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1.
目的:研究支链对魔芋葡甘聚糖(KGM)分子螺旋结构的影响规律及脱支链KGM分子链构象形态.方法:采用不同外场条件下真空中分子动力学模拟的研究方法.结果:研究表明支链是维持KGM分子螺旋结构的重要基团,脱支链KGM分子链的螺旋构象是由局部的折叠片段组合而成;脱除支链后的KGM的构象更稳定,且真空中对分子链构象影响最大的非键合作用力仍是静电作用,当温度高于343K时脱支链KGM的螺旋构象消失,分子链呈现直链伸展状态.结论:分子动力学模拟方法是研究脱支链KGM螺旋结构的一种有效手段. 相似文献
2.
Iron(II) EDTA used to measure the helical twist along any DNA molecule 总被引：43，自引：0，他引：43
A new method has been devised to measure the number of base pairs per helical turn along any DNA molecule in solution. A DNA restriction fragment is adsorbed onto crystalline calcium phosphate, fragmented by reaction with iron(II) EDTA, and subjected to electrophoresis on a denaturing polyacrylamide gel. A modulated cutting pattern results, which gives directly the helical periodicity of the DNA molecule. A 150-base pair sequence directly upstream of the thymidine kinase gene of the type 1 herpes simplex virus was found to have an overall helical twist of 10.5 base pairs per turn, which is characteristic of the B conformation of DNA. In addition, purines 3' to pyrimidines showed lower than expected reactivity toward the iron cutting reagent, which is evidence for sequence-dependent variability in DNA conformation. 相似文献
3.
Alkanes adopt extended conformations in solution that minimize steric interactions and maximize surface area. Folding can reduce the amount of hydrophobic surface exposed to solvent, but sterically unfavorable gauche interactions result. However, we found that the alkyl chains of two common surfactants in aqueous solution adopt helical conformations when bound within a synthetic receptor. The receptor recognizes the helical alkane better than the extended conformation, even though 2 to 3 kilocalories per mole of strain is introduced. The proper filling of space and burial of hydrophobic surface drive the molecular recognition between the receptor and the coiled alkane. 相似文献
4.
Gelatin: a poor substrate for a mammalian collegenase 总被引：1，自引：0，他引：1
A rabbit tumor collagenase was purified more than 5000-fold. In this form it degrades native collagen in helical conformation at 37 degrees C, pH 7.6, into two fragments, but it had little capacity to cleave gelatin, an indication of the importance of higher-order structure of substrate for this enzyme in pure form. It is likely that, in vivo, enzymes other than collagenase degrade gelatin polypeptides produced by primary collagenolysis. 相似文献
5.
Metals and DNA: molecular left-handed complements 总被引：23，自引：0，他引：23
J K Barton 《Science (New York, N.Y.)》1986,233(4765):727-734
Chiral metal complexes provide unique molecular probes for DNA. Chiral reagents that "recognize" different local structures along the DNA strand have been designed by a process in which the asymmetry in shape and size of the complex is matched to that of the DNA helical groove. As a result, the chiral metal complexes provide very sensitive probes for local helical structure, both left- and right-handed. Direct coordination of chiral complexes to the DNA bases adds an element of sequence selectivity to the probe design. With a suitable reactive metal center, reagents that target chemically specific sites along the strand may be developed. One such chiral reagent, which cleaves left-handed DNA sites with photoactivation, has been useful in mapping this distinct conformation and examining its biological role. The conformation-specific molecular cleaver, much like a DNA-binding enzyme, recognizes and reacts at discrete sites along the DNA strand. These site-specific chiral metal complexes provide exciting new tools for probing the local variations in DNA structure and its role in the regulation of gene expression. 相似文献
6.
Using a domain elongation strategy, we decoupled internal motions in RNA from overall rotational diffusion. This allowed us to site-specifically resolve a manifold of motional modes in two regulatory RNAs from HIV-1 with the use of nuclear magnetic resonance spin relaxation methods. Base and sugar librations vary on a picosecond time scale and occur within helical domains that move collectively at diffusion-limited nanosecond time scales. Pivot points are short, functionally important, and highly mobile internal loops. These spontaneous changes in RNA conformation correlate quantitatively with those that follow adaptive recognition of diverse targets. Thus, ligands may stabilize existing RNA conformations rather than inducing new ones. 相似文献
7.
We studied the mechanical process of seed pods opening in Bauhinia variegate and found a chirality-creating mechanism, which turns an initially flat pod valve into a helix. We studied con?gurations of strips cut from pod valve tissue and from composite elastic materials that mimic its structure. The experiments reveal various helical con?gurations with sharp morphological transitions between them. Using the mathematical framework of "incompatible elasticity," we modeled the pod as a thin strip with a flat intrinsic metric and a saddle-like intrinsic curvature. Our theoretical analysis quantitatively predicts all observed con?gurations, thus linking the pod's microscopic structure and macroscopic conformation. We suggest that this type of incompatible strip is likely to play a role in the self-assembly of chiral macromolecules and could be used for the engineering of synthetic self-shaping devices. 相似文献
8.
The structure of the complex involving one polyadenylic acid and two polyinosinic acid chains has been determined by x-ray diffraction. The three coaxial, helical chains have conformations like conventional RNA double helices despite the absence of purine-pyrimidine pairing. Formation of hypoxanthine pairs in codon-anticodon interactions therefore requires only trivial changes in the conformation of a standard nucleotide. Evolution of the contemporary genetic code involving purine-pyrimidine complementarity from a primeval code with only adenine-hypoxanthine pairing would have been possible without major discontinuities in molecular geometry. 相似文献
9.
The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins 总被引：563，自引：0，他引：563
A 30-amino-acid segment of C/EBP, a newly discovered enhancer binding protein, shares notable sequence similarity with a segment of the cellular Myc transforming protein. Display of these respective amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The periodic array of at least four leucines was also noted in the sequences of the Fos and Jun transforming proteins, as well as that of the yeast gene regulatory protein, GCN4. The polypeptide segments containing these periodic arrays of leucine residues are proposed to exist in an alpha-helical conformation, and the leucine side chains extending from one alpha helix interdigitate with those displayed from a similar alpha helix of a second polypeptide, facilitating dimerization. This hypothetical structure is referred to as the "leucine zipper," and it may represent a characteristic property of a new category of DNA binding proteins. 相似文献
10.
Three-dimensional structure of yeast phenylalanine transfer RNA: folding of the polynucleotide chain 总被引：40，自引：0，他引：40
S H Kim G J Quigley F L Suddath A McPherson D Sneden J J Kim J Weinzierl A Rich 《Science (New York, N.Y.)》1973,179(70):285-288
At 4 A resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 A apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a secondary structure consistent with the cloverleaf conformation; however, its folding is different from that proposed in any model. The molecule is made of two double-stranded helical regions oriented at right angles to each other in the shape of an L. One end of the L has the CCA acceptor; the anticodon loop is at the other end, and the dihydrouridine and TpsiC loops form the corner. 相似文献
11.
Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA. 相似文献
12.
Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease 总被引：57，自引：0，他引：57
A Wlodawer M Miller M Jaskólski B K Sathyanarayana E Baldwin I T Weber L M Selk L Clawson J Schneider S B Kent 《Science (New York, N.Y.)》1989,245(4918):616-621
The rational design of drugs that can inhibit the action of viral proteases depends on obtaining accurate structures of these enzymes. The crystal structure of chemically synthesized HIV-1 protease has been determined at 2.8 angstrom resolution (R factor of 0.184) with the use of a model based on the Rous sarcoma virus protease structure. In this enzymatically active protein, the cysteines were replaced by alpha-amino-n-butyric acid, a nongenetically coded amino acid. This structure, in which all 99 amino acids were located, differs in several important details from that reported previously by others. The interface between the identical subunits forming the active protease dimer is composed of four well-ordered beta strands from both the amino and carboxyl termini and residues 86 to 94 have a helical conformation. The observed arrangement of the dimer interface suggests possible designs for dimerization inhibitors. 相似文献
13.
14.
Stereodynamic complexes of copper were found to undergo inversion of a helical chiral element upon oxidation or reduction. The amino acid methionine was derivatized by the attachment of two chromophores to the nitrogen atom. The resultant ligands formed stable complexes with Cu(I) and Cu(II) salts. For a derivative of a given absolute chirality, the complexes afford nearly mirror image circular dichroism spectra. The spectral changes originate from reorientation of the nitrogen-attached chromophores due to a conformation interconversion driven by the exchange of a carboxylate for a sulfide ligand. The electrically induced chirality inversion coupled with strong interactions with polarized light is unique and may lead to novel chiral molecular devices. 相似文献
15.
The molecular structure of a DNA-triostin A complex 总被引：31，自引：0，他引：31
A H Wang G Ughetto G J Quigley T Hakoshima G A van der Marel J H van Boom A Rich 《Science (New York, N.Y.)》1984,225(4667):1115-1121
The molecular structure of triostin A, a cyclic octadepsipeptide antibiotic, has been solved complexed to a DNA double helical fragment with the sequence CGTACG (C, cytosine; G, guanine; T, thymine; A, adenine). The two planar quinoxaline rings of triostin A bis intercalate on the minor groove of the DNA double helix surrounding the CG base pairs at either end. The alanine residues form hydrogen bonds to the guanines. Base stacking in the DNA is perturbed, and the major binding interaction involves a large number of van der Waals contacts between the peptides and the nucleic acid. The adenine residues in the center are in the syn conformation and are paired to thymine through Hoogsteen base pairing. 相似文献
16.
Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase 总被引：69，自引：0，他引：69
D R Knighton J H Zheng L F Ten Eyck N H Xuong S S Taylor J M Sowadski 《Science (New York, N.Y.)》1991,253(5018):414-420
The structure of a 20-amino acid peptide inhibitor bound to the catalytic subunit of cyclic AMP-dependent protein kinase, and its interactions with the enzyme, are described. The x-ray crystal structure of the complex is the basis of the analysis. The peptide inhibitor, derived from a naturally occurring heat-stable protein kinase inhibitor, contains an amphipathic helix that is followed by a turn and an extended conformation. The extended region occupies the cleft between the two lobes of the enzyme and contains a five-residue consensus recognition sequence common to all substrates and peptide inhibitors of the catalytic subunit. The helical portion of the peptide binds to a hydrophobic groove and conveys high affinity binding. Loops from both domains converge at the active site and contribute to a network of conserved residues at the sites of magnesium adenosine triphosphate binding and catalysis. Amino acids associated with peptide recognition, nonconserved, extend over a large surface area. 相似文献
17.
Ionically conducting polymers (polymer electrolytes) are under intensive investigation because they form the basis of all solid-state lithium batteries, fuel cells, and electrochromic display devices, as well as being highly novel electrolytes. Little is known about the structures of the many crystalline complexes that form between poly(ethylene oxide) and a wide range of salts. The crystal structure is reported of the archetypal polymer electrolyte poly(ethylene oxide)(3):LiCF(3)SO(3), which has been determined from powder x-ray diffraction data. The poly(ethylene oxide) (PEO) chain adopts a helical conformation parallel to the crystallographic b axis. The Li(+) cation is coordinated by five oxygen atoms-three ether oxygens and one from each of two adjacent CF(3)SO(3)(-) groups. Each CF(3)SO(3)(-) in turn bridges two Li(+) ions to form chains running parallel to and intertwined with the PEO chain. There are no interchain links between PEO chains, and the electrolyte can be regarded as an infinite columnar coordination complex. 相似文献
18.
Cornelissen JJ Donners JJ de Gelder R Graswinckel WS Metselaar GA Rowan AE Sommerdijk NA Nolte RJ 《Science (New York, N.Y.)》2001,293(5530):676-680
Polymerization of isocyanopeptides results in the formation of high molecular mass polymers that fold in a proteinlike fashion to give helical strands in which the peptide chains are arranged in beta-sheets. The beta-helical polymers retain their structure in water and unfold in a cooperative process at elevated temperatures. The peptide architecture in these polymers is a different form of the beta-helix motif found in proteins. Unlike their natural counterparts, which contain arrays of large beta-sheets stacked in a helical fashion, the isocyanopeptide polymers have a central helical core that acts as a director for the beta-sheet-like arrangement of the peptide side arms. The helical structure of these isocyanopeptide polymers has the potential to be controlled through tailoring of the side branches and the hydrogen-bonding network present in the beta-sheets. 相似文献
19.
Jaakola VP Griffith MT Hanson MA Cherezov V Chien EY Lane JR Ijzerman AP Stevens RC 《Science (New York, N.Y.)》2008,322(5905):1211-1217
The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A2A adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors. 相似文献
20.
Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp) 总被引：65，自引：0，他引：65
M Ruff S Krishnaswamy M Boeglin A Poterszman A Mitschler A Podjarny B Rees J C Thierry D Moras 《Science (New York, N.Y.)》1991,252(5013):1682-1689
The crystal structure of the binary complex tRNA(Asp)-aspartyl tRNA synthetase from yeast was solved with the use of multiple isomorphous replacement to 3 angstrom resolution. The dimeric synthetase, a member of class II aminoacyl tRNA synthetases (aaRS's) exhibits the characteristic signature motifs conserved in eight aaRS's. These three sequence motifs are contained in the catalytic site domain, built around an antiparallel beta sheet, and flanked by three alpha helices that form the pocket in which adenosine triphosphate (ATP) and the CCA end of tRNA bind. The tRNA(Asp) molecule approaches the synthetase from the variable loop side. The two major contact areas are with the acceptor end and the anticodon stem and loop. In both sites the protein interacts with the tRNA from the major groove side. The correlation between aaRS class II and the initial site of aminoacylation at 3'-OH can be explained by the structure. The molecular association leads to the following features: (i) the backbone of the GCCA single-stranded portion of the acceptor end exhibits a regular helical conformation; (ii) the loop between residues 320 and 342 in motif 2 interacts with the acceptor stem in the major groove and is in contact with the discriminator base G and the first base pair UA; and (iii) the anticodon loop undergoes a large conformational change in order to bind the protein. The conformation of the tRNA molecule in the complex is dictated more by the interaction with the protein than by its own sequence. 相似文献