectroscopy, while the stereochemical features of the diastereomeric encounter intermediates were investigated by theoretical conformational analysis. The results collectively emphasize the environmental contraol of the polypeptide matrix on the stability of cysteinate sulfur axial ligation. Implications of the absence of stereoselectivity in the reaction investigated are also discussed in the light of a few general considerations concerning chiral discrimination in reactions between optically

ISSN:0006-3525    

DOI:10.1002/bip.360290605

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractThe peptide N‐Boc‐L‐Phe‐dehydro‐Leu‐L‐Val‐OCH3was synthesized by the usual workup procedure and finally by coupling the N‐Boc‐L‐Phe‐dehydro‐Leu‐OH to valine methyl ester. It was crystallized from its solution in methanol–water mixture at 4°C. The crystals belong to the triclinic space group P1 witha= 5.972(5) Å,b= 9.455(6) Å,c= 13.101(6) Å, α = 103.00(4)°, β = 97.14(5)°, γ = 102.86(50)°,V= 690.8(8) Å,Z= 1, dm = 1.179(5) Mg m−3and dc = 1.177(5) Mg m−3. The structure was determined by direct methods using SHELXS86. It was refined by block‐diagonal least‐squares procedure to anRvalue of 0.060 for 1674 observed reflections. The C 2α–C 2βdistance of 1.323(9) Å in dehydro‐Leu is an appropriate double bond length. The bond angle Cα–Cβ–Cγin the dehydro‐Leu residue is 129.4(8)°. The peptide backbone torsion angles are θ1= −168.6(6)°, ω0= 170.0(6)°, ϕ1= −44.5(9)°, ψ1= 134.5(6)°, ω1= 177.3(6)°, ϕ2= 54.5(9)°, ψ2= 31.1(10)°, ω2= 171.7(6)°, ϕ3= 51.9(8)°, ψ 3T= 139.0(6)°, θT= −175.7(6)°. These values show that the backbone adopts a β‐turn II conformation. As a result of β‐turn, an intramolecular hydrogen bond is formed between the oxygen of theith residue and NH of the (i+ 3)th residue at a distance of 3.134(6) Å. The Boc group has atrans–transconformation. The side‐chain torsion angles of the Phe residue are χ1= 171.6(6)°, χ 12,1= −102.1(9)°, and χ 12,2= 78.6(10)°. The side‐chain conformational angles of dehydro‐Leu residue are χ2= 2.7(13)°, χ 22,1= −107.3(11)°, and χ 22,2= 131.3(10)°. The torsion angles χ 31,1and χ 31,2that define the conformation of the valyl side chain are −166.16(6)° and 69.1(9)°, respectively. The cr

ISSN:0006-3525    

DOI:10.1002/bip.360290606

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractIn a continuation of our program to study the structure–activity relationship of peptide opiates, we report the conformational analysis of two cyclic tetrapeptides related to dermorphin—Tyr‐c[D‐Orn‐Phe‐Asp]‐NH2and Tyr‐c[D‐Asp‐Phe‐Orn]‐NH2. These analogues have similar binding properties marked by a high selectivity for the μ‐opioid receptors because of a drastic decrease in the affinity for the δ‐opioid receptor. The conformational preferences of these analogues of dermorphin determined from proton nmr, molecular dynamics, and energy minimizations are quite similar. The constraint of the 13‐membered ring formed from cyclization is quite evident from the conformational analysis. The constrained ring system acts as a template maintaining the relative orientation of the exocyclic tyrosine and side chain of phenylalanine. Two intramolecular hydrogen bonds measured for theD‐Orn analogue in DMSO were disrupted upon the addition of water. For theD‐Asp analogue, two intramolecular hydrogen bonds were found stable in DMSO and water. The global conformations of the two peptides determined from nuclear Overhauser effects did not change with the solvent titration. The difference in the hydrogen bonding within the 13‐membered ring may account for the slight differences observed in the efficacy of th

ISSN:0006-3525    

DOI:10.1002/bip.360290607

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractHomonuclear two‐dimensional (J,δ) proton spectroscopy has been suggested as a method for the measurement of1H‐31P coupling constants in oligonucleotides. The technique has been applied to a dinucleoside monophosphate G2′p5′C and a deoxydecanucleotide d(ACATCGATGT). PCILO energy calculations have been carried out to find minimum energy conformations with respect to the DNA backbone torsion angle ε, and these have been considered for the interpretation of the observed H3′‐31P coupling constants in oli

ISSN:0006-3525    

DOI:10.1002/bip.360290608

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractConstrained conformational energy minimizations have been used to calculate an adiabatic (ϕ, ψ) potential energy surface for the disaccharide sucrose. The inclusion of molecular flexibility in the conformational energy analysis of this disaccharide was found to have a significant effect upon the allowed conformational space of the molecule. Three low‐energy regions were identified on the adiabatic energy surface, and two of these regions were found to contain two related local minimum‐energy conformations, with similar energies, differing only in the directionality of the intra–residue hydrogen bonds of the glucose portion of the molecule. The known crystal structures of seven molecules containing the sucrose moiety all fall within the region of the primary allowed minimum and are consistent with the relaxed energy map, while these crystal conformations could not be rationalized using energy maps for rigid residue geometries. The greater flexibility of the furanoid ring relative to that of the pyranoid ring contributed significantly to the enlargement of the low‐energy region on the adiabatic map. However, in spite of the importance of limited flexibility in understanding the conformation and fluctuations of sucrose, this molecule was found to be considerably more rigid that some other disaccharides, such as maltose and cellobiose, in accord with experimenta

ISSN:0006-3525    

DOI:10.1002/bip.360290609

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractMolecular dynamics simulations have been used to study the motions in vacuum of the disaccharide sucrose. Ensembles of trajectories were calculated for each of the five local minimum energy conformations identified in the adiabatic conformational energy mapping of this molecule. The model sucrose molecules were found to exhibit a variety of motions, although the global minimum energy conformation was found to be dynamically stable, and no transitions away from this structure were observed to occur spontaneously. In all but one of these vacuum trajectories, the intramolecular hydrogen bond between residues was maintained, in accord with recent nmr studies of this molecule in aqueous solution. Considerable flexibility of the furanoid ring was found in the trajectories. No “flips” to the opposite puckering for this ring were found in the simulations starting from the global minimum, although such a transition was observed for a trajectory initiated with one of the higher local minimum energy conformations. Overall, the observed structural fluctuations were consistent with the experimental picture of sucrose as a relatively rigid molec

ISSN:0006-3525    

DOI:10.1002/bip.360290610

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY

摘要:

AbstractWe have shown previously that the N‐methylpridyl group vibrations of water‐soluble porphyrins, M(TMpy‐P4), are shifted to lower frequencies (0.5–2.6 cm−1) as a result of coulombic interaction between the N+‐CH3group of M(TMpy‐P4) and the PO2group of a nucleic acid. We have now turned over our attention to the effect of this coulombic interaction on the PO2group vibrations of nucleic acids. Using Fourier transform ir and Raman spectroscopy, we found that the νa(PO2) at 1221 cm−1is shifted 12 ∼ 17 cm−1to higher frequencies, whereas the νs(PO2) at 1087 cm−1is shifted 18 ∼ 26 cm−1to lower frequencies, when DNA is mixed with M(TMpy‐P4). These results indicate that the N+‐CH3group of M(TMpy‐P4) interacts preferentially with one of the two oxygen atoms

ISSN:0006-3525    

DOI:10.1002/bip.360290611

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1990

数据来源: WILEY