ISSN:0006-3525    

DOI:10.1002/bip.360250602

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

年代:1986

数据来源: WILEY

摘要:

AbstractDomain effects on the pseudo‐first‐order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction‐diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse‐sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site‐based and molecule‐based elements to the rat

ISSN:0006-3525    

DOI:10.1002/bip.360250603

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

年代:1986

数据来源: WILEY

摘要:

AbstractNongelling solutions of structurally regular chain segments of agarose sulphate show disorder–order and order–disorder transitions (as monitored by the temperature dependence of optical rotation) that are closely similar to the conformational changes that accompany the sol–gel and gel–sol transitions of the unsegmented polymer. The transition midpoint temperature (Tm) for formation of the ordered structure on cooling is ∼25 K lower thanTmfor melting. Salt‐induced conformational ordering, monitored by polarimetric stopped‐flow, occurs on a millisecond time scale, and follows the dynamics expected for the process 2 coil ⇌ helix. The equilibrium constant for helix growth (s) was calculated as a function of temperature from the calorimetric enthalpy change for helix formation (ΔHcal= −3.0 ± 0.3 kJ per mole of disaccharide pairs in the ordered state), measured by differential scanning calorimetry. The temperature dependence of the nucleation rate constant (knuc), calculated from the observed second‐order rate constant (kobs) by the relationshipkobs=knuc(1 − 1/s) gave the following activation parameters for nucleation of the ordered structure of agarose sulphate (1 mg mL−1; 0.5MMe4NCl or KCl): ΔH* = 112 ± 5 kJ mol−1; ΔS* = 262 ± 20 J mol−1K−1; ΔG*298= 34 ± 6 kJ mol−1; (knuc)298= (7.5 ± 0.5) × 106dm3mol−1s−1. The endpoint of the fast relaxation process corresponds to the metastable optical rotation values observed on cooling from the fully disordered form. Subsequent slow relaxation to the true equilibrium values (i.e., coincident with those observed on heating from the fully ordered state) was monitored by conventional optical rotation measurements over several weeks and follows second‐order kinetics, with rate constants of (2.25 ± 0.07) × 10−4and (3.10 ± 0.10) × 10−4dm3mol−1s−1at 293.7 and 296.2 K, respectively. This relaxation is attributed to the sequential aggregation processes helix + helix → dimer, helix + dimer → trimer, etc., with depletion of isolated helix driving the much faster coil–helix equilibrium to completion. Light‐scattering measurements above and below the temperature range of the conformat

ISSN:0006-3525    

DOI:10.1002/bip.360250604

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

年代:1986

数据来源: WILEY

摘要:

AbstractValues for the thermodynamic quantities, ΔH° = 11.8 ± 2.0 Kcal/mole and ΔS° = 43.6 ± 6.0 e.u., of the 3‐13 helix–coil equilibrium of isolated S‐peptide (19 residue N‐terminal fragment of ribonuclease A) in aqueous solution (3 mM, 1MNaCl, pD 5.4) have been determined from a joint analysis of the Thr 3γ, Ala 6β, Phe 8meta, and Phe 8para1H chemical shift vs temperature curves (−7 to 80°C) in several aqueous–trifluorethanol mixtures. Chemical shifts in the coil and in the helix have been determined for up to 16 protons belonging to the 3‐13 fragment. Thermodynamic parameters have also been determined for C‐peptide (13 residue fragment) and a number of S‐peptide derivatives. From the variation of the values of the thermodynamic parameters at pD2.5, 5.4, and 8.0, a quantitation of the two helix‐stabilizing side‐chain interactions can be made: (1) Δ(ΔH°) ≃ 5 Kcal/mole and Δ(ΔS°) ≃ 18 e.u. for the salt bridge Glu 2−… Arg 10+and (2) Δ(ΔH°) ≃ 3 Kcal/mole and Δ(ΔS°) = 9 e.u. for the one in which the His 12+imidazolium group is involved, pre

ISSN:0006-3525    

DOI:10.1002/bip.360250605

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

年代:1986

数据来源: WILEY

摘要:

AbstractPeptide gels usable as protein model systems have been synthesized by a cross‐linking copolymerization of acryloyl substituted peptides with 1,4‐tetramethylene dimethacrylate. A specially adapted approach to peptide synthesis allows the removal of the amino terminal Cbo group at the end of the peptide synthesis, followed by the introduction of an acryloyl group. The polymerizable peptide monomers obtained can be transferred into insoluble peptide gels by radical copoylmerization with cross‐linking agents. After cleavage of the protecting groups of the side chains, these peptide gels can be used both as protein model systems for investigating peptide–oligonucleotide interaction and as sorbents for affinity chromatography. The preparation and characterization of the peptide gels Ala‐Lys‐Glu‐Lys‐Ala‐OMe (I), Ala‐Arg‐Glu‐Arg‐Ala‐OMe (II), Ala‐Arg‐Glu‐Lys‐Ala‐OMe (III), and Ala‐Arg‐Ala‐Lys‐Ala‐OMe (IV) as well as the conditions for the removal of the protecting groups is presented. Gel III contains the natural peptide sequence Arg‐Glu‐Ly

ISSN:0006-3525    

DOI:10.1002/bip.360250606

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe amino acid sequence of the collagen α1(I) chain (calf) is analyzed. Deviations of random tripeptide distribution leads to the definition of clusters. Inside these regions, collagen‐typical tripeptides are located. Besides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, and Gly‐Ala‐Hyp, the polar sequences Gly‐Glu‐Hyp, Gly‐Ala‐Arg, Gly‐Glu‐Arg, and Gly‐Pro‐Lys form typical sequences. The neighborhood of each tripeptide is analyzed and classified. The proximity to the collagen‐typical tripeptides is registered. Cluster theory: Less‐typical sequences also fold as members of the collagen triple helix and they are as reasonable as well as important for the collagen structure as the cluster tripeptides, but only the latter are important for the nuclea

ISSN:0006-3525    

DOI:10.1002/bip.360250607

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

年代:1986

数据来源: WILEY

摘要:

AbstractA collagen model peptide comprising three covalently cross‐linked chains (Ala‐Gly‐Pro)8with a stable triple‐helix conformation was utilized as the constant part of elongated model peptides of different composition. The tripeptides Gly‐Pro‐Hyp, Gly‐Pro‐Ala, Gly‐Pro‐Pro, Gly‐Pro‐Ser, Gly‐Ala‐Hyp, Gly‐Phe‐Hyp, Gly‐Glu‐Hyp, Gly‐Ala‐Lys, and Gly‐Pro‐Phe were coupled at the N‐terminal to the cross‐linked peptide. The transition temperatures determined by CD measurements are higher for the peptides containing the Gly‐X‐Hyp sequences followed by those with the Gly‐Pro‐Y sequences. In experiments with combinations of two different tripeptides coupled to the constant part of the cross‐linked model peptides higher transition temperatures were observed if the se

ISSN:0006-3525    

DOI:10.1002/bip.360250608

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

年代:1986

数据来源: WILEY

摘要:

AbstractSolvent accessible peptide bonds in proteins exhibit a 1–3° compression of the OCN bond angle and a corresponding expansion of the NCCa bond angle, relative to buried peptide bonds. These changes are consistent with an increase in hydrogen bonding to the carbonyl oxygen accompanying solvent exposure (J. D. Dunitz and F. K. Winkler, (1975)Acta Cryst.B31, 251–263). For amphiphilic structures such as α‐helices, systematic differences in peptide‐bond geometry between solvent‐exposed and buried residues will generate significant curvature. A decrease of 4° in the OCN bond angle between hydrophilic and hydrophobic sides of an amphiphilic helix will lead to smooth bending, with a radius of curvature of about 70 Å. This curvature is in the range observed for α‐helices in proteins. Helix curvature is estimated to have only a small effect on the magnitude and direction of the helic

ISSN:0006-3525    

DOI:10.1002/bip.360250609

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

年代:1986

数据来源: WILEY

摘要:

AbstractCartilage proteoglycan was isolated from bovine nasal septum and fractionated according to buoyant density after dissociative CsCl density gradient centrifugation. Gel‐exclusion chromatography showed that hyaluronic acid was present in fractions of density lower than 1.69 g/mL. The molecular weight, assessed by sedimentation equilibrium analysis, of the proteoglycan present in the fractions with density>1.69 g/mL, which appeared chromatographically homogeneous and constituted 54% of the preparation, ranged from 1.0 to 2.6 × 106forv= 0.55 cm3g−1. Carbodiimide‐induced modification of the carboxyl groups by methylamine resulted in a reduction of the molecular weight to 0.74 – 1.25 × 106. An analogous reduction in molecular weight was obtained after equilibration of this proteoglycan fraction with hyaluronic acid oligomers containing five disaccharide units. Since both procedures are known to cause inhibition of the interaction between proteoglycans and hyaluronic acid, it is suggested that this lower molecular‐weight range represents the true degree of polydispersity of the sub‐units of hyaline cartilage proteoglycan constituting this fraction, while the higher values obtained for the intact proteoglycan are the result of the presence of hyaluronic acid in the sample. The molecular‐weight range of the whole proteoglycan subunit preparation, assessed after carboxyl group modification, was 0.5–1.2 × 106. Apparently normal and abnormal cartilage was excised from single human osteoarthrosic femoral heads. Proteoglycans extracted by 4Mguanidine hydrochloride were isolated after dissociative density gradient centrifugation and subjected to carboxyl group modification. Preparations from normal tissue exhibited molecular‐weight averages ranging from 5 to 9 × 105. A molecular‐weight reduction was observed with proteoglycans isola

ISSN:0006-3525    

DOI:10.1002/bip.360250610

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

年代:1986

数据来源: WILEY

摘要:

AbstractWe show that the bridges and clusters of the kind found earlier in rubredoxin also occur in myoglobin. The familiar acid–base(salt) bridges are at the heart of many of the clusters. The data reported by Takano [(1977)J. Mol. Biol.,110, 537–508] on sperm whale metmyoglobin reveals ten clusters together with the heme structure and some unidentified fragments. The data reported by Hanson and Schoenborn [(1981)J. Mol. Biol.153, 117–146] on carbonmonoxymyoglobin shows numerous bridges that generally fit into the cluster picture derived from Takano's data. The data reported by S. E. V. Phillips (personal communication) on oxymyoglobin also fits into the same pattern of cluster. All but one of the myoglobin clusters are formed from two pieces of local structure each of which covers up to fifteen consecutive aminoacid residues. A “long‐range” union joins the two pieces of local structure. The clusters are generally involved with the nonhelical structure and with the junctions of the two helices. Two applications of the theory are suggested. First, the clusters offer an explanation for the formation of the α‐helices and second the unfolding of the myoglobin molecule at pH 3.8 to 5.3 is readily interpreted as the protonation at this pH of the carboxylate ions that generate the clusters that in turn support

ISSN:0006-3525    

DOI:10.1002/bip.360250611

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

年代:1986

数据来源: WILEY