摘要:

AbstractElectrostatic effects are believed to determine the molecular structure and function of macromolecules in many ways. In metallo‐based enzymes and in metal–macromolecule interactions in solution, these effects may predominate. In order to tackle metal ion–nucleic acid interactions theoretically, we propose a modification of Debye's distance‐dependent dielectric function first proposed more than 50 years ago. This function more closely approximates physical reality at small interatomic separations. Our theory yields a dielectric function that gives reasonable agreement with experimental data in preliminary calcu

ISSN:0006-3525    

DOI:10.1002/bip.360240302

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

年代:1985

数据来源: WILEY

摘要:

AbstractSelf‐diffusion coefficients have been obtained over a range of concentrations for both polymer and solvent in amylopectin/dimethylsulfoxide and amylopectin/water systems. The measurements were made using pulsed‐field gradient nuclear magnetic resonance (PFG‐nmr). The implications of macromolecule polydispersity to the interpretion of the PFG‐nmr experiment have been considered. Measurements of the self‐diffusion coefficients of solute and solvent are shown to provide an effective probe of polymer size and shape. Such measurements demonstrate that in dimethylsulfoxide, wheat starch amylopectin molecules are highly planar withMwof order 106. In contrast, amylopectin in water is an aggregate with a more spherical shape and has a volume some 400 times larger than the single

ISSN:0006-3525    

DOI:10.1002/bip.360240303

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

年代:1985

数据来源: WILEY

摘要:

AbstractMechanical creep and creep recovery in small shearing deformations have been studied in unligated clots formed with both thrombin and ancrod. In thrombin clots, both A binding sites (which interact with “a” sites to link monomer units within a protofibril) and B sites (which interact with “b” sites to form links between protofibrils) are exposed to enable formation of linkages; in ancrod clots, only the A sites are exposed. Fine clots (with minimal lateral aggregation of protofibrils), coarse clots (with substantial aggregation of fibril bundles), and clots of intermediate coarseness were compared. Fine thrombin clots showed less creep at short times but more creep at long times than coarse or intermediate clots and had more irrecoverable deformation relative to the initial elastic deformation. Ancrod clots had greater irrecoverable deformation than the corresponding thrombin clots, both fine and coarse. The permanent deformation in fine ancrod clots was enormous, corresponding almost to fluid character; the rate of permanent deformation was larger than that in fine thrombin clots by more than two orders of magnitude. For all types of clots, differential measurements of compliance (or its reciprocal, elastic modulus), as well as the applicability of the Boltzmann superposition principle to calculation of creep recovery, showed that the overall density of structure remained constant throughout the mechanical history; i.e., if structural elements were breaking, they were reforming at the same rate in different configurations. The possibility that the weakness of ancrod clots is attributable to partial degradation of α‐chains rather than absence of Bb linkages was eliminated by comparisons of clots made with thrombin, ancrod, and ancrod plus thrombin; the last two showed identical partial degradation of α‐chains (by gel electrophoresis), but the first and third had essentially identical initial elastic moduli and creep behavior. Two alternative mechanisms for irrecoverable deformation in fine clots are discussed, involving rupture of protofibrils and slippage of twisted segments,

ISSN:0006-3525    

DOI:10.1002/bip.360240304

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

年代:1985

数据来源: WILEY

摘要:

AbstractLight‐scattering measurements were carried out on chick‐embryo cartilage proteoglycan type H (PG‐H) in three different media. The number of uronates per PG‐H was obtained as a measure of the molecular weight: 2.3 × 103in 4MGdnHCl, 7.1 × 103in 0.3MNaCl, and 5.7 × 103in 0.04 g/dL SDS + 0.1MNaCl (GdnHCl, guanidine hydrochloride; SDS, sodium dodecylsulfate). Self‐association of PG‐H occurred in 0.3MNaCl and 0.04 g/dL

ISSN:0006-3525    

DOI:10.1002/bip.360240305

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

年代:1985

数据来源: WILEY

摘要:

AbstractIt is suggested that the three‐dimensional structure of globular proteins is partly determined by a framework of strengthened hydrogen bonds that involves both ionic side chains and water molecules in addition to the polypeptide backbone. This conclusion follows from a combination of the results ofab initiomolecular‐orbital computations on small model molecules and high‐accuracy x‐ray data on the rubredoxin molecule. The computations yield the idea of hydrogen‐bonded bridges that are built from tens of atoms, and the experimental information yields the idea that the bridges are assembled into clusters, each of which is built from hundreds of atoms. Some 10 such clusters then form a globula

ISSN:0006-3525    

DOI:10.1002/bip.360240306

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

年代:1985

数据来源: WILEY

摘要:

AbstractWe perform a computer simulation of the quaternary structure change during the allosteric transition of hemoglobin. The simulation is based on a docking procedure by which αβ dimers of human hemoglobin are associated into tetramers after being rotated in various orientations. The stability of tetramers thus reconstituted is estimated from the values of asimplified energy functiondescribing nonbonded interactions and from the area of the surface buried in dimer–dimer contacts (theirinterface area), which we take to represent stabilizing interactions and solvent contribution. A systematic analysis of tetramers reconstituted with twofold symmetry reveals that when the dimers have the Rtertiary structure, only tetramers having R‐likequaternary structuresare stable. When the dimers have the T tertiary structure, they may associate into T‐like tetramers or a variety of quaternary structures ranging from T to near R, thus tracing a plausible reaction pathway for the allosteric transition. We subject intermediates of this pathway to energy refinement with rigid αβ dimers. The refinement demonstrates that symmetrical structures are more stable than non symmetrical ones. A detailed analysis of dimer–dimer contacts in intermediates shows how close packing is maintained over large interfaces throughout the quaternary structure change, especially in the “switch region” of contact between the C helix of α‐chains and the FG

ISSN:0006-3525    

DOI:10.1002/bip.360240307

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

年代:1985

数据来源: WILEY

摘要:

AbstractA powerful Monte Carlo method is described to simulate thermal conformational fluctuations in native proteins by using an empirical conformational energy function in which bond lengths and bond angles are kept fixed and only dihedral angles are independent variables. In this method, collective variables corresponding to eigenvectors of the second‐derivative matrix of the energy function at its minimum point are scaled according to corresponding eigenvalues in such a way that the energy function in terms of the scaled collective variables is isotropic at the minimum point. Simulation is carried out with an isotropic step size in the space of these scaled collective variables. This simulation method is applied to a small protein, bovine pancreatic trypsin inhibitor (BPTI), and its model harmonic system defined by a quadratic energy function with the same second‐derivative matrix as that of BPTI at its minimum point. Efficiency of the simulation method with an isotropic step size in the space of the scaled collective variables is found to be about 500–50 times greater than the conventional method with with an isotropic step in the space of the usual nonscaled variables. One step of this new method generates conformational changes that occur in the real‐time range of 0.05 ps. In a record of 5 × 105step simulation, the BPTI molecule is observed to migrate beyond a single minimum‐ene

ISSN:0006-3525    

DOI:10.1002/bip.360240308

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

年代:1985

数据来源: WILEY

摘要:

AbstractDerivatives of calmodulin have been prepared in which tyrosine‐99 and tyrosine‐138 have been converted to their aminotyrosine derivatives. Significant changes in microenvironment occur in the presence of Ca2+. Both groups have a significant degree of mobility with respect to the protein matrix; this is Ca2+depend

ISSN:0006-3525    

DOI:10.1002/bip.360240309

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

年代:1985

数据来源: WILEY

摘要:

AbstractA matrix treatment of the formation of intramolecular anti‐parallel β‐sheets from a statistical coil has been extended to incorporate interstrand loops of arbitrary size. The behavior of the model is compared with a simpler version in which all pairs of contiguous strands were connected by β‐bends. When large interstrand loops are allowed, there are many more types of sheets than is the case when all contiguous strands must be connected by tight or β‐bends. For this reason, the larger interstrand loops make it easier to introduce the initial sheet into a statistical coil, and the sheet content is enhanced in the early stages of stages of sheet formation (i.e., at small values of the growth parametert). As the transition continues (i.e., astincreases), a stage will be reached where occupancy of the statistical coil state is negligible because nearly all residues are in sheets or interstrand loops. Now, additional sheet formation can be accomplished only at the expense of residues in the interior of interstrand loops. For this reason, the larger interstrand loops make it more difficult to complete the final stages of sheet formation. These effects are especially dramatic in the formation of cros

ISSN:0006-3525    

DOI:10.1002/bip.360240310

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

年代:1985

数据来源: WILEY

ISSN:0006-3525    

DOI:10.1002/bip.360240312

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

年代:1985

数据来源: WILEY