摘要:

AbstractThe calculated spectrum of longitudinal compressional waves on DNA polymer chains is shown to be in excellent agreement with recently performed inelastic neutron scattering measurements in hydrated, oriented DNA crystals. This opens up a previously unexplored frequency regime of DNA science and establishes the validity of the phonon extended wave description of DNA elementary excitations in this region.

ISSN:0006-3525    

DOI:10.1002/bip.360280702

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

年代:1989

数据来源: WILEY

摘要:

AbstractA build‐up technique has been devised that permits prediction of DNA structure form sequence. No experimental information is employed other than the force field parameters. This strategy for dealing with the multiple minimum problem requires a supercomputer to make the necessary global searches. The number of energy minimization trials that were made for each of the 16 deoxydinucleoside monophosphate conformational building blocks of DNA was 1944. As a test case, the minimum energy conformations of d(GpC) and d(CpG) to 5.5 kcal/mole were then combined to generate energy‐minimized structures for d(CpGpC). The number of trials that were made for d(CpGpC) was 3752. Minima for this single‐stranded trimer to 15 kcal/mole were then employed to search for minimum energy conformations of the duplex d(CpGpC) · d(GpCpG). The number of starting conformations that were utilized at this stage was 1514. The lowest energy duplex had a Z‐II‐DNA conformation, followed by a B‐DNA form at 1.2 kcal/mole. The A‐ and Z‐I‐forms as well as many novel Watson–Crick base‐paired structures were found at higher energy. Finally, energy‐minimized structures of d(CG)6in Z‐II and B‐DNA conformations were computed using torsion angles from the an

ISSN:0006-3525    

DOI:10.1002/bip.360280703

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

年代:1989

数据来源: WILEY

摘要:

AbstractWe have studied, by conformational analysis, the sequence dependence of DNA conformational transition between B‐ and A‐forms. We have considered intramolecular interactions between base pairs, without backbone, to examine their role in the conformational transition between B‐ and A‐forms, and found that base pairs themselves usually have intrinsic conformational preferences for the B‐ or A‐form. Calculation of all ten possible base steps shows that the base combinations, CC (or GG), GC, AT, and TA, have tendencies to assume the A‐conformation. Results show that it is particularly easy to slide along the long axis of the base pair for these steps, with AT and CC showing especially flat energies. These calculations show that a preference for the B‐ or A‐conformation depends on the electrostatic energy parameters, in particular, on dielectric and shielding constants; the A‐conformations are mainly stabilized by electrostatic interactions between favorably juxtaposed atomic charges on base pairs; however, the B‐conformation generally has more favorable van der Waals interactions than the A‐form. These sequence‐dependent conformational preference and environmental effects agree roughly with experimental observations, suggesting that the origin of the conformational polymorphism is attributable to the intrinsic conformational

ISSN:0006-3525    

DOI:10.1002/bip.360280704

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

年代:1989

数据来源: WILEY

摘要:

AbstractCyclic octapeptides having alternating Sar and hydrophobic amino acid sequences, such as cyclo[Lys(Z)‐Sar‐Leu‐Sar‐Leu‐Sar‐Leu‐Sar] (C8KL), cyclo[Glu(OMe)‐Sar‐Lys(Z)‐Sar‐Leu‐Sar‐Leu‐Sar](C8KE), and cyclo[Lys(Suc)‐Sar‐Leu‐Sar‐Leu‐Sar‐Leu‐Sar][C8K(Suc)L, Suc represents succinic acid], were synthesized. These cyclic octapeptides formed a complex selectively with Ca2+. Upon complexation,transpeptide bonds of Sar residues were isomerized tocispeptide bonds. C8KL and C8KE showed very similar characteristics of Ca2+binding, extraction of Ca2‐from an aqueous solution to a chloroform solution, and Ca2+transport through a liquid chloroform membrane. C8KL transported Ca2+across the lipid bilayer membrane above the phase‐transition temperature, while C8KE and C8K(Suc)L did not. Therefore, the transport of Ca2+through the lipid bilayer membrane is very sensitive

ISSN:0006-3525    

DOI:10.1002/bip.360280705

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

年代:1989

数据来源: WILEY

摘要:

AbstractEffects of the nature and orientation of a side chain in cyclic octapeptides on Ca2+transport were examined by using cyclo[L‐Lys(Z)‐Sar‐LLeu‐Sar]2(C8‐L), cyclo[L‐Lys(Z)‐Sar]4(C8KS), and their diastereomer cyclic octapeptides, cyclo[L‐Lys(Z)‐Sar‐D‐Leu‐Sar]2(C8‐D) and cyclo[L‐Lys(Z)‐Sar‐D‐Lys(Z)‐Sar]2(C8Kk). All these cyclic octapeptides were found to take a single conformation in CDCl3,and the conformation was C2‐symmetric for C8‐L and C8‐D, and C4‐symmetric for C8KS and C8Kk. They formed a complex with Ca2+. Upon complexation, C8KS accompanied isomerization of peptide bonds, but C8‐D retained the arrangement of peptide bonds. The amount of Ca2+extracted from an aqueous solution to a chloroform solution by allLcyclic octapeptide C8‐L or C8KS was about twice that of Na+, but 6 ∼ 8‐fold smaller than that by C8‐D or C8Kk includingDunits. These cyclic octapeptides were capable of transporting Ca2+through a lipid membrane above the phase transition temperature, and the transport

ISSN:0006-3525    

DOI:10.1002/bip.360280706

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe synthetic peptide Gly‐L‐Ala‐L‐Phe (C14H19N3O4· 2H2O; GAF) crystallizes in the monoclinic space group P21, witha= 5.879(1),b= 7.966(1),c= 17.754(2) Å, β = 95.14(2)°,Dx= 1.321 g cm−3, andZ= 2. The crystal structure was solved by direct methods using the program SHELXS‐86 and refined to anRvalue of 0.031 for 1425 reflections (>3σ). The tripeptide exists as a zwitterion in the crystal and assumes a near α‐helical backbone conformation with the following torsion angles: ψ1= −147.8°; ϕ2, ψ2= −71.2°, −33.4°; ϕ3ψ3= −78.3°, −43.3°. In this structure, one water molecule bridges the COO−and NH3+terminii to complete a turn of an α‐helix and another water molecule participates in head‐to‐tail intermolecular hydrogen bonding, so that the end result is a column of molecules that looks like an α‐helix. Thus, the two water molecules of crystallization play a major role in stabilizing the near α‐helical conformation of each tripeptide molecule and in elongating the helix throughout the crystal. An analysis of all protein sequences around regions containing a GAF fragment by Chou‐Fasman's secondary structure prediction method showed that those regions are likely to assume an α‐helical conformation with twice the probability they are likely to adopt a β‐sheet conformation. It is conceivable that a GAF fragment may be a good part of the nucleation site for forming α‐helical fragments in a polypeptide, with the aqueous me

ISSN:0006-3525    

DOI:10.1002/bip.360280707

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe solution conformation of [D‐Ala2]‐leucine enkephalin in its zwitterionic form in DMSO‐d6has been monitored by one‐ and two‐dimensional proton magnetic resonance spectroscopy at 500 MHz. The resonances from the labile amide protons and the nonlabile protons have been assigned from the shift correlated spectroscopy. The chemical shift of the amide and C‐α protons are found to vary with temperature but in opposite directions, except the C‐α proton of the terminal tyrosine residue. This behaviour has been explained by the shifting of equilibrium between the zwitterionic and neutral forms of the [D‐Ala2]‐leucine enkephalin and probably conformational changes accompanying temperature variation. The low values of the temperature coefficients of leucine and glycine amide protons indicate that these protons are either intramolecularly hydrogen bonded or solvent shielded. The observation of sequential cross peaks in the nuclear Overhauser effect spectra obtained at various mixing times, τm(200–900 ms), indicate an extended backbone, which does not corroborate with the presence of a folded structure, i.e., β‐bend type structure. The estimate of interproton distances in conjunction with the low values of temperature coefficients of the leucine and glycine amide protons and vicinal coupling constants3J HN‐C αHhave been rationalized by the predominance of two γ‐bends in the backbone conformation of [D‐Ala2]‐leucine enkephalin. The γ‐bend around theD‐Ala residue has Φ = 80° and ψ = 270°, whil

ISSN:0006-3525    

DOI:10.1002/bip.360280708

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe peptide N‐Boc‐L‐Gly‐dehydro‐Phe‐NHCH3was synthesized by the combination of N‐Boc‐L‐Gly‐dehydro‐Phe azlactone and methylamine. The peptide crystallizes in orthorhombic space group P212121witha= 5.679(2) Å,b= 16.423(9) Å,c= 19.198(10) Å,V= 1791(2) Å3,Z= 4, dm = 1.212(5) Mg m−3, dc = 1.237(1) Mg m−3. The structure was determined by direct methods using SHELXS 86. The structure was refined by full‐matrix least squares procedure to anRvalue of 0.049 for 1509 observed reflections. The molecular dimensions are, in general, in good agreement with the standard values. The bond angle Cα–Cβ–Cγin the dehydro‐Phe residue is 133.6(5)°. The peptide backbone torsion angles are θ1= −171.4(4)°, ω0= 178.2(4)°, ϕ1= −57.2(6)°, ψ1= 141.2(4)°, ω1= −174.4(4)°, ϕ2= 71.5(6)°, ψ2= 7.2(6)°, and ω2= −179.8(5)°. These values show that the backbone adopts the β‐bend type II conformation. The Boc group has atrans‐transconformation. The side‐chain torsion angles in dehydro‐Phe are χ2= 1.6(9)°, χ 22,1= 0.5(9)°, and χ 22,2= 179.8(6)°. The plane ofC 2α–C 2β–C 2γis rotated with respect to the plane of the phenyl ring at 0.5(6)°, which indicates that the atoms of the side chain of the dehydro‐Phe residue are essentially coplanar. As a result of the β‐bend in the structure, an intramolecular hydrogen bond is formed between the oxygen of theith residue and the NH of the (i+ 3)th residue at a distance of 2.940(

ISSN:0006-3525    

DOI:10.1002/bip.360280709

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe proteodermatan sulfate (PDS) of bovine skin is a low molecular weight proteoglycan with a molecular structure consisting of a protein chain and a sulfated polysaccharide chain covalently linked at the 4‐serine of the protein. Static and dynamic laser light scattering methods have been used to determine the weight‐average molecular weight,Mw,z‐average radius of gyration,R g z′, andz‐average translational diffusion coefficient,Dt,z°, of bovine skin PDS. We have also characterized the two components of PDS, i.e., the protein core and the dermatan sulfate (DS) chain. (The latter contained an N‐terminal‐linked penta‐ or tetrapeptide.) Interpretation of the PDS data is complicated by the block copolymer nature of its structure. When appropriate corrections are made, our results indicate thatMwfor PDS monomer is 62,000 when dissolved in 4Mguanidine hydrochloride (GdnHCl), and increases to 610,000 in 0.15MNaCl.Mwfor the core protein in 4MGdnHCl is 39,000, and this also increases substantially to 650,000 in 0.15MNaCl. In contrast,Mwfor the DS chain is 24,000 in 0.15MNaCl, indicating that there is minimal self‐association of DS in 0.15MNaCl. Thus we conclude that the self‐association of PDS involves the protein core. Comparison ofR g zandRh, the average hydrodynamic radius, suggests that trace amounts of aggregation persist for the PDS and its core protein even in 4MGdnHCl. This conclusion is supported by evaluation of the second moments of the dynamic light scattering correlation function. Comparisons of the observedDt,z° for PDS with predicted values using hydrodynamic theory are consistent with a “lollipop

ISSN:0006-3525    

DOI:10.1002/bip.360280710

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

年代:1989

数据来源: WILEY

摘要:

AbstractThe present paper is a systematic first approach to the problem of solvation thermodynamics of biomolecules.Most previous approaches have been only crude estimates of solvent contributions, and have simply assessed solvation free energy as proportional to surface areas.Here we estimate the various contributions and divide them into (a) hard‐core interactions dependent upon the entire volume of solute and (b) the remainder of interactions manifested through surfaces, such as van der Waals, charge—charge, or hydrogen bonds. We have estimated the work to create a cavity with scaled‐particle theory (SPT), the van der Waals interactions on the surface, and hydrogen bonds between the surface and the solvent. The conclusion here is that this latter term is the largest component of the solvation free energy of proteins.From estimates on nine diverse proteins, it is clear that the larger the protein, the more dominant is the hydrogen‐bond term. In the next paper, we indicate that correlations between hydrogen‐bonding groups on the surfaces could increase the magnitude of the hydrogen‐bond c

ISSN:0006-3525    

DOI:10.1002/bip.360280711

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

年代:1989

数据来源: WILEY