摘要:

AbstractComplexation of positively charged sites in a protein with the negative DNA phosphate groups shields the phosphate charges. This diminishesinterstrand electrostatic repulsions, which stabilizes the duplex. When phosphate shidlding is present in one DNA strand only, the conformation of this strand changes due to a decrease ofintrastrand phosphate–phosphate repulsions. This destabilizes the duplex since then the strands differ in conformation. A thermodynamic model is formulated to describe this stabilization/destabilization effect in terms of changed enthalpies and entropies of hybridization. It is found that protein complexation with one DNA strand can indeed lower theTMvalue of a duplex. The model is applied to the action of helicases (replication), RNA polymerases (transcription), and restriction endonucleases. Mechanisms with unilateral charge shielding are proposed for their duplex‐destabilizing propert

ISSN:0006-3525    

DOI:10.1002/bip.360281002

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

年代:1989

数据来源: WILEY

摘要:

AbstractA theory of equilibrium denaturation of proteins is suggested. According to this theory, a cornerstone of protein denaturation is disruption of tight packing of side chains in protein core. Investigation of this disruption is the object of this paper. It is shown that this disruption is an “all‐or‐none” transition (independent of how compact is the denatured state of a protein and independent of the protein–solvent interactions) because expansion of a globule must exceed some threshold to release rotational isomerization of side chains. Smaller expansion cannot produce entropy compensation of nonbonded energy loss; this is the origin of a free‐energy barrier (transition state) between the native and denatured states. The density of the transition state is so high that the solvent cannot penetrate into protein in this state. The results obtained in this paper make it possible to present in the following paper a general phase diagram of protein molecule

ISSN:0006-3525    

DOI:10.1002/bip.360281003

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe thermodynamically stable states of denatured protein in solution are investigated. These states are distinguished from the native state by the absence of tight packing of side chains while the compactness of denatured protein may vary within a wide region. The following regimes are outlined:1the “wet” molten globule, i.e., the compact state with pores occupied by solvent;2the swollen globule (“wet,” of course); and3the coil.The “dry” molten globule, when solvent does not penetrate inside the protein, is excluded for all experimental conditions. All the transitions within the denatured globule state are gradual while the denatured globule–coil phase transition is a second order one. The conditions of protein denaturation as well as conditions of transitions and crossovers within the denatured state

ISSN:0006-3525    

DOI:10.1002/bip.360281004

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe magnitude and uniformity of the torsion elastic constant (α) of linear and supercoiled pBR322 DNAs are measured in 3 mMTris as a function of added chloroquine/basepair ratio (chl/bp) by studying the fluorescence polarization anisotropy of intercalated ethidium dye. The time‐resolved FPA is measured using a picosecond dye‐laser for excitation and time‐correlated single‐photon counting detction. For both linear and supercoiled DNAs, α remains uniform except at the very highest chl/bp ratio examined. For the linear DNA, α decreases from 5.0 × 10−12dyne‐cm at chl/bp = 0 to about 3.5 × 10−12dyne‐cm at chl/bp = 0.5, and remains at that value up to chl/bp = 5, whereupon it increases back up to its original value. For the supercoiled DNA, α remains constant at about 5.2 × 10−12dyne‐cm from chl/bp = 0 up to chl/bp = 5, whereupon it increases in parallel with the linear DNA. The effect of chloroquine on the secondary structure, torsion constant, and torsional dynamics evidently differs substantially between linear and supercoiled DNAs, even under conditions where the supercoiled DNA is completely relaxed and both DNAs bind the same amount of dye. This strongly contradicts any notion that the local structures of linear and relaxed supercoiled DNA/dye complexes with the same binding ratio are identical. The increase in apparent α at chl/bp = 5 for both DNAs may be due to stacking of the chloroquine in the major groove and consequent

ISSN:0006-3525    

DOI:10.1002/bip.360281005

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

年代:1989

数据来源: WILEY

摘要:

AbstractWe examine the effects of concentration (aggregation), buffers, and ligation, under conditions of either constant ligand activity or limited total amount of ligand, upon thermal denaturation of macromolecules as measured by scanning calorimetry. In doing so we utilize and extend an earlier generalized allosteric treatment [S. J. Gill, B. Richey, G. Bishop, and J. Wyman (1985)Biophys. Chem.21, 1–14], applicable to ligand binding, enthalpy changes, and volume changes in a macromolecular system. The approach is contrasted with formulations based on the idea of structural domains. We show how information from the full scanning calorimetric curves can be utilized in arriving at and testing appropriate models for observed behavior in selected example

ISSN:0006-3525    

DOI:10.1002/bip.360281006

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

年代:1989

数据来源: WILEY

摘要:

AbstractConformational transitions of basic sequential polytripeptides (Lys‐Ala‐Leu)n, (Arg‐Ala‐Ala)n, (Arg‐Leu‐Ala)n, and (Arg‐Ala‐Leu)n, induced by elevated salt concentrations and/or temperatures in aqueous solutions, were investigated by CD, sedimentation equilibrium, and viscometry. The behavior of (Lys‐Ala‐Leu)nwas compared with that of the sequential isomer (Lys‐Leu‐Ala)n, studied previously. It was found that both polypeptides are highly helical with a tendency to aggregate in high salt solutions. Although the hydrophobic interactions between Lys and Leu residues play an important role in both cases, the final effect on helix stabilization and aggregation is different. The Arg‐containing polypeptides were found to assume the α‐helical conformation. Compared to the Lys‐containing polypeptides (Lys‐Ala‐Leu)nand (Lys‐Leu‐Ala)n, a very

ISSN:0006-3525    

DOI:10.1002/bip.360281007

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe influence of inverted repeat sequences on the melting transitions of linear of DNAs has been examined. Derivative melting curves (DMC) of a 514 base pair (bp) DNA, seven subfragments of this DNA, and four other DNAs have been compared to predictions of DNA melting theory. The 514‐bp DNA contains three inverted repeat sequences that can form cruciform structures in supercoiled DNA. We refer to these sequences as c‐inverted repeats. Previous work showed that the DMC of this DNA, unlike a number of other DNAs, is not accurately predicted by DNA melting theory. Since the theoretical model does not include hairpin‐like structures, it was suggested that hairpin or cruciform formation in these inverted repeats may be responsible for this discrepancy. Our results support this hypothesis. Predicted DMCs are in good agreement with DNAs with no inverted repeats, or inverted repeats not evident in supercoiled DNA. Differences between the theoretical and experimentalTm's are ≤ 0.3°C. DNA molecules that contain one or more of the three c‐inverted repeats are not as accurately predicted. ExperimentalTmvalues are lower than predicted values by 0.7–3.8°C. It is concluded that some inverted repeat sequences can form hairpin‐like structures during the melting of linear DNAs. These structures appear to lower overal

ISSN:0006-3525    

DOI:10.1002/bip.360281008

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

年代:1989

数据来源: WILEY

摘要:

AbstractInfrared vibrational CD (VCD) of a small peptide,L‐alanyl‐L‐alanyl‐L‐alanine (Ala3), and a peptide model, N‐acetyl‐L‐alanine‐N′‐methyl‐amide (AAMA), in the 1550–1750‐cm−1region has been observed. The “coupled oscillator” VCD feature observed for Ala3in the amide I region is interpreted in terms of a solution structure stabilized by the electrostatic interaction of the zwitterionic groups. No such interactions are possible in basic aqueous solution of Ala3nor in AAMA in neutral solution. Thus, the coupled oscillator features are lost in the latter two cases, indicating the absence of

ISSN:0006-3525    

DOI:10.1002/bip.360281009

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

年代:1989

数据来源: WILEY

摘要:

AbstractA detailed description of the two observed solution conformations of the pentapeptide lactone fragment of actinomycin D is presented using the distance constraints obtained from two‐dimensional nuclear Overhauser enchancement spectra in combination with minimum energy calculations. Low energy conformational states that are compatible with the experimental distances are found for each of the two conformers. For one conformer, an alltranspeptide bond conformation is found with no intramolecular hydrogen bonds. For the other conformer, theD‐Val–Pro and Pro–Sar peptide bonds werecis; this solution conformation is the same as that found in both the crystal structure of the pentapeptide lactone as well as of the native actinomycin D itself. These results are discussed in terms of the combined influence of conformation and the effects of mutual intramolecular association of the pentapeptide lactone moieties in native actinomycin D on its cytotoxic a

ISSN:0006-3525    

DOI:10.1002/bip.360281010

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe biased reptation model provides a good framework for interpreting the results of continuous field DNA electrophoresis experiments performed in agarose gels. Here we discuss the main features of the mobility–molecular size and mobility–gel concentration diagrams as obtained from new extensive computer simulations of the model. Our aim is to suggest a global and coherent picture of this widely used yet poorly understood experimental technique, and to point out the areas where a systematic experimental study is still nee

ISSN:0006-3525    

DOI:10.1002/bip.360281011

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

年代:1989

数据来源: WILEY