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1.
C S Wu  J T Yang 《Biopolymers》1988,27(3):423-430
The conformation of a 13-residue C-peptide analogue of ribonuclease A——in surfactant solutions was studied by CD. The CD spectrum of the peptide in excess NaDodSO4 solution was typical for a helical conformation; the spectrum appeared to be virtually independent of pH (2.5–6) and temperature (3–25°C). Analysis of the CD data indicated a helicity of about 65–70% with no α-sheet and β-turn; this corresponded to 8 or 9 residues in the helical form or slightly more than two turns of α-helix. This compares with an average of about one turn of α-helix for the C-peptide analogue in water at pH 4.7 and 7°C. The conformation of the peptide in cationic surfactant, dodecyl ammonium chloride, and nonionic surfactant, dodecyl heptaoxyethylene ether, solution resembled that in water. We concluded that the C-peptide analogue can develop a maximum helicity close to the corresponding segment in ribonuclease A in hydrophobic environment provided by the clustering of NaDodSO4 molecules to the cationic side groups of the peptide, except that the end effects may destabilize two or three residues each at both ends of the helix. Thus, in the interior of a protein molecule this hydrophobic effect may overshadow the charged-group effect than can be explained by the helix dipole model for the helical segments on the exterior of the protein molecule.  相似文献   

2.
Kunio Takeda 《Biopolymers》1985,24(4):683-694
Conformational changes of poly(L-ornithine) [(Orn)n] were studied in a sodium dodecyl sulfate (NaDodSO4) solution by CD. (Orn)n adopted an unstable and a stable helical structure below and above the NaDodSO4 concentration range where β-structure was favored, respectively. CD stopped-flow was used to monitor the transitions from coil to the unstable helix, from the helix to β-structure, and from coil to β-structure. Only the rate of the helix to β-structure transition was accelerated by an increase in NaDodSO4 concentration, whereas the rates of the others were independent of NaDodSO4 concentration. The fractions of coil, α-helix, and β-structure in each conformation of (Orn)n caused by NaDodSO4 were computed by simulating a mixed spectrum of typical CD spectra for these structures to the experimentally obtained spectrum. The contents of the unstable and stable helical structures were less than 50 and 73%, respectively.  相似文献   

3.
S Kubota  K Ikeda  J T Yang 《Biopolymers》1983,22(10):2237-2252
A series of sequential polypeptides (LysiRj)n (R is Leu, Ser, or Gly) and random copolypeptides, (Lysx, Leuy)n, were synthesized. Their conformation in NaDodSO4 solution was determined by CD. Only (Lys-Leu)n, (Lys-Ser)n, and (Lys3-Ser)n adopt a stable β-form in the surfactant solution; (Lys-Ser2)n, (Lys-Ser3)n, (Lys2-Ser2)n, and (Lys2-Ser)n have an unstable β-form, which reverts to an unordered form in high NaDodSO4 concentrations, even though both Ser and DodSO-bound Lys+ are β-formers. In contrast, (Lys-Gly)n remains unordered in NaDodSO4 solution. On the other hand, Lys-rich (Lys2-Leu)n forms an unstable helix and (Lys2-Leu2)n a stable helix in NaDodSO4 solution. In 25 mM NaDodSO4 (Lysx, Leuy)n also forms a helix up to x = 75 and reverts to the β-form at x = 90. This compares with the helical conformation of (Lysx, Alay)n up to x = 65 and its β-form at x = 90, suggesting that Leu is an even stronger helix-former than Ala. Our results may provide a plausible explanation for the increase in helicity and disruption of the β-form for many proteins in NaDodSO4 solution, that is, the polypeptide chain of a protein usually favors a helical conformation over a β-form in the presence of excess surfactant.  相似文献   

4.
Synthesis and characterization of poly(LysAla3)   总被引:1,自引:0,他引:1  
The synthesis and characterization of poly(LysAla3) are described. The polytetrapeptide is a model for short sequences found in proelastin, and is presumably involved in desmosine or isodesmosine cross-link formation in the native protein. Poly(LysAla3) is found to possess a mixture of conformations in aqueous solution dependent on molecular weight and pH. Low-molecular-weight (ca. 3000) material appears to be a mixture of random and extended helix at neutral pH. However, as the molecular weight is increased an increasing amount of α-helix is observed rising to >50% for mol wt = 21,000. The α-helical chain segments are thermally stable, melting to a mixture of extended and random forms at Tm = 25°C. High pH (10.5) promotes further α-helix formation but at pH >11.0 the polypeptide becomes insoluble. The inference is that short chain segments of the peptide in elastin are unlikely to be α-helical in the equilibrium state but may fluctuate through such a conformation.  相似文献   

5.
S Kubota  K Ikeda  J T Yang 《Biopolymers》1983,22(10):2219-2236
A series of sequential polypeptides, (Lysi-Alaj)n, and random copolypeptides, (Lysx, Alay)n, were synthesized. The competitive effect of Ala, a helix former, and Lys, whose homopolymer has a β-form in neutral NaDodSO4 solution, was determined by CD and absorption spectroscopy. All the polypeptides studied were unordered in neutral solution without the surfactant. Of the six sequential polypeptides only (Lys-Ala)n adopted a stable β-form in NaDodSO4 solution. Most striking is the difference between this polypeptide, (Lys2-Ala2)n and (Lysx, Alay)n, even though they all have equimolar Lys and Ala. (Lys2-Ala2)n was partially helical in 2.5–5 mM NaDodSO4 but approached the unordered form in 50 mM NaDodSO4, whereas (Lys50, Ala50)n was completely helical in all NaDodSO4 concentrations. Even Lysrich (Lys2-Ala)n and (Lys3-Ala)n formed a partial helix and a trace of the β-form, respectively, in low NaDodSO4 concentrations; both reverted to the unordered form in high NaDodSO4 concentrations. These results can be explained by Pauling-Corey's model for β-pleated sheets. Only (Lys-Ala)n has all DodSO-bound Lys+ residues on one side and Ala residues on the other side of the polypeptide chain. They can nestle quiet efficiently in a β-sheet and between neighboring β-sheets. Our results further imply that random copolypeptides are not completely random; they comprise varying segments of (Lysk-Alam), where k and m could vary from zero to a small integer.  相似文献   

6.
The solution characterization of poly(Lys-Ala-Glu) is described. This polytripeptide is zwitterionic at neutral pH and is shown to take on a conformation which is dictated by the state of ionization, molecular weight, temperature, and solvent. The polypeptide is almost entirely α-helical at low pH and temperature for polymers of greater than 25,000 molecular weight. Melting profiles for these conditions show tm ~ 20°C. Analysis of circular dichroism curves shows the α-helical content to vary in a linear manner with molecular weight in the range 3000–30,000. At neutral pH the charged polypeptide is essentially random, but substantial α-helix could be induced by addition of methanol or trifluoroethanol. At temperatures where the sequential polypeptide is a random coil, addition of trifluoroethanol produces a polymer which is mostly α-helical but also contains an appreciable ammount of β-structure. The infrared spectrum of a low-molecular-weight fraction assumed to be cyclo(Lys-Ala-Glu)2 was tentatively assigned a β-pleated sheet structure. A comparison of this polytripeptide in various ionization states with other polytripeptides containing L -alanine and L -glutamate or L -lysine shows the α-helix directing properties for the (uncharged) residues to lie in the order Ala > Glu > Lys.  相似文献   

7.
In the presence of sodium poly(L -glutamate) at pH = 7.5 the dye pseudoisocyanine in dilute aqueous solution (Cd = 1.10 × 10?5 M) and low P/D values exhibits an absorption spectrum with a very sharp red-shifted J-band. Under the same conditions circular dichroism (CD) in the visible region is observed with an extremely sharp peak at the position of the J-band. At pH = 4.6, where the polypeptide is in the α-helix conformation, no such J-band is observed and no CD spectrum can be detected at the same P/D values. CD spectra in the uv range demonstrate that the occurrence of the dye–polypeptide complex which gives rise to the J-band at slightly alkaline pH is not accompanied by a conformational transition of the polypeptide towards the α-helical form.  相似文献   

8.
Raman and polarized ir spectra have been obtained on built-up monomolecular films of poly(α-aminoisobutyric acid), and analyzed in the context of normal mode calculations on 310-, α-, and α′-helix conformations of this molecule. The average discrepancy between observed and calculated frequencies is significantly smaller for the 310-helix than for the other structures. This, together with the more satisfactory explanation of several special features of the spectra, indicates that this polypeptide adopts a 310-helix conformation in such thin films.  相似文献   

9.
Circular dichroic spectra of metmyoglobin and apomyoglobin were measured in neutral and acidic solution. Addition of sodium dodecyl sulfate (NaDodSO4) slightly reduces the helicity (based on the circular dichroic magnitude) of both proteins probably because of the loss of long-range interactions among helical segments. Lowering the pH of the protein-surfactant solution to 3 slightly enhances the helical conformation of myoglobin due to the protonation of acidic side groups and thereby the reduction of coulombic repulsion among negative charges. For BrCN-digested fragments the COOH-terminal peptide (22 residues) loses its helicity which can be restored by addition of NaDodSO4. The middle fragment (76 residues) retains a considerable amount of helicity in water alone, which further increases in the presence of NaDodSO4. The NH2-terminal fragment (55 residues) also has some helical conformation in water, which is enhanced by the addition of NaDodSO4. The circular dichroic spectrum of an equimolar mixture of the three peptides in NaDodSO4 solution is the same as that calculated from the spectra of isolated peptides under similar conditions.  相似文献   

10.
The structure of the peptide Boc-Val-Ala-Leu-Aib-Val-Ala-Leu-OMe has been determined in crystals obtained from a dimethylsulfoxide–isopropanol mixture. Crystal parameters are as follows: C38H69N7O10 · H2O · 2C3H7OH, space group P21, a = 10.350 (2) Å, b = 26.084 (4) Å, c = 10.395(2) Å, β = 96.87(12), Z = 2, R = 8.7% for 2686 reflections observed > 3.0 σ (F). A single 5 → 1 hydrogen bond is observed at the N-terminus, while two 4 → 1 hydrogen bonds characteristic of a 310-helix are seen in the central segment. The C-terminus residues, Ala(6) and Leu(7) are expended, while Val(5) is considerably distorted from a helical conformation. Two isopropanol molecules make hydrogen bonds to the C-terminal segment, while a water molecule interacts with the N-terminus. The structure is in contrast to that obtained for the same peptide in crystals from methanol-water [ I. L. Karle, J. L. Flippen-Anderson, K. Uma, and P. Balaram (1990) Proteins: Structure, Function and Genetics, Vol. 7, pp. 62–73] in which two independent molecules reveal an almost perfect α-helix and a helix penetrated by a water molecule. A comparison of the three structures provides a snapshot of the progressive effects of solvation leading to helix unwinding. The fragility of the heptapeptide helix in solution is demonstrated by nmr studies in CDC13 and (CD3)2SO. A helical conformation is supported in the apolar solvent CDCl3, whereas almost complete unfolding is observed in the strongly solvating medium (CD3)2SO. © 1993 John Wiley & Sons, Inc.  相似文献   

11.
Abstract

The crystal structure of the dehydro octapeptide Boc-Val-ΔPhe-Phe-Ala-Leu-Ala-ΔPhe-Leu-OH has been determined to atomic resolution by X-ray crystallographic methods. The crystals grown by slow evaporation of peptide solution in methanol/water are orthorhombic, space group P212121. The unit cell parameters are a= 8.404 (3), b= 25.598(2) and c = 27.946(3) Å, Z=4. The agreement factor is R= 7.58% for 3636 reflections having (IF0I) ≥ 3σ (IF0I). The peptide molecule is characterised by a 310-helix at the N-terminus and a π-turn at the C-terminus. This conformation is exactly similar to the helix termination features observed in proteins. The π-turn conformation observed in the octapeptide is in good agreement with the conformational features of π-turns seen in some proteins. The αL-position in the π-turn of the octapeptide is occupied by ΔPhe7, which shows that even bulky residues can be accommodated in this position of the π-turns. In proteins, it is generally seen that aL- position is occupied by glycine residue. No intermolecular head-to-tail hydrogen bonds are observed in solid state structure of the octapeptide. A water molecule located in the unit cell of the peptide molecule is mainly used to hold the peptide molecule together in the crystal. The conformation observed for the octapeptide might be useful to understand the helix termination and chain reversal in proteins and to construct helix terminators for denovo protein design.  相似文献   

12.
Abstract

The genetic algorithm is a technique of function optimization derived from the principles of evolutionary theory. We have adapted it to perform conformational search on polypeptides and proteins. The algorithm was first tested on several small polypeptides and the 46 amino acid protein crambin under the AMBER potential energy function. The probable global minimum conformations of the polypeptides were located 90% of the time and a non-native conformation of crambin was located that was 150kcal/mol lower in potential energy than the minimized crystal structure conformation. Next, we used a knowledge-based potential function to predict the structures of melittin, pancreatic polypeptide, and crambin. A 2.31 Å ΔRMS conformation of melittin and a 5.33 Å ΔRMS conformation of pancreatic polypeptide were located by genetic algorithm-based conformational search under the knowledge-based potential function. Although the ΔRMS of pancreatic polypeptide was somewhat high, most of the secondary structure was correct. The secondary structure of crambin was predicted correctly, but the potential failed to promote packing interactions. Finally, we tested the packing aspects of our potential function by attempting to predict the tertiary structure of cytochrome b 562 given correct secondary structure as a constraint. The final predicted conformation of cytochrome b 562 was an almost completely extended continuous helix which indicated that the knowledge-based potential was useless for tertiary structure prediction. This work serves as a warning against testing potential functions designed for tertiary structure prediction on small proteins.  相似文献   

13.
By means of conformational energy calculations, we previously showed that the antigenic strength of a series of oligopeptides (derived from the carboxyl terminal sequence of cytochrome c) in a T-lymphocyte proliferation assay depends on their ability to adopt the α-helix conformation. Using experimentally determined statistical weights (within the framework of the Zimm–Bragg theory for the helix–coil transition), here we present a simple free energy analysis of the ability of these peptides to adopt the α-helix conformation in water. The experimental statistical weights have been modified to include the effect of long-range charge–dipole interactions on helix stability. We find that there is a close correlation between the tendency of a peptide to adopt the α-helix conformation and its ability to stimulate antigen-primed T cells. The shortest peptide with a tendency to adopt the α-helix conformation is also the shortest one that exhibits antigenic activity. The rapid and simple method presented here can thus be used to predict relative antigenicities for different peptides derived from cytochrome c.  相似文献   

14.
The stepwise synthesis and conformational studies of the N-terminal helical partial sequence of the membrane-modifying polypeptide antibiotic alamethicin are described. The polyoxyethylen esters of the fragments N-t-Boc-L -Pro-Aib-Ala-Gln-Aib-Val-Aib-Gly-OH and N-Ac-Aib-L -Pro-Aib-Ala-Aib-Ala-Gln-Aib-Val-Aib-Gly-OH are synthesized using polyoxyethylene (molecular mass 10,000) as solubilizing support. CD spectra of each intermediate in ethanol show α-helix formation of the N-protected peptide polymers beginning with the nonapeptide and of the N-protonated sequences beginning with the decapeptide. Compared to the helix of alamethicin, temperature- and solvent-dependent CD measurements indicate analogous conformational behavior. The results suggest that in lipophilic media the alamethicin helix can extend the full length of the partial sequence between the two proline residues and that aqueous media favor an increase of random-coil conformation. For model studies of the particular lipid interaction of alamethicin, the stepwise synthesis of peptides with the alternating (Aib-L -Ala)n sequence (n = 1–7) was carried out on a polyoxyethylene support (molecular mass 6000). CD and ORD studies in ethanol showed a change from the random coil to a right-handed α-helix with increasing peptide length. This change is observed for the N-protected peptides at a chain length of 8 residues and for the N-protonated peptides at a length of 9 residues. The comparison of the CD data of free and polyoxyethylene-bound peptides revealed that the solubilizing polymeric support cannot induce conformational changes. The intensities of the CD bands of t-Boc-(Aib-L -Ala)n-OPOE (n ≥ 6) are higher than those of alamethicin, and these model peptides show similar temperature and solvent inducible changes of their helix contents.  相似文献   

15.
The conformational transitions of synthetic basic polytripeptides (Lys-Leu-Gly)n, (A2bu-Leu-Gly)n, (Lys-Leu-Ala)n, and (A2bu-Leu-Ala)n induced by high salt concentrations and elevated pH were investigated by CD, ir, and 1H-nmr spectroscopy, sedimentation analysis, viscometry, and light scattering. Sheet aggregates of chains in a conformation similar to the polyglycine II (polyproline II) helix, bound together by hydrogen bonds, are the most probable form of (Lys-Leu-Gly)n and also, partly, of (A2bu-Leu-Gly)n in a high-pH or high-salt solutions. The conformation (Lys-Leu-Ala)n, in a low-salt concentration, is an α-helix. Since (A2bu-Leu-Ala)n is disordered under similar conditions, it appears that this α-helix is stabilized by hydrophobic interactions between Lys and Leu side chains. In a high concentration of water structure-making ions, CD data for (Lys-Leu-Ala)n indicate distortion of the α-helix, with a parallel increase in the average molecular weight corresponding to trimer formation. Hydrodynamic data are consistent with a model of bundles of three closely touching spherocylinders. (A2bu-Leu-Ala)n shows a limited tendency to α-helix formation.  相似文献   

16.
The crystal structure of N-acetyl-L -4-hydroxyproline (Hyp) was determined by direct methods. (The crystal is orthorhombic with the space group P212121.) The acetyl group is in the trans conformation and the pyrrolidine ring puckers at Cγ (CsCγ envelope), as in most Hyp residues. According to the rotation angle ψ = ?30°, the N-acetyl-L -4Hyp has the same conformation as an α-helix of prolyl residues. The crystal packing is stabilized by hydrogen bonds between three different molecules and the same molecule of water. One of the water bridges involves the carbonyl of the N-acetyl group of one molecule and the hydrogen atom of the 4-OH group of another. Such an arrangement has been proposed to explain the high stability of (Gly-L -Pro-L -4Hyp)n. A second bridge involves the two hydrogens of the water molecule and the carbonyl groups of two neighbouring molecules, as already proposed in a dihydrated model of collagen. These experimental features, which are discussed in relation to the different models of collagen, allow us to propose an hypothetical arrangement for the water molecule which is strongly retained in the triple helix of (Gly-L -Pro-L -4Hyp)n.  相似文献   

17.
Jake Bello 《Biopolymers》1993,33(3):491-495
The helix content of [L -Lys(Me3)]n · ClO4, and [L -Lys(Me3)50, L -Ala50]n · ClO4 in water is markedly increased by the presence of sucrose and glycerol. For [L -Lys(Me3)]n · ClO4 the ellipticity at 222 nm changes from +2 × 103 deg cm2 dmole?1 in water to ?44 × 103 in 50% glycerol. Sucrose does not promote helix formation in melittin at pH 7.2, but glycerol does. At pH 5.5 sucrose and, more so, glycerol, induce helix in melittin. Glycerol induces some helix in methylated melittin, but less than in melittin. The results are discussed in relation to excluded volume effects, ΔG of transfer of peptide and hydrophobic groups from water to mixed solvents, electrostatic effects, and preferential hydration. © 1993 John Wiley & Sons, Inc.  相似文献   

18.
X-ray diffraction and energy-minimization results are reported for poly(γ-phenethyl-L -glutamate). Orthorhombic unit-cell parameters of drawn fibers are a = 15.4 Å, b = 26.6 Å, c = 54.4 Å. Atomic coordinates are derived for an α-helix peptide conformation that corresponds to a calculated side-chain internal energy minimum. The side-chain conformation correlates well with the electron density projection; the side chains wrap around the α-helical main chain with the phenethyl ester group directed toward the N-terminus. The para-axis of the benzene ring is inclined at an angle nearly nearly normal to the helix axis. The x-ray structure factors calculated for this model, when compared to the 10 observed structure factors, yield a crystallographic reliability index of R = 0.23.  相似文献   

19.
Poly(L -arginine) assumes the α-helix in the presence of the tetrahedral-type anions or some polyanions by forming the “ringed-structure bridge” between guanidinium groups and anions which is stabilized by a pair of hydrogen bonds and electrostatic interaction [Ichimura, S., Mita, K. & Zama, M. (1978) Biopolymers 17 , 2769–2782; Mita, K., Ichimura, S. & Zama, M. (1978) Biopolymers 17 , 2783–2798]. This paper describes the parallel CD studies on the conformational effects on poly (L -homoarginine) of various mono-, di-, polyvalent anions and some polyanions, as well as alcohol and sodium dodecylsulfate. The random coil to α-helix transition of poly(L -homoarginine) occurred only in NaClO4 solution or in the presence of high content of ethanol or methanol. The divalent and polyvalent anions of the tetrahedral type (SO, HPO, and P2O), which are strong α-helix-forming agents for poly(L -arginine), failed to induce the α-helical conformation of poly(L -homoarginine). By complexing with poly(L -glutamic acid) or with polyacrylate, which is also a strong α-helix-forming agent for poly(L -arginine), poly(L -homoarginine) only partially formed the α-helical conformation. Monovalent anions (OH?, Cl?, F?, and H2PO) did not change poly(L -homoarginine) to the α-helix, and in the range of pH 2–11, the polypeptide remained in an unordered conformation. In sodium dodecylsulfate, poly(L -homoarginine) exhibited the remarkably enlarged CD spectrum of an extended conformation, while poly(L -arginine) forms the α-helix by interacting with the agent. Thus poly(L -homoarginine), compared with poly(L -arginine), has a much lower ability to form the α-helical conformation by interacting with anions. The stronger hydrophobicity of homoarginine residue in comparison with the arginine residue would provide unfavorable conditions to maintain the α-helical conformation.  相似文献   

20.
Spiders can produce up to seven different types of silks or glues with different mechanical properties. Of these, flagelliform (Flag) silk is the most elastic, and aciniform (AcSp1) silk is the toughest. To produce a chimeric spider silk (spidroin) FlagR-AcSp1R, we fused one repetitive module of flagelliform silk from Araneus ventricosus and one repetitive module of aciniform silk from Argiope trifasciata. The recombinant protein expressed in E. coli formed silk-like fibers by manual-drawing. CD analysis showed that the secondary structure of FlagR-AcSp1R spidroin remained stable during the gradual reduction of pH from 7.0 to 5.5. The spectrum of FTIR indicated that the secondary structure of FlagR-AcSp1R changed from α-helix to β-sheet. The conformation change of FlagR-AcSp1R was similar to other spidroins in the fiber formation process. SEM analysis revealed that the mean diameter of the fibers was around 1 ~ 2 μm, and the surface was smooth and uniform. The chimeric fibers exhibited superior toughness (~33.1 MJ/m3) and tensile strength (~261.4 MPa). This study provides new insight into design of chimeric spider silks with high mechanical properties.  相似文献   

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