摘要:

AbstractGelled agarose was observed by freeze‐fracture and electron microscopy. Aggregated double helices of agarose form a fibrous network that showed conformational variations over a range of agarose concentrations (0.3–2%). Diameters of fibers tend to increase with rising concentrations and the appearance of protuberances or cul‐de‐sacs in the network increases with falling concen

ISSN:0006-3525    

DOI:10.1002/bip.360310902

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

年代:1991

数据来源: WILEY

摘要:

AbstractAn epitope of human chorionic somatomammotropin for one of the monoclonal antibodies raised against the whole antigen has been identified. We compared the release of peptides from limited proteolysis of the antigen in the presence and absence of the related antibody. Using enzymes of different specificity, we could determine the amino acid sequence that can be considered at least inclusive of the epitope. The monoclonal antibody selected is 100% cross‐reactive with human growth hormone, so the antigenic determinant identified is shared by the two protein hormone

ISSN:0006-3525    

DOI:10.1002/bip.360310903

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

年代:1991

数据来源: WILEY

摘要:

AbstractClusters of ionizable groups are examined for conditions that develop cooperativity (1) on the binding of protons, and (2) on the binding of an associated ligand when the clusters are shared between domains or subunits in macromolecules. Cooperative binding isotherms for protons have long been observed (but not emphasized as cooperative binding) when studies have been done on clusters for the evaluation of metal ion complexation [A. E. Martell&M. Calvin (1952)Chemistry of the Metal Chelate Compounds, Prentice‐Hall, Englewood Cliffs, New Jersey]. Reactions are formulated in this paper to show that anions, chelating to positively charged clusters, are also capable of developing the cooperative binding of protons. Extension of these simple reactions to those where clusters of ionizable groups are shared between domains of macromolecules provides models for cooperative binding, which include the allosteric, Bohr, anion, and cation effects in protein

ISSN:0006-3525    

DOI:10.1002/bip.360310904

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

年代:1991

数据来源: WILEY

摘要:

AbstractIn this paper we examine the distance geometry (DG) algorithm in the form used to determine the structure of proteins. We focus on three aspects of the algorithm: bound smoothing with the triangle inequality, the random selection of distances within the bounds, and the number of distances needed to specify a structure. Computational experiments are performed using simulated and real data for basic pancreatic trypsin inhibitor (BPTI) from nmr and crystallographic measurements. We find that the upper bounds determined by bound smoothing to be a linear function of the true crystal distance. A simple model that describes the results obtained with randomly selected trial distances is proposed. Using this representation of the trial distances, we show that BPTI DG structures are more compact than the true crystal structure. We also show that the DG‐generated structures no longer resemble test structures when the number of these interresidue distance constraints is less than the number of degrees of freedom of the protein backbone. While the actual model will be sensitive the way distances are chosen, our conclusions are likely to apply to other versions of the DG algorith

ISSN:0006-3525    

DOI:10.1002/bip.360310905

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe interaction of the La(III) and Tb(III) ions with adenosine‐5′‐monophosphate (5′‐AMP), guanosine‐5′‐monophosphate (5′‐GMP), and 2′‐deoxyguanosine‐5′‐monophosphate (5′‐dGMP) anions with metal/nucleotide ratios of 1 and 2 has been studied in aqueous solution in acidic and neutral pHs. The solid complexes were isolated and characterized by Fourier transform ir and1H‐nmr spectroscopy.The lanthanide(III)–nucleotide complexes are polymeric in nature both in the solid and aqueous solutions. In the metal‐nucleotide complexes isolated from acidic solution, the nucleotide binding is via the phosphate group (inner sphere) and an indirect metal‐N‐7 interaction (outer‐sphere) with the adenine N‐1 site protonated. In the complexes obtained from neutral solution, metal chelation through the N‐7 and the PO 32−group is prevailing. In aqueous solution, an equilibrium between the inner and outer sphere metal‐nucleotide interaction has been observed. The ribose moiety shows C2′‐endo/antipucker in the free AMP anion and in the lanthanide(III)–AMP complexes, whereas the GMP anion with C2′‐endo/antisugar conformation exhibits a mixture of the C2′‐endo/antiand C3′‐endo/antisugar puckers in the lanthanide(III)–GMP salts. The deoxyribose has O4′‐endo/antisugar pucker in

ISSN:0006-3525    

DOI:10.1002/bip.360310906

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

年代:1991

数据来源: WILEY

摘要:

AbstractA modified molecular dynamics (MD) method in which atomic masses are weighted was developed previously for studying the conformational flexibility of neuroregulating tetra‐peptide Phe‐Met‐Arg‐Phe‐amide (FMRF‐amide). The method has now been applied to longer and constrained molecules, namely a disulfide‐linked cyclic hexapeptide, c [CYFQNC], and its linear and [pseudo‐cyclic]analogues. The sampling of dihedral conformational space of the linear hexapeptide in mass‐weighted MD simulations was found to be improved significantly over conventional MD simulations, as in the case of the shorter FMRF‐amide molecule studied previously. In the cyclic hexapeptide, the internal constraint of the molecule due to the intramolecular disulfide bond (hence the absence of free terminals in the molecule) does not adversely affect the significant improvement of conformational sampling in mass‐weighted MD simulations over normal MD simulations. The pseudo‐cyclic polypeptide is identical to the linear CYFQNC molecule in amino acid sequence (i.e., side chains of the cysteine residues are reduced), but the positions of its two terminal heavy atoms were held fixed in space such that the molecule has a nearly cyclic conformation. For this molecule, the mass‐weighted MD simulation generated a wide range of polypeptide backbone conformations covering the internal dihedral degrees of freedom; moreover, the physical space of the pseudo‐cyclic structure was also sampled in a complete revolution of the entire molecular fragment about the two fixed termini during the simulation. These characteristics suggest that mass‐weighted MD can also be an extremely useful method for conformational analyses of constrained molecules and, in particular, for model

ISSN:0006-3525    

DOI:10.1002/bip.360310907

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

年代:1991

数据来源: WILEY

摘要:

AbstractUltraviolet hyperchromicity experiments indicate that in DNA duplex formation, a C–T mismatch is destabilizing in the center of a duplex, but behaves as a stable base pair at the terminus of a duplex. The C–T base pair is thought to contain two hydrogen bonds, but has thermodynamic parameters (ΔH° and ΔG° of dissociation) that are similar to a G‐C base pair. AMBER molecular mechanics calculations were performed to study the possible structural properties of DNA duplexes with central and terminal C–T combinations. These calculations also indicate that a central C–T pair destabilizes a duplex, while terminal C–T forms a stable base pair. Hydrogen bonding between cytosine and thymine occurs only in the energy‐minimized structures when the helix diameter decreases and the propeller twist angle between the bases increases. These changes are found to occur only at the end of a duplex in the calculations, which may explain the exp

ISSN:0006-3525    

DOI:10.1002/bip.360310908

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

年代:1991

数据来源: WILEY

摘要:

AbstractTime‐resolved and steady‐state electric birefringence imaging with a slow‐scan video camera is used to study orientation during DNA agarose gel electrophoresis. The hydrodynamically induced gel distortion is shown to be the major source of birefringence under electrophoresis running conditions and to generate a birefringence image that approximates the image of the DNA concentration gradient in the electric field direction. A fluid kinematic model is presented to describe the spatial distribution of steady‐state birefringence and is verified with fluorescence measurements of DNA distribution. The stress‐optic coefficient of 1% agarose gel is measured by mechanical compression and used to evaluate the magnitude of the induced strain on the gel during electr

ISSN:0006-3525    

DOI:10.1002/bip.360310909

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

年代:1991

数据来源: WILEY

摘要:

AbstractN‐(3‐dimethylaminopropyl) naphtho [2, 1‐b] thiophene‐4‐carboxamide and the 6‐substituted methoxy, methyl, fluoro, chloro, bromo, trifluoromethyl, and cyano derivatives have been shown to bind to DNA via intercalation with binding constants in the 35–900 × 103range at 25°C, pH 7, and [Na+] = 0.019M. Both electron‐donating and ‐withdrawing substituents enhance intercalation binding, but the binding affinity is most enhanced by the cyano substituent. Calorimetric titrations for calf thymus DNA differ dramatically from those reported for ethidium [Hopkins et al. (1990)BiopolymersVol. 29, pp. 449–459]. Apparent enthalpy parameters (ΔHB) for intercalation are constant only at low coverage of sites and become much more positive as saturation is approached. In the plateau region, ΔHBvalues for the parent and the cyano‐, fluoro‐, chloro‐, and bromo‐substituted compounds are nearly the same (∼ −5.9 kcal/mol). For the methyl‐ (−6.8 kcal/mol) and methoxy‐ (−7.5 kcal/mol) substituted compounds, the ΔHBvalues are more exothermic than that for the un‐substituted compound, whereas ΔHBfor the trifluoromethyl compound is approximately 1 kcal/mol less exothermic. The corresponding ΔSBvalues, corrected for mixing effects, are in the 7–15‐cal/deg/mol range and are approximately linear

ISSN:0006-3525    

DOI:10.1002/bip.360310910

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

年代:1991

数据来源: WILEY

摘要:

AbstractAn understanding of helix dynamics can aid in interpreting the motions of proteins. The conformational transitions that occur also appear to play a role in protein folding. Structural studies of isolated peptides in solution are just becoming available. However, detailed analysis of the helix–coil transition is still not available and will be difficult to obtain experimentally. For these reasons, we performed a long molecular dynamics simulation of polyalanine at high temperature. Using this approach, we obtain a description of the overall structure and inherent flexibility of the chain as well as a structural picture of the conformational changes that occur. In this way, we can address both equilibrium properties of the peptide and the dynamics and mechanism of the structural transitions. Our results correlate fairly well with the available experimental data and previous simulations aimed at addressing α‐helix dynamics. The peptide spends the bulk of its time fluctuating between different conformations with intermediate helix contents. Transitions between highly ordered and highly disordered structures were rare, but they occurred rapidly. Our distribution of conformations favored collapsed states. Hence, our transitions to structures with high helical content were from fluctuating compact structures. The conversion between helix and coil occurred sequentially on a residue‐by‐residue basis. However, there was local cooperativity; the transition of a residue to the coil state was facilitated after a neighboring group became non‐helical. The relevance of our results to protein folding is also

ISSN:0006-3525    

DOI:10.1002/bip.360310911

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

年代:1991

数据来源: WILEY