摘要:

AbstractThe vibrational Raman optical activity (ROA) spectra of di‐ and tri‐L‐alanine in the range 650–1750 cm−1have been measured in H2O and D2O solution at high, neutral, and low pH and pD. Corresponding ROA spectra for tetra‐ and penta‐L‐alanine have also been obtained, but over a more restricted set of pH and pD conditions. There are similarities with the ROA spectrum ofL‐alanine below ∼ 1200 cm−1, but the spectra are very different above this wavenumber due to the influence of the vibrational coordinates of the peptide group. The similar overall appearance of the di‐, tri‐, and tetrapeptide ROA under selected conditions of pH and pD, and of all four peptide ROA spectra in DCl and HCl solutions, in the backbone skeletal stretch region ∼ 1050–1200 cm−1and the extended amide III region ∼ 1250–1350 cm−1, suggests that the backbone conformation is approximately the same in all four structures. One difference, however, is a shift of a large positive ROA band in H2O at ∼ 1341 cm−1in the dipeptide, assigned to Cα–H and in‐plane N–H deformations, down to ∼ 1331 cm−1in the tripeptide and to ∼ 1315 cm−1in the tetrapeptide and pentapeptide (the last in HCl due to insufficient solubility in H2O), which indicates increasing delocalization of the corresponding normal mode with increasing chain length. Our results do not support the suggestion that stabilizing interactions of the zwitterionic end groups in tri‐L‐alanine at neutral pH leads to a different soluti

ISSN:0006-3525    

DOI:10.1002/bip.360340302

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe development of Flory–Huggins (FH) theory is reviewed, particularly with regard to the molecular significance of the interaction parameter that scales the contact interaction of solute and solvent. The chemical potential given by FH theory for an “idealute” solute is then compared with that provided by a more general, statistical thermodynamic approach. It is found that the FH contact term does not directly correspond to the solvation free energy. The significance of this result for the interpretation of free energies of transfer of a solute from one solvent to another is examined. It is shown that neither the earlier recommended standard free energy change for the process (using the infinitely dilute reference state, mole fraction units) nor the recently recommended FH‐corrected standard free energy change provides the solvation energy desired. Instead, the standard free energy using the infinitely dilute reference state and molarity units, as long advocated by Ben‐Naim, provides the desired solvation free energy. Correction of extant values, based on mole fraction units, is easily made. However, application of such results to problems of protein folding is not straightforward. © 1994 John Wiley

ISSN:0006-3525    

DOI:10.1002/bip.360340303

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

年代:1994

数据来源: WILEY

摘要:

AbstractA study of the component synthesis method (CSM) for analyzing the normal mode dynamics of macromolecules is reported. The procedure involves a reduction of the dimensions of the normal mode problems for large molecular systems and the accurate extraction of the low‐frequency modes. A macromolecule is divided into small components based on a hierarchical clustering of the residues in the structure. Interactions between coupled components are treated by the method of static correlation. The normal modes of the components are obtained first, and a fraction of the low‐frequency normal modes of the components under mutual correlations are then used as a reduced basis for solving for the normal modes of the whole molecule. Multiple components are introduced for large macromolecules so that the dimensions of the eigenvalue problems at the component level are small. The method is applied to the protein crambin. In test calculations in which the dimensions of the eigenvalue equations are reduced to 1/6 of their natural size, the errors in the normal mode frequencies calculated by the CSM procedure are only about 1–2% when compared with the exact values. The rms fluctuations of all atoms in crambin calculated by the CSM procedure are basically identical to the exact results. The CSM procedure is shown to be accurate for calculating the normal modes of large macromolecules with a significant reduction of the size of the problem. © 1994 John Wiley&Son

ISSN:0006-3525    

DOI:10.1002/bip.360340304

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

年代:1994

数据来源: WILEY

摘要:

AbstractWe present a new method for measuring the widths and depths of the grooves formed within DNA helices. This method overcomes the limitations of simply measuring interstrand phosphate–phosphate distances and has the advantage of yielding continuous values for groove geometry along a DNA fragment. In the case of oligonucleotides, it also clearly indicates the zones in which grooves exist, bounded by two phosphodiester backbones. The methodology has been developed within the Curves algorithm for studying irregular DNA geometries and is based on the optimal, and generally curved, helical axis obtained by this analysis. © 1994 John Wiley&Sons, I

ISSN:0006-3525    

DOI:10.1002/bip.360340305

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe free energy difference between two states of a molecular system separated by an energy barrier can generally be computed using the technique of umbrella sampling along a chosen reaction coordinate or pathway. The effect of a particular choice of pathway upon the obtained free energy difference is investigated by molecular dynamics simulation of a model system consisting of a glycine dipeptide in aqueous solution. Two different reaction coordinates connecting the so‐called C5and C7conformations, one involving intramolecular hydrogen bonds and the other involving the peptide ϕ, ψ angles, are considered.The Gibbs free energy differences ΔG(C5– C7) are small in both cases, 1.5 ± 1 kJ mol−1and 2.2 ± 1 kJ mol−1, respectively. The two different reaction coordinates yield free energy differences that are identical to within their statistical error. It is found that the exchange of solute–solute, solute–water, and water–water hydrogen bonds involves free energy changes of less thankBT, which points at the existence of a multitutde of low free energy pathways connecting the C5and C7dipeptide conformations. © 1994 J

ISSN:0006-3525    

DOI:10.1002/bip.360340306

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

年代:1994

数据来源: WILEY

摘要:

AbstractA dielectric relaxation peak due to bound water of globule proteins in aqueous solution was observed at first by the use of a time domain reflectometry. This peak locates around 100 MHz as well as that of the aqueous DNA solution and the moist collagen, and has a relaxation strength in proportion to surface of the globule protein except for trypsin and pepsin of hydrolase. It is suggested that this peak is caused by orientation of bound water molecules on the protein surface. The number of bound water molecules estimated is in good agreement with that obtained by other method such as x‐ray analysis. The solution exhibits another peak below 100 MHz, which is caused by the rotation of globule protein supplemented by migration of the counterion. Its relaxation time is completely proportional to the molecular weight of the protein. © 1994 John Wiley&Sons, I

ISSN:0006-3525    

DOI:10.1002/bip.360340307

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

年代:1994

数据来源: WILEY

摘要:

AbstractWater loss during lyophilization of a 49.4 mg/mL solution of lysozyme in D2O was studied with ir spectroscopy using a low‐temperature, single reflection, horizontal, attenuated, total reflectance accessory. Four regions of water loss were identified and assignable to different forms of bound water. The amide I band begins to shift to higher frequency while the amide II concurrently shifts to lower frequency and broadens after the first stage of water loss (sublimation) at −10°C. Additionally, the carboxylate band (at 1584 cm−1) shifts slightly to lower frequency. A second stage at 17°C is characterized by continued shifts in the carboxylate and amide II bands to low frequency, further broadening in the amide II and greater shift to high frequency in the amide I (ascribed to the removal of periphery water around the protein). At the third stage of water loss, the carboxylate band decreases substantially in relative absorbance (consistent with the removal of water from the carbonyl backbone). In the fourth and last stage, the carboxylate band nearly disappears and water loss is very slow. Based upon a final level of hydration of 0.037 h, the last stage corresponds to 25% completion of the removal of water associated with ionizable side chains. From start to finish, the amide I shifts 9 cm−1to higher frequency. © 1994 John Wiley

ISSN:0006-3525    

DOI:10.1002/bip.360340308

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

年代:1994

数据来源: WILEY

摘要:

AbstractA study of gellan has been made using the technique of photon correlation spectroscopy. It has been confirmed that gellan gels are largely stationary at a molecular level like other polysaccharide gels and quite unlike the gels of flexible polymers such as polyacrylamide. Solution‐gel transitions of deacetylated gellan in 0.025MNaCl have been studied both as a function of concentration and temperature, and the results compared with those of a parallel investigation of agarose. The interstitial spaces within gellan gels have also been studied by measuring the diffusion coefficients of dextran fractions within the gels. Since all gels are nonergodic systems, the theory of dynamic light scattering from such systems is discussed insofar as it affects the present work.It has been shown that the gellan and agarose aqueous systems are fundamentally different, in that agarose does not from a solution at very low concentrations, but splits up into macroscopic gel particles. At very low concentrations, gellan forms a solution in the presence of both gelleing and nongelling ions, the molecules of which shows little change in hydrodynamic diameter with temperature in the range 20–80°C.At higher concentrations where gels are formed, both gellan and agarose exhibit hystersis in their tempertature transitions from gel to solution and solution to gel, the solution being of large molecular aggregates. The transitions are sharp, but in both cases ther is a continous rearrangement in the structural morphology over the entire temperature range on heating, rendering the system more homogeneous prior to dissociation. In the case of gellan, however, there are two distincit phases in these structural changes—this is not true of agarose. The mean mass per unit length of the gellan fibre in the presence of 0.025MNaCl is 19 k daltons/nm at 0.7% concentration and varies with concentration to the power 0.15. The mass per unit length of the agarose fibre is much larger (ca. 110 k Daltons/nm), this difference being consistent with the difference in properties at very low concentrations. © 1994 John Wiley&So

ISSN:0006-3525    

DOI:10.1002/bip.360340309

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

年代:1994

数据来源: WILEY

摘要:

AbstractUsing internal conformational degrees of freedom for biopolymers as natural variables, and introducing a Lagrangian dynamics approach, one can simulate time‐dependent processes over a much longer time scale than in classical Newtonian molecular dynamics (MD) techniques. Two factors contribute to this: a substantial reduction in the number of degrees of freedom and a very large increase in the size of the time step. We present the Lagrangian equations of motion for repuckering transitions in model furanose (F), ribose (R), and 2′‐deoxyribose (dR) ring systems using the pseudorotation phase angle as the single dynamic variable. As in most Lagrangian analyses, the effective masses for theRanddRmodels are dependent on conformation, and we test the behavior of this variable mass (VM) model. Since the variation in effective mass is small, the VM model is compared with a simplified constant mass (CM) model, which is shown to be an excellent approximation. The equations of motion for the CM and VM models are integrated with the leapfrog and the iterative leapfrog algorithms, respectively. The Lagrangian dynamics approach reduces the number of degrees of freedom from about 40 to 1, and allows the use of time steps on the order of 20 fs, about an order of magnitude greater than is used in conventional MD simulations. © 1994 John Wiley&Son

ISSN:0006-3525    

DOI:10.1002/bip.360340310

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

年代:1994

数据来源: WILEY

摘要:

AbstractThe enthalpies of interactions of porcine arterial elastin with alkali metal and alkali earth halides and sulphates were investigated by means of flow microcalorimetry and the stoichiometry measured using radiotracer techniques. In aqueous solutions, all alkali earth halides interacted exothermically at concentrations ranging from 0.01 to 2.5M. All the alkali metal halides, particularly NaCl, exhibited complex concentration‐dependent interactions, exothermic at low concentrations and endothermic at high concentrations. Both the anion and cation contributed to the response, although the anion seemed to dominate. SO 42−interacted most strongly of the anions tested. All interactions were reversible in the sense that repeat experiments gave identical results, but the enthalpy of “adsorption” was generally different from that of “desorption.” The enthalpy of interaction depended on the conformation of the elastin in a salt‐specific manner. For example, CaCl2and MgCl2interacted similarly in water but very differently in 1 : 1 water : methanol. © 1994 John

ISSN:0006-3525    

DOI:10.1002/bip.360340311

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

年代:1994

数据来源: WILEY