Molecular mechanical studies on left- and right-handed B-DNA

Molecular mechanical simulations on base-paired deoxyhexanucleoside phosphates, (dAdT)₃ · (dAdT)₃, (dTdA)₃ · (dTdA)₃, (dGdC)₃ · (dGdC)₃, and (dCdG)₃ · (dCdG)₃, have been carried out to assess their energetic stabilities in left- and right-handed forms. These hexamers have also been simulated with alternating sugar-puckering profiles with the combinations (purine : C2′-endo–pyrimidine : C3′-endo) and (purine : C3′-endo–pyrimidine C2′-endo). The right-handed models have been found to be the energetically most stable structures and the left-handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar-phosphate backbone on the other.     

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5′-CGCGCGCGCGCG-3′)₂ dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na⁺, K⁺ and Mg^{2 +}, with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H₂O)₆]²⁺ ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H₂O)₆]²⁺ to distant phosphates, resulting in acute bending of A-RNA; tight ‘ion traps’ in Z-RNA between C-O2 and the C-O2′ atoms in GpC steps; and others.     

The transitions between left- and right-handed forms of poly(dG-dC).

The circular dichroism study of water/trifluoroethanol (TFE) solutions of poly(dG-dC) has revealed the following: The polynucleotide is present as a B form up to a TFE content of 60% (v/v) or less. Then, a cooperative transition into a left-handed Z form occurs. Within the region of 66-78% TFE, a continuous non-cooperative change is going on which can be attributed to an intrafamily transition within the family of Z forms. At last, in the interval of 80-84% TFE, a second cooperative transition, probably, Z - A is realized. Both transitions, Z - A and Z - B, show slow kinetics (10-60 min) while the direct transitions from the A to B form taking less than 10 sec. The length of cooperativity for the B - Z transition, Vo = 25 base pairs was estimated using spermine molecules. Spermine was found to induce the B to Z transition in the (dG-dC) sequences even in the absence of TFE which might be biologically interesting.     

Biologically addressable monolayer structures formed by templates of sulfur-bearing molecules.

We demonstrate that the combined application of Langmuir-Blodgett and self-assembly techniques allows the fabrication of patterns with contrasting surface properties on gold substrates. The process is monitored using fluorescence microscopy and surface plasmon spectroscopy and microscopy. These structures are suitable for the investigation of biochemical processes at surfaces and in ultrathin films. Two examples of such processes are shown. In the first example, the structures are addressed through the binding of a monoclonal antibody to a peptide. This demonstrates the formation of self-assembled monolayers by cysteine-bearing peptides on gold, and the directed binding of proteins to the structured layers. A high contrast between specific and unspecific binding of proteins is observed by the patterned presentation of antigens. Such films possess considerable potential for the design of multichannel sensor devices. In the second example, a structured phospholipid layer is produced by controlled self-assembly from vesicle solution. The structures created--areas of phospholipid bilayer, surrounded by a matrix of phospholipid monolayer--allow formation of a supported bilayer which is robust and strongly bound to the gold support, with small areas of free-standing bilayer which very closely resemble a phospholipid cell membrane.     

A designed protein with packing between left-handed and right-handed helices

A common motif in protein structures is the assembly of alpha-helices. Natural alpha-helical assemblies, such as helical bundles and coiled coils, consist of multiple right-handed alpha-helices. Here we design a protein complex containing both left-handed and right-handed helices, with peptides of D- and L-amino acids, respectively. The two peptides, D-Acid and L-Base, feature hydrophobic heptad repeats and are designed to pack against each other in a "knobs-into-holes" manner. In solution, the peptides form a stable, helical heterotetramer with tight packing in the most solvent-protected core. This motif may be useful for designing protease-resistant, helical D-peptide ligands against biological protein targets.     

Rhizobium meliloti swims by unidirectional, intermittent rotation of right-handed flagellar helices.

The 5 to 10 peritrichously inserted complex flagella of Rhizobium meliloti MVII-1 were found to form right-handed flagellar bundles. Bacteria swam at speeds up to 60 microns/s, their random three-dimensional walk consisting of straight runs and quick directional changes (turns) without the vigorous angular motion (tumbling) seen in swimming Escherichia coli cells. Observations of R. meliloti cells tethered by a single flagellar filament revealed that flagellar rotation was exclusively clockwise, interrupted by very brief stops (shorter than 0.1 s), typically every 1 to 2 s. Swimming bacteria responded to chemotactic stimuli by extending their runs, and tethered bacteria responded by prolonged intervals of clockwise rotation. Moreover, the motility tracks of a generally nonchemotactic ("smooth") mutant consisted of long runs without sharp turns, and tethered mutant cells showed continuous clockwise rotation without detectable stops. These observations suggested that the runs of swimming cells correspond to clockwise flagellar rotation, and the turns correspond to the brief rotation stops. We propose that single rotating flagella (depending on their insertion point on the rod-shaped bacterial surface) can reorient a swimming cell whenever the majority of flagellar motors stop.     

Racemic twin crystals containing left- and right-handed polyoxometalate chains induced by the asymmetric coordination of metal-organic units

Two racemic twin crystals containing left- and right-handed polyoxometalates (POMs) chains [Cu(en)₂][Cu(en)₂(H₂O)]₂ [SiW₁₁CuO₃₉] · 5H₂O (D-1 and L-1; en = ethylenediamine) have been synthesized and structurally characterized. Both chiral compounds (D-1 and L-1) were constructed from the achiral building blocks [SiW₁₁CuO₃₉]⁶⁻ and [Cu(en)₂(H₂O)_n]²⁺ (n = 0 or 1). The structural chirality is induced by the [Cu(en)₂(H₂O)_n]²⁺ units asymmetrically coordinated on the chainlike [SiW₁₁CuO₃₉]_n⁶ⁿ⁻ polyoxoanions, leading to the whole molecules crystallized in the chiral P1 space group. The chiroptical activities of D-1 and L-1 were confirmed by the solid-state circular dichroism spectroscopy. Their electrochemical and electrocatalytic properties were also investigated.     

Microtubules: dissipative structures formed by self-assembly

Microtubules are hollow fibres that form the track upon which chromosomes or proteins, such as kinesins, are transported in the cell. They are formed by the self-assembly of the protein tubulin both in vitro and in vivo. In the cell, their appearance in time and space is strictly controlled by the presence of nucleation centres. Microtubules are very dynamic structures, a property that is obtained by coupling the self-assembly process to the hydrolysis of the nucleotide, guanosine 5′-triphosphate, (GTP). After assembly, GTP is hydrolysed and guanosine 5′-diphosphate, (GDP)-microtubule structure is formed which, although intrinsically very unstable, is stabilised by a small remaining tubulin-GTP-cap at both ends. As such, the ends of microtubules can be considered as gates for entry into the polymeric state. These gates can be blocked by sub-stoichiometric amounts of drugs such as colchicine.

As biological devices, microtubules differ considerably from man-made devices: they are dynamic dissipative structures, made by spontaneous self-assembly. It has been suggested that microtubules could play a role in the conduction and dynamic storage of information. This implies the existence of different conformational states of tubulin.     

Triple helices formed by polyuridylic acid with some adenosine derivatives

We have prepared a variety of derivatives of adenosine which, at neutral pH's, carry protonated amine functions. These derivatives form stable helical structures with polyuridylic acid, but the melting points are not substantially higher than those of helical complexes formed by adenosine derivatives lacking cationic groups.     

Properties of triple helices formed by oligonucleotides containing 8-aminopurines

The synthesis of parallel hairpins carrying 8-aminopurines is described. These hairpins have a high affinity for specific polypyrimidine sequences resulting in the formation of very stable triplexes.     

ATP synthase b subunit dimerization domain: a right-handed coiled coil with offset helices

The dimerization domain of Escherichia coli ATP synthase b subunit forms an atypical parallel two-stranded coiled coil. Sequence analysis reveals an 11-residue abcdefghijk repeat characteristic of right-handed coiled coils, but no other naturally occurring parallel dimeric structure of this class has been identified. The arrangement of the helices was studied by their propensity to form interhelix disulfide linkages and analysis of the stability and shape of disulfide-linked dimers. Disulfides formed preferentially between cysteine residues in an a position of one helix and either of the adjacent h positions of the partner. Such heterodimers were far more stable to thermal denaturation than homodimers and, on the basis of gel-filtration chromatography studies, were similar in shape to both non-covalent dimers and dimers linked through flexible Gly(1-3)Cys C-terminal extensions. The results indicate a right-handed coiled-coil structure with intrinsic asymmetry, the two helices being offset rather than in register. A function for the right-handed coiled coil in rotational catalysis is proposed.     

Properties of triple helices formed by parallel-stranded hairpins containing 8-aminopurines

Parallel-stranded hairpins with a polypyrimidine sequence linked to a complementary purine carrying 8-aminopurines such as 8-aminoadenine, 8-aminoguanine and 8-aminohypoxanthine bind polypyrimidine sequences complementary (in an antiparallel sense) to the purine part by a triple helix. The relative stabilities of triplexes were assessed by UV-absorption melting experiments as a function of pH and salt concentration. Hairpins carrying 8-aminopurines give very stable triple helical structures even at neutral pH, as confirmed by gel-shift experiments, circular dichroism and nuclear magnetic resonance spectroscopy. The modified hairpins may be redesigned to cope with small interruptions in the polypyrimidine target sequence.     

Circular dichroism of helices formed by purine monomers with pyrimidine polynucleotides

The CD spectra of a number of helical complexes formed by purine monomers and complementary pyrimidine polyribonucleotides have been observed over the range 200–400 nm. Each of these spectra is quite similar to that of the corresponding polymer–polymer helix. The spectra are evidently determined by the geometry of the asymmetric array of bases, largely unperturbed by the ribose–phosphate backbone. The helix structure (A-form), on the other hand, is determined by the backbone of the pyrimidine homopolymer. Data on the monomer–polymer complexes support the conclusion that the CD spectra of ribohomopolymer helices depend primarily on interastrand interactions of the same transition within a given base and are relatively unaffected by transitions of the complementary base.     

Triple helices formed by polyuridylic acid with some amino deoxyadenosine derivatives

Summary The stability of helical structures formed by polyuridylic acid with nucleosides and nucleotides derived from adenosine is not significantly affected by replacing hydroxyl groups by hydrogen, amino, or azido functions. Stability is affected by the position of the phosphate group.     

Polyproline helices in protein structures: A statistical survey

A statistical survey of polyproline II (PPII) helices extracted from protein crystal structures is here reported. The average hydrophobicity of these helices is intermediate between those displayed by beta-strands and coil regions and is similar to that of alpha-helices. PPII helices with amphipathic properties have been identified and classified. Amino acid propensities for PPII helices derived in this study differ significantly from those previously reported. They show a little albeit significant correlation with propensities for alpha-helices whereas they are fully non-correlated to propensities for beta-sheets. Finally, PPII propensities have been correlated with amino acid frequencies in structural proteins, such as collagen and extensins.     

基于融合双亲短肽提高葡萄糖氧化酶的热稳定性

葡萄糖氧化酶(Glucose oxidase,简称GOD)可氧化葡萄糖生产葡萄糖酸及其衍生物,在新型无抗饲料添加剂的开发中具有良好的应用潜力,但其生产加工过程中尚存在热稳定差的瓶颈问题。本研究采用融合双亲短肽技术提高葡萄糖氧化酶的热稳定性,分别选取8种不同氨基酸长度、不同Linker连接的双亲短肽(Self-assembling peptides,SAPs)融合至黑曲霉来源的葡萄糖氧化酶的N端,构建了8种融合型酶SAP1-GS-GOD、SAP1-PT-GOD、SAP2-PT-GOD、SAP3-PT-GOD、SAP4-PT-GOD、SAP5-PT-GOD、SAP6-PT-GOD、SAP7-PT-GOD,并在毕赤酵母GS115中异源表达。获得的连接PT Linker的融合酶在60℃下孵育60 min后的相对酶活均高于初始酶。其中,融合酶SAP5-PT-GOD在60℃下孵育30 min的相对酶活为67%,是相同处理条件下初始酶相对酶活的10.9倍。同时,融合酶SAP1-PT-GOD、SAP2-PT-GOD、SAP3-PT-GOD、SAP5-PT-GOD的K_(cat)/K_m值较初始酶均有进一步的提高。研究表明,在葡萄糖氧化酶的N端融合以PT为Linker的目标双亲短肽能有效提高葡萄糖氧化酶的热稳定性,通过对融合酶分子内作用力进行分析,酶分子内氢键的增加对融合酶热稳定性的提高效果最为显著。上述研究获得的热稳定性提高的融合葡萄糖氧化酶及其效果机制分析对提高酶在加工和应用过程中的活性具有重要的研究意义和应用价值。     

Omega amino acids in peptide design: incorporation into helices

Incorporation of easily available achiral ω-amino acid residues into an oligopeptide results in substitution of amide bonds by polymethylene units of an aliphatic chain, thereby providing a convenient strategy for constructing a peptidomimetic. The central Gly-Gly segment of the helical octapeptide Boc-Leu-Aib-Val-Gly-Gly-Leu-Aib-Val-Ome(1) has been replaced by δ-amino-valeric acid (δ-Ava) residue in the newly designed peptide Boc-Leu-Aib-Val-δ-Ava-Leu-Aib-Val-OMe(2). ¹H-nmr results clearly suggest that in the apolar solvent CDCl₃, the δ-Ava residue is accommodated into a folded helical conformation, stabilized by successive hydrogen bonds involving the NH groups of Val(3), δ-Ava(4), and Leu(5). The δ-Ava residue must adopt a gauche-gauche-trans-gauche-gauche conformation along the central polymethylene unit of the aliphatic segment, a feature seen in an energy-minimized model conformation based on nmr parameters. The absence of hydrogen bonding functionalities, however, limits the elongation of the helix. In fact, in CDCl₃, the folded conformation consists of an N-terminal helix spanning residues 1–4, followed by a Type II β-turn at residues 5 and 6, whereas in strongly solvating media like (CD₃)₂SO, the unfolding of the N-terminal helix results in β-turn conformations at Leu(1)-Aib(2). The Type II β-turn at the Leu(5)-Aib(6) segment remains intact even in (CD₃)₂SO. CD comparisons of peptides 1 and 2 reveal a “nonhelical” spectrum for 2 in 2,2,2-trifluoroethanol. © 1996 John Wiley & Sons, Inc.     

Characteristics of Z-DNA helices formed by imperfect (purine-pyrimidine) sequences in plasmids

The capacities of three synthetic sequences to adopt left-handed helices were evaluated in recombinant plasmids. The sequences consisted of very short runs of (CG)n (n = 2-4) interspersed with runs of alternating A.T base pairs and/or with regions of non-alternating base pairs. The plasmids were studied by two-dimensional gel electrophoresis to determine the natures of the conformational transitions and their free energies of formation. These results coupled with analyses with chemical (diethyl pyrocarbonate, osmium tetroxide, and bromoacetaldehyde) and enzymatic (S1 nuclease, T7 gene 3 product, and MHhaI) probes indicated that the entire sequence was adopting a left-handed helix in each case. In one of these sequences, Z-DNA formation necessitated the retention of the anti conformation of one of the guanines in a region of non-alternation. In a sequence which contains out-of-phase regions of alternation, our results indicate the formation of a separate left-handed helix in the central (CG)2 region, thus forming two Z-Z junctions. In summary, we conclude that only very short regions of alternating CG are necessary to effect the B to Z transition and that this conformational change can be transmitted through non-alternating regions. A set of empirical rules governing the characteristics of the B to Z transition and the types of left-handed helices in supercoiled plasmids was derived from studies on a systematic series of 17 plasmids.