金属硫蛋白及其结构域突变体的紫外和圆二色光谱学研究

采用 p GEX- 4T- 1融合表达载体高效表达所得的金属硫蛋白及其结构域突变体 ,包括 α结构域 ,β结构域 ,α- KKS- α和 β- KKS- β( KKS为金属硫蛋白结构域之间的天然连接区氨基酸 ) ,经纯化和纯度鉴定后 ,利用紫外和圆二色光谱进行结构研究 .在脱金属的上述蛋白中 ,固定 p H为中性 ,改变加入 Cd2 + 的比例 ,或固定 Cd2 + 浓度 ,逐渐调节 p H至中性 ,观察紫外和圆二色光谱中镉硫金属簇吸收峰的形成 .研究结果表明 :镉硫金属簇的形成依赖于加入金属的比例和 p H值 ,所有蛋白均于p H3.1 5以上开始形成明显的吸收峰 .紫外图谱中的吸收峰位于 2 54nm附近 ,但在圆二色图谱中不同蛋白形成的峰的位置不同 ,MT,α结构域和 α- KKS- α在 2 2 5nm和 2 58nm处有吸收 ,β结构域在 2 60 nm处有吸收 ,而 β- KKS- β在 2 4 5nm处有吸收 ;向 α结构域 ,β结构域 ,MT,α- KKS- α和 β-KKS- β中分别加入 4eq,3eq,7eq,8eq和 6eq( eq:equivalent,当量 )的 Cd2 +时 ,吸收峰可达到最大值 .同时发现 α结构域的吸收峰强于 β结构域 ,而且双结构域突变体的镉硫金属簇则明显强于相应的单结构域突变体 ,这表明吸收峰的强弱与金属结合力的大小相关 ,而且结构域之间存在相互作用 ,从而影响与金属的结合 .     

Domain 3 of non-structural protein 5A from hepatitis C virus is natively unfolded

Hepatitis C virus (HCV) non-structural protein 5A (NS5A) is involved both in the viral replication and particle production. Its third domain (NS5A-D3), although not absolutely required for replication, is a key determinant for the production and assembly of novel HCV particles. As a prerequisite to elucidate the precise functions of this domain, we report here the first molecular characterization of purified recombinant HCV NS5A-D3. Sequence analysis indicates that NS5A-D3 is mostly unstructured but that short structural elements may exist at its N-terminus. Gel filtration chromatography, circular dichroism and finally NMR spectroscopy all point out the natively unfolded nature of purified recombinant NS5A-D3. This lack of stable folding is thought to be essential for primary interactions of NS5A-D3 domain with other viral or host proteins, which could stabilize some specific conformations conferring new functional features.     

Circular dichroism investigation of the effect of plasmid DNA structure on retention in histidine chromatography

The effect of temperature-induced changes in secondary and tertiary structures of plasmid DNA (pDNA) and on the retention behaviour of open circular (oc) and supercoiled (sc) isoforms in histidine-agarose chromatography was investigated by Circular dichroism (CD) spectroscopy. Chromatographic experiments performed with three plasmids (2.7, 6.1 and 7.4 kbp) and with a decreasing ammonium sulphate gradient (2.3--2.0 M) showed that the retention of sc pDNA increased as temperature decreased from 24 to 5 °C. Such behaviour was attributed to the temperature-induced removal of negative superhelical turns in sc pDNA which is accompanied by a decrease in the number of dissociated base pairs responsible for interaction with the histidine ligands. CD spectroscopy showed that temperature has an important effect on plasmid secondary structure if adenine-rich inserts are present in the plasmid structure. Chromatographic experiments also suggested that base composition could also be responsible for the induction of specific interactions with histidine ligands.     

Secondary structure analyses of protein films on gold surfaces by circular dichroism

In order to analyze the secondary structures of protein molecules adsorbed on gold surfaces, circular dichroism (CD) spectra were measured and the secondary structure contents of protein ultra-thin films were estimated quantitatively. A disulfide group was introduced to cytochrome b(562) (cyt.b562), which is a water-soluble b-type heme protein. The cyt.b562 molecules self-assembled to form an ultra-thin protein film both on a gold substrate modified with 2,2(')-dithiodiacetic acid and on a bare gold surface. CD measurements were carried out both in solution and in air, and these results were compared. The protein denaturation was partially prevented, not only in solution but also in air, by both the modification of the substrate and the introduction of the anchor group to the protein molecule. The secondary structure contents of ultra-thin protein films on flat gold surfaces were observed for the first time both in solution and in air by CD spectra.     

The biological activity of Humanin analogs correlates with structure stabilities in solution

A single mutation has resulted in large differences in neuroprotective activity of a 24 amino acid Humanin (HN). A mutation of Ser7Ala (S7A-HN) resulted in loss of activity, while a mutation of Ser14Gly (S14G-HN) resulted in about 1000-fold increase. The mechanism of the effects conferred by these mutations have been totally unclear, although our recent structure analysis suggested a possibility of the effect of mutation on the structure stability. Here, we have studied the effects of buffer and temperature on the structure of these three HN peptides. These peptides showed a similar disordered structure at 10 °C in 10 mM phosphate, pH 6.0. They were also similar in phosphate-buffered saline (PBS) as long as the temperature was kept low at 10 °C. However, a large difference was observed in both phosphate buffer and PBS between the peptides, when the temperature was raised to a physiological temperature of 37 °C. While S14G-HN showed small changes in both solutions at 37 °C, the less active HN and inactive S7A-HN showed much larger changes under the identical conditions. In addition, it appeared that structure change at 37 °C was faster for S7A-HN than HN. These results show that the structure stability at 37 °C increases in the order of S7A-HN, HN and S14G-HN, in correlation with their neuroprotective activities.     

Protein secondary structure from circular dichroism spectra

Circular dichroism spectra of proteins are extremely sensitive to secondary structure. Nevertheless, circular dichroism spectra should not be analyzed for protein secondary structure unless they are measured to at least 184 nm. Even if all the various types ofβ-turns are lumped together, there are at least 5 different types of secondary structure in a protein (α-helix, antiparallelβ-sheet, parallelβ-sheet,β-turn, and other structures not included in the first 4 categories). It is not possible to solve for these 5 parameters unless there are 5 equations. Singular value decomposition can be used to show that circular dichroism spectra of proteins measured to 200 nm contain only 2 pieces of information, while spectra measured to 190 nm contain about 4. Adding the constraint that the sum of secondary structures must equal 1 provides another piece of information, but even with this constraint, spectra measured to 190 nm simply do not analyze well for the 5 unknowns in secondary structure. Spectra measured to 184 nm do contain 5 pieces of information and we have used such spectra successfully to analyze a variety of proteins for their component secondary structures.     

A sensitive method based on fluorescence-detected circular dichroism for protein local structure analysis

We report an improved fluorescence-detected circular dichroism (FDCD)-based analytical method that is useful for probing protein three-dimensional structures. The method uses a novel FDCD device with an ellipsoidal mirror that functions on a standard circular dichroism (CD) spectrometer and eliminates all artifacts. Our experiments demonstrated three important findings. First, the method is applicable to any proteins either by using intrinsic fluorescence derived from tryptophan residues or by introducing a fluorescent label onto nonfluorescent proteins. Second, by using intrinsic fluorescence, FDCD spectroscopy can detect a structural change in the tertiary structure of metmyoglobin due to stepwise denaturation on a change in pH. Such changes could not be detected by conventional CD spectroscopy. Third, based on the typical advantages of fluorescence-based analyses, FDCD measurements enable observation of only the target proteins in a solution even in the presence of other peptides. Using our ellipsoidal mirror FDCD device, we could observe structural changes of fluorescently labeled calmodulin on binding with Ca²⁺ and/or interacting with binding peptides. Because FDCD appears to reflect the protein’s local structure around the fluorophore, it may provide a useful means for “pinpoint analysis” of protein structures.     

The role of prion peptide structure and aggregation in toxicity and membrane binding

Prion diseases are neurodegenerative disorders associated with a conformational change in the normal cellular isoform of the prion protein, PrP(C), to an abnormal scrapie isoform, PrP(SC). Unlike the alpha-helical PrP(C), the protease-resistant core of PrP(SC) is predominantly beta-sheet and possesses a tendency to polymerize into amyloid fibrils. We performed experiments with two synthetic human prion peptides, PrP(106-126) and PrP(127-147), to determine how peptide structure affects neurotoxicity and protein-membrane interactions. Peptide solutions possessing beta-sheet and amyloid structures were neurotoxic to PC12 cells in vitro and bound with measurable affinities to cholesterol-rich phospholipid membranes at ambient conditions, but peptide solutions lacking stable beta-sheet structures and amyloid content were nontoxic and possessed less than one tenth of the binding affinities of the amyloid-containing peptides. Regardless of structure, the peptide binding affinities to cholesterol-depleted membranes were greatly reduced. These results suggest that the beta-sheet and amyloid structures of the prion peptides give rise to their toxicity and membrane binding affinities and that membrane binding affinity, especially in cholesterol-rich environments, may be related to toxicity. Our results may have significance in understanding the role of the fibrillogenic cerebral deposits associated with some of the prion diseases in neurodegeneration and may have implications for other amyloidoses.     

Terbium(3 +) as a probe of nucleic acids structure. Does it alter the DNA conformation in solution?

At low ionic strength, Tb³⁺ binding strongly alters the secondary structure of DNA. Circular dichroism and electro-optical techniques are more sensitive than fluorescence to study these alterations in double-stranded DNA, at low Tb³⁺/DNA phosphate ($\text{I}\text{P}$) ratios. Both techniques yield the following conclusion: as $\text{I}\text{P}$ is increased, native and sonicated DNA undergo a transition from the B- to ψ-form, the latter being a compact structure characteristic of aggregated DNA. Our study of alkylated DNA establishes that the accessibility of N-7 guanine to Tb³⁺ is clearly required for structural alterations in an aggregated state to occur. The chelation of the phosphate group and of the N-7 guanine by Tb³⁺ simultaneously alters the geometry of the sugar-phosphate backbone and the stacking interaction between the bases in double-stranded DNA.     

Potential application of the Clostridium tyrobutyricum flagellin as substrate for proteinase detection

Denatured Clostridium tyrobutyricum flagellin is rapidly degraded during incubation with commercial preparations of -amylase, dextranase, endo-1,3,(4)--glucanase, chitinase and hyaluronidase indicating the presence of contaminating proteinases. Electrophoretic and solid-phase assay, with bovine serum albumin as substrate, revealed proteolytic activities in these preparations. In comparison to bovine serum albumin, the damaging of flagellin by proteolysis indicates that this protein would be useful as a general substrate in proteinase detection. © Rapid Science Ltd. 1998     

Nascent structure in the kinase anchoring domain of microtubule-associated protein 2

Biological processes are often viewed as highly ordered interactions between well-folded protein domains. The specific interactions exhibited by certain highly abundant neuronal proteins such as microtubule-associated protein 2 (MAP2) and tau stand in stark contrast because these proteins do not show evidence of structure by standard biophysical assays, yet they do bind to specific targets. It is conceivable that there are regions of MAP2 and tau with propensity to form structural domains upon binding a target. To search for evidence of such regions, limited proteolysis experiments were carried out on MAP2c, the smallest MAP2 isoform. Increased protease resistance was observed around the binding site for the RII subunit of cAMP-dependent protein kinase. Protein constructs spanning this region were produced based on the long-lived tryptic fragments Ser44-Arg93 and Ile94-Arg182, and were probed for structure using spectroscopic methods. The results support the existence of regions of nascent structure in the N-terminal region of MAP2c, which are believed to contribute to its regulatory function.     

The dynamic structure of Rab35 is stabilized in the presence of GTP under physiological conditions

Rab proteins, a family of small guanosine triphosphatases, play key roles in intracellular membrane trafficking and the regulation of various cellular processes. As a Rab isoform, Rab35 is crucial for recycling endosome trafficking, cytokinesis and neurite outgrowth. In this report, we analyzed dynamic structural changes and physicochemical features of Rab35 in response to different external conditions, including temperature, pH, salt concentration and guanosine triphosphate (GTP), by circular dichroism (CD) spectroscopy. CD spectra revealed that the α-helix content of Rab35 varies under different conditions considerably. The addition of GTP increases the α-helix content of Rab35 when the temperature, pH and salt concentration match physiological conditions. The results suggest that the external environment affects the secondary structure of Rab35. In particular, the presence of GTP stabilized the α-helices of Rab35 under physiological conditions. These structural changes may translate to changes in Rab35 function and relate to its role in membrane trafficking.     

Solution structure of amphibian tachykinin Uperolein bound to DPC micelles

Uperolein, a physalaemin-like endecapeptide, has been shown to be selective for Neurokinin 1 receptor. As a first step towards understanding the structure-activity relationship, we report the membrane-induced structure of Uperolein with the aid of circular dichroism and 2D (1)H NMR spectroscopy. Sequence-specific resonance assignments of protons have been made using correlation spectroscopy (TOCSY, DQF-COSY) and NOESY spectroscopy. The interproton distance constraints and dihedral angle constraints have been utilized to generate a family of structures using torsion angle molecular dynamics within program DYANA. The conformational range of the peptide revealed by NMR and CD studies has been analysed in terms of characteristic secondary features. Analysis of NMR data indicates that the global fold of Uperolein can be explained in terms of equilibrium between 3(10)-helix and alpha-helix from residues 5 to 11. An extended highly flexible N-terminus displays some degree of order and a possible turn structure. A comparison between the structures of Uperolein and Substance P, a prototype and endogenous Neurokinin 1 receptor agonist, indicates several common features in the distribution of hydrophobic and hydrophilic residues. Both the peptides show an amphiphilic character towards the middle region. The similarities suggest that the molecules interact with the receptor in an analogous manner.     

天花粉蛋白小结构域N端TCS182—200同源片段的构象研究

以天花粉蛋白小结构域Ｎ端ＴＣＳ１８２－２００同源片段序列为基础,设计Ｔ１４,Ｔ１８和ＴＤＫ３个模型肽。本文分析了模型肽的肽链柔性和侧链两亲性,预测二级结构形成势,并通过多肽固相合成和圆二色性研究模型肽的溶液二级结构,比较理论预测和实测结果。在水溶液中,Ｔ１８为β－折叠,ＴＤＫ含有一定量α－螺旋;而Ｔ１４基本上为无规卷曲,但在碱性条件下有类似螺肇的亚稳结构存在。     

Method of addition of acetonitrile influences the structure and stability of collagen

Collagen has been extensively used as a biomaterial in many biomedical applications. Recently, collagen based biomaterials were prepared using organic solvents. In this context, the method of addition of organic solvent described in the present study will be an important contribution in the preparation of collagen-based biomaterials. The effect of acetonitrile on collagen structure and stability was investigated using biophysical methods. Collagen undergoes solvent-induced denaturation with increasing concentration of acetonitrile. It was observed that addition of acetonitrile (50–90%) to a collagen solution in a single shot (method 1) led to precipitation. Contrary, collagen remained in the solution when acetonitrile content was increased to 90% in a collagen solution that had been formerly equilibrated with 20% acetonitrile (method 2). Interestingly, triple helical structure was retained when precipitated collagen, obtained from method 1, was re-dissolved in acetic acid solution. The re-dissolved collagen exhibits comparable melting temperature as that of native collagen. Re-dissolved collagen also showed fibril formation, but with decreased rate. The soluble collagen in 90% acetonitrile, prepared by method 2, is found to be unordered. The above results thus suggest that the method of addition of acetonitrile plays an important role in the folding and unfolding of collagen.     

Quantitative spectral comparison by weighted spectral difference for protein higher order structure confirmation

Previously, different approaches of spectral comparison were evaluated, and the spectral difference (SD) method was shown to be valuable for its linearity with spectral changes and its independence on data spacing (Anal. Biochem. 434 (2013) 153–165). In this note, we present an enhancement of the SD calculation, referred to as the “weighted spectral difference” (WSD), by implementing a weighting function based on relative signal magnitude. While maintaining the advantages of the SD method, WSD improves the method sensitivity to spectral changes and tolerance for baseline inclusion. Furthermore, a generalized formula is presented to unify further development of approaches to quantify spectral difference.     

Physical methods to determine the binding mode of putative ligands for hepatitis C virus NS3 helicase

Several small molecules identified by high-throughput screening (HTS) were evaluated for their ability to bind to a nonstructural protein 3 (NS3) helicase from hepatitis C virus (HCV). Equilibrium dissociation constants (K(d)'s) of the compounds for this helicase were determined using several techniques including an assay measuring the kinetics of isothermal enzyme denaturation at several concentrations of the test molecule. Effects of two nonhydrolyzable ATP analogs on helicase denaturation were measured as controls using the isothermal denaturation (ITD) assay. Two compounds, 4-(2,4-dimethylphenyl)-2,7,8-trimethyl-4,5-quinolinediamine and 2-phenyl-N-(5-piperazin-1-ylpentyl)quinazolin-4-amine, were identified from screening that inhibited the enzyme and had low micromolar dissociation constants for NS3 helicase in the ITD assay. Low micromolar affinity of the quinolinediamine to helicase was also confirmed by nuclear magnetic resonance experiments. Unfortunately, isothermal titration calorimetry (ITC) experiments indicated that a more water-soluble analog bound to the 47/23-mer oligonucleotide helicase substrate with low micromolar affinity as did the substituted quinazolinamine. There was no further interest in these templates as helicase inhibitors due to the nonspecific binding to enzyme and substrate. A combination of physical methods was required to discern the mode of action of compounds identified by HTS and remove undesirable lead templates from further consideration.     

Inaugural structure from the DUF3349 superfamily of proteins, Mycobacterium tuberculosis Rv0543c

The first structure for a member of the DUF3349 (PF11829) family of proteins, Rv0543c from Mycobacterium tuberculosis, has been determined using NMR-based methods and some of its biophysical properties characterized. Rv0543c is a 100 residue, 11.3 kDa protein that both size exclusion chromatography and NMR spectroscopy show to be a monomer in solution. The structure of the protein consists of a bundle of five α-helices, α1 (M1 – Y16), α2 (P21 – C33), α3 (S37 – G52), α4 (G58 – H65) and α5 (S72 – G87), held together by a largely conserved group of hydrophobic amino acid side chains. Heteronuclear steady-state {¹H}–¹⁵N NOE, T₁, and T₂ values are similar through-out the sequence indicating that the backbones of the five helices are in a single motional regime. The thermal stability of Rv0543c, characterized by circular dichroism spectroscopy, indicates that Rv0543c irreversibly unfolds upon heating with an estimated melting temperature of 62.5 °C. While the biological function of Rv0543c is still unknown, the presence of DUF3349 proteins predominately in Mycobacterium and Rhodococcus bacterial species suggests that Rv0543 may have a biological function unique to these bacteria, and consequently, may prove to be an attractive drug target to combat tuberculosis.     

Deciphering the molecular structure of cryptolepain in organic solvents

Solvent composition plays a major role in stabilizing/destabilizing the forces that are responsible for the native structure of a protein. Often, the solvent composition drives the protein into non-native conformations. Elucidation of such non-native structures provides valuable information about the molecular structure of the protein, which is unavailable otherwise. Inclusion of methanol (non-fluorinated alcohol) or TFE (fluorinated alcohol) in the solvent composition drove cryptolepain, a serine protease and an all-β-protein, into a non-native structure with an enhanced β-sheet or induction of α-helix. These solvents did not much affect cryptolepain under neutral conditions, even at higher concentrations, but the effects were predominant at lower pH, when the protein molecule is under stress. The organic solvent-induced state is partially unfolded with similar characteristics to the molten globule state seen with protein under a variety of conditions. Chemical- or temperature-induced unfolding of cryptolepain in the presence of organic solvent is distinctly different from that in the absence of organic solvent. Such different unfolding provided evidence of two structural variants in the molecular structure of the protein as well as the differential stabilization/destabilization of such structural variants and their sequential unfolding.     

Stabilization of the fibrous structure of an alpha-helix-forming peptide by sequence reversal

The alpha3-peptide, which comprises three repeats of the sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala and forms an amphipathic alpha-helix, is unique among various alpha-helix-forming peptides in that it assembles into fibrous structures that can be observed by transmission electron microscopy. As part of our investigation of the structure-stability relationships of the alpha3-peptide, we synthesized the r3-peptide, whose amino acid sequence is the reverse of that of the alpha3-peptide, and we investigated the effects of sequence reversal on alpha-helix stability and the formation of fibrous structures. Unexpectedly, the r3-peptide formed a more-stable alpha-helix and longer fibers than did the alpha3-peptide. The stability of the r3-peptide helix decreased when the ionic strength of the buffer was increased and when the pH of the buffer was adjusted to 2 or 12. These results suggest that the r3-peptide underwent a "magnet-like" oligomerization and that an increase in the charge-distribution inequality may be the driving force for the formation of fibrous structures.