摘要:

AbstractThe dehydropeptide Ac‐ΔPhe‐L‐Ala‐ΔPhe‐NH‐Me, containing two dehydro‐phenylalanine (ΔPhe) residues, crystallizes from methanol/water in space group P212121, witha= 12.508 (2),b= 12.746(1) andc= 15.465(9).In the crystalline state, the peptide chain assumes a right‐handed 310‐helical conformation stabilized by two intramolecular hydrogen bonds, between the N‐terminal acetyl group and the NH of ΔPhe3, and between the CO of ΔPhe1and the NH of the C‐terminal methylamide group, respectively. The two consecutive 10‐membered rings formed by the hydrogen bonds have torsion angles quite close to the standard values for type III β‐bends. ΔPhe1is located in the (i+ 1) position of the first β‐bend, while ΔPhe2is located in the (i+ 2) position of the other β‐bend.In the crystal, the molecules are linked head to tail by intermolecular hydrogen bonds to form long helical chains. The axes of the helices are parallel to thecaxis, but neighboring helices run in antiparallel directions. This crystal packing is similar to the packing motifs frequen

ISSN:0006-3525    

DOI:10.1002/bip.360320702

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

年代:1992

数据来源: WILEY

摘要:

AbstractWe present a systematic analysis of water structure around nucleic acid bases. We have examined 28 crystal structures of oligonucleotides, and have studied the patterns of water around the four bases, guanine, cytosine, adenine, and thymine. The geometries of water positions were calculated up to 4.00 Å from base atoms. We have found conformation‐dependent differences in both the geometry and extent of hydration of the bas

ISSN:0006-3525    

DOI:10.1002/bip.360320703

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe kinetics of folding random coils of αα‐tropomyosin (Tm) subsequences to two‐chain coiled coils was studied by stopped‐flow CD. Subsequences studied were those comprising residues 11–127 (11Tm127), 142–281 (142Tm281), 1–189 (1Tm189), and 190–284 (190Tm284) of the parent 284‐residue α‐tropomyosin chain. Unlike the parent, subsequences1Tm189and11Tm127fold within the dead time of the instrument (<0.04 s). Like the parent, subsequences142Tm281and19Tm284fold in two phases. In the fast phase, 45% and 32%, respectively, of the equilibrium helical content form. In the time‐resolvable, first‐order slow phase (k−l= 2.7 s at 20°C for142Tm281andk−l= 2.0 s at 15°C for190Tm284), the remaining structure forms. Neither reduced142Tm281nor190Tm284show any dependence of the rate on concentration, so chain association occurs in the fast phase. Like the parent,142Tm281forms more helical content in the fast phase when cross‐linked at C‐190, and the remaining structure forms slowly with rate parameters similar to those of the reduced species. Comparison of the folding behavior of C‐ and N‐terminal subsequences with that of the parent protein suggests that the slow phase in the parent is caused by a folding bottleneck somewhere nearer the C‐terminus. However, rapid association and partial folding near the N‐terminus is not necessary for prompt folding, since even190Tm284chains associate and partially fold very rapidly (<0.04 s)

ISSN:0006-3525    

DOI:10.1002/bip.360320704

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe crystal structure of a synthetic analogue of valinomycin, cyclo [‐(D‐Val‐L‐Hyi‐L‐Val‐D‐Hyi)2‐] (octa‐meso‐valinomycin) (I) (C40H68N4O12· 1.5 · C4H8O2,Mr= 937.01 + 88.10), has been determined. Crystals grown from dioxane are monoclinic, space group P21/a, with cell parametersa= 21.487(8),b= 16.836(5),c= 16.089(4) Å, β = 111.70(4), andZ= 4. The atomic coordinates for nonhydrogen atoms were refined in the anisotropic thermal motion approximation. H atom positions were included in the structure factor calculations at their geometrically expected positions. Values of the standard and weightedRfactors after refinement are 0.11 and 0.13, respectively. The conformation of the depsipeptide crystallized from dioxane is different from that crystallized from chloroform (II). The molecule adopts a rectangular shape with two type IV β–turns containing a hydrogen bond and possesses pseudorotational symmetry. The side chains are located on the molecular periphery. The orientation of the carbonyl groups of the molecule is not conducive for efficient metal‐ion coordination and in the observed conformation cannot behave as an ionophore.In the crystal the molecules form infinite chains parallel to thecaxis, and are stabilized by two intermolecular hydrogen bonds that are shorter and have better geometry than the intramolecular hydrogen bonds.A ϕ/Ψ plot for dodecadepsipeptides with a (DLLD)3sequence has well‐defined areas for Val and Hyi residues only in cases when the crystals have been grown from nonpolar or medium‐polar solvents. The Φ/Ψ plot for octadepsipeptides crystallized from chloroform (II) shows this behavior also. There also is a correlation between the polarity of the solvent from which crystals of octa‐meso‐valinomycin or valinomycin analogues with a (DLLD) sequence of configuration have been grown and the number of the intramolecular hydrogen bonds that are formed. The more polar the solvent the fewer the number of intramolecular hydrogen bonds.Empirical energy calculations on octa‐meso‐valinomycin indicate that for isolated molecules, the energy of the bracelet form (II) is 4.7 kcal/mo

ISSN:0006-3525    

DOI:10.1002/bip.360320705

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe solution conformations of three trispeptides—L,L,L‐1,3,5‐C6H3[CH2NHCOCH(X)‐NHBoc]3, X = CH3(Ala) or CH2CH (CH3)2(Leu), andL,L,L‐N{CH2CH2NHCOCH [CH2‐CH(CH3)2]NHBoc}3—have been determined from their ir and vibrational CD (VCD) spectra in the NH stretching and carbonyl stretching regions in apolar solution. The compounds containingL‐Leu are shown to occur primarily in a propeller conformation with C3symmetry that is stabilized by interchain hydrogen bonds. Through application of the coupled oscillator model of VCD, a right‐handed sense for the hydrogen‐bonded chains in the propeller is deduced, in agreement with previous empirical force field calculations. The spectra also provide evidence for interchain association between two chains, resulting in a C10‐ring. For chains not involved in interchain association, the spectra reveal the presence of C7‐rings within a chain. The trispeptide containingL‐Ala is found to occur p

ISSN:0006-3525    

DOI:10.1002/bip.360320706

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe TT mismatch region in duplex d(CGCGATTCGCG) was studied using a 500‐ps molecular dynamics (MD) simulation in water, and a series of 1‐ps MD simulations and energy minimizations in vacuum. The DNA maintained its duplex structure, although the mismatch region showed significantly higher flexibility than the GC regions. The predominant conformation in the 500‐ps MD simulation involved an average −42° propeller twist between T6and T′6, and a −22° buckle between A5and T′7, One hydrogen bond was formed between T6and T′6, and another between T6and the O2 of T′7with both Watson‐Crick hydrogen bonds between A5and T′7remaining intact. The minimizations resulted in conformations with the equivalent hydrogen‐bonding pattern, as well as ones with “wobble pair” hydrogen bonds between T6and T′6. However, the wobble pair conformation was found to be u

ISSN:0006-3525    

DOI:10.1002/bip.360320707

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

年代:1992

数据来源: WILEY

摘要:

AbstractIn this study, we have separated the contributions of DNA and protein to the absorption and linear dichroism (LD) of each of four phages: fd, IKe, Pf1, and Pf3. We have found that the DNA packaged in each of the phages is hypochromic relative to the purified single stranded DNA, suggesting that bases are stacked in all of the phages. We have oriented the phages by flow and for the first time report the intrinsic LD from 320 to 190 nm for each of these phages. From the intrinsic LD of the phages and the isotropic absorption of the individual components, we have determined the reduced dichroism of the DNA within the phages and, subsequently, the maximum angle of inclination of the DNA bases (from the helix axis) for the packaged DNA. The maximum angles were 63° and 64° for the DNAs of class I phages fd and IKe, respectively. The angles were significantly less, 51° and 49°, for the DNAs of the class II phages Pf1 and Pf3, respectively. Thus, the two classes of phage differ in the structures of their packaged DNA, the DNA bases of the class II phages being more parallel to the long axis of the phage than are the DNA bases of the class I pha

ISSN:0006-3525    

DOI:10.1002/bip.360320708

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe interaction between poly(9‐vinyladenine) (PVAd) and poly[r (U)] was investigated by means of uv, CD,1H‐, and31P‐nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly [r(U)] by complementary hydrogen bonding. The interaction of PVAd with double‐ and triple‐stranded helices of RNA was also investigated by uv melting behavior and31P‐nmr spectroscopy. The results suggested that PVAd could not interact with the double‐stranded poly [r (A)] · poly[r(U)]but did with the tripl

ISSN:0006-3525    

DOI:10.1002/bip.360320709

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe crystal structure of a synthetic depsipeptide ionophore hexadecaisoleucinomycin, cyclo[‐(D‐Ile‐L‐Lac‐L‐Ile‐D‐Hyi)4‐] (C80H136N8O24), has been determined by single crystal x‐ray diffraction techniques. The crystals are orthorhombic, space group P212121, number of molecules per unit cellz= 4, and cell parametersa= 11.195,b= 17.853,c= 54.835 Å. The values of the standard (R) and weighted (Rw) discrepancy factors after refinement are 0.122 and 0.135, respectively. The structure is characterized by an elongated bracelet form with a twofold axis of pseudosymmetry. It is stabilized by eight intramolecular 4 → 1 hydrogen bonds between the amide CO and NH groups. The ester carbonyls are directed toward the inside of the molecule, their oxygen atoms forming an ellipsoidal internal cavity. The side chains are located on the molecular periphery. The conformational states of hexadecaisoleucinomycin in solution are discussed in the

ISSN:0006-3525    

DOI:10.1002/bip.360320710

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

年代:1992

数据来源: WILEY

摘要:

AbstractScaled quantum mechanical force fields have been calculated using the 4‐31G basis fortransand cis conformers of both isolated and water‐solvated N‐methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between thetransandcisconformers. This is also true of a single set of scale factors fortransandcisNMA in water. The total standard deviation between measured and calculated frequencies fortransNMA in both isolated and solvated states is 6 cm−1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA ·nH2O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water‐solvated or otherwise hydrogen‐bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen‐bonded to water, using frequencies measured from water‐solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen‐bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be gene

ISSN:0006-3525    

DOI:10.1002/bip.360320711

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

年代:1992

数据来源: WILEY