Conformation of branched polypeptides based on poly(L-lysine). Effect of the ionic strength and of the presence of alcohols

CD spectra of branched polypeptides based on poly(L-lysine) containing in the side chains approximately, 3, 5 and 8.5 DL-alanine residues or 3 DL-alanine residues and another terminal L-amino acid were measured at pH 7.4, and in the uncharged state in various ionic strengths, and also in water-methanol and water-trifluoroethanol mixtures. At pH 7.4 and in low ionic strength (0.02M and 0.2M-NaCl) the polypeptides assume an unordered conformation, except for the L-leucine containing polypeptide, which is helical to a considerable extent. Increase of the ionic strength to 2.0M-NaCl leads to the formation of the α-helical structure. In the uncharged state all polypeptides are at least partly helical. The content of the α-helix increases with increasing ionic strength and depends also on the nature of the side chain. Formation of the α-helix is supported by the presence of L-leucine and L-proline, some limitation of the α-helix formation by histidine is manifested mainly in low ionic strength. The presence of methanol and trifluoroethanol has an effect similar to the increase of ionic strength, i.e. increases the α-helix content.

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Conformation of branched polypeptides based on poly(L-lysine): The effect of terminal amino acids in the branches

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19850228 ◽

1985 ◽

Vol 50 (1) ◽

pp. 228-244 ◽

Cited By ~ 16

Author(s):

Hana Votavová ◽

Ferenc Hudecz ◽

Judit Kajtár ◽

Jaroslav Šponar ◽

Karel Bláha ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Ionic Strength ◽

Glutamic Acid ◽

Amino Acid Residues ◽

Ordered Structure ◽

Cd Spectra ◽

Helix Formation ◽

Terminal Amino ◽

Α Helix

CD Spectra of branched polypeptides based on poly(L-lysine) and containing three DL-alanine residues and one to three other L- or D-amino acid residues in the branches were measured in water, water-methanol and water-trifluoroethanol mixtures. In aqueous solutions dependence of the CD spectra on pH and ionic strength was studied. The effect of branch elongation was followed mainly with compounds containing glutamic acid. One terminal D-amino acid residue and also an extension by two L- or D-amino acid residues does not hinder the α-helix formation in the backbone but affects the conditions of its formation. In polypeptides with three L- or D-amino acids additional α-helical segments in the branches are assumed to be formed. For branches with L-amino acids the CD curves express additively the contributions of both helical components, in the case of D-amino acids the increasing population of the ordered structure in branches is manifested by compensation of dichroic contribution of the L-amino acid backbone leading even to enantiomorphous curves.

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Synthesis and conformation of sequential basic polypeptides with branched and linear side chains

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19852925 ◽

1985 ◽

Vol 50 (12) ◽

pp. 2925-2936 ◽

Cited By ~ 2

Author(s):

Štěpánka Štokrová ◽

Jan Pospíšek ◽

Jaroslav Šponar ◽

Karel Bláha

Keyword(s):

Amino Acid ◽

Salt Concentration ◽

Salt Solution ◽

Theoretical Work ◽

Side Chain ◽

Amino Acid Residues ◽

Cd Spectra ◽

Low Salt ◽

Conformational Freedom ◽

Basic Polypeptides

Polypeptides (Lys-X-Ala)n and (Lys-X-Gly)n in which X represents residues of isoleucine and norleucine, respectively, and polypeptide (Tle-Lys-Ala)n, were synthesized via polymerization of 1-hydroxysuccinimidyl esters of the appropriate tripeptides to complete previously studied series. Circular dichroism (CD) spectra of the respective polymers were measured as a function of pH and salt concentration of the medium. The results were correlated with those obtained previously with the same series containing different amino acid residues at the X-position. The helix forming ability of the polypeptides (Lys-X-Ala)n with linear X side chain was found to be independent of the length. In the series (Lys-X-Gly)n the unordered conformation was the most probable one except (Lys-Ile-Gly)n. This polymer assumed the β conformation even in low salt solution at neutral pH. An agreement with some theoretical work concerned with the restriction of conformational freedom of amino acid residue branching at Cβ atom with our experimental results is evident.

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Development of Antimicrobial Stapled Peptides Based on Magainin 2 Sequence

Molecules ◽

10.3390/molecules26020444 ◽

2021 ◽

Vol 26 (2) ◽

pp. 444

Author(s):

Motoharu Hirano ◽

Chihiro Saito ◽

Hidetomo Yokoo ◽

Chihiro Goto ◽

Ryuji Kawano ◽

...

Keyword(s):

Antimicrobial Activity ◽

Amino Acid ◽

Hemolytic Activity ◽

Helical Structure ◽

Antimicrobial Activities ◽

Side Chain ◽

Membrane Disruption ◽

Amino Acid Residues ◽

Electrophysiological Measurements ◽

Cell Membrane Disruption

Magainin 2 (Mag2), which was isolated from the skin of the African clawed frog, is a representative antimicrobial peptide (AMP) that exerts antimicrobial activity via microbial membrane disruption. It has been reported that the helicity and amphipathicity of Mag2 play important roles in its antimicrobial activity. We investigated and recently reported that 17 amino acid residues of Mag2 are required for its antimicrobial activity, and accordingly developed antimicrobial foldamers containing α,α-disubstituted amino acid residues. In this study, we further designed and synthesized a set of Mag2 derivatives bearing the hydrocarbon stapling side chain for helix stabilization. The preferred secondary structures, antimicrobial activities, and cell-membrane disruption activities of the synthesized peptides were evaluated. Our analyses revealed that hydrocarbon stapling strongly stabilized the helical structure of the peptides and enhanced their antimicrobial activity. Moreover, peptide 2 stapling between the first and fifth position from the N-terminus showed higher antimicrobial activity than that of Mag2 against both gram-positive and gram-negative bacteria without exerting significant hemolytic activity. To investigate the modes of action of tested peptides 2 and 8 in antimicrobial and hemolytic activity, electrophysiological measurements were performed.

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Free energies of amino acid side-chain rotamers in α-helices, β-sheets and α-helix N-caps 1 1Edited by A. R. Fersht

Journal of Molecular Biology ◽

10.1006/jmbi.1997.1250 ◽

1997 ◽

Vol 272 (3) ◽

pp. 456-464 ◽

Cited By ~ 25

Author(s):

Benjamin J Stapley ◽

Andrew J Doig

Keyword(s):

Amino Acid ◽

Side Chain ◽

Amino Acid Side Chain ◽

Free Energies ◽

Β Sheets ◽

Α Helix

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The composition of cartilage proteoglycans. An investigation using high-and low-ionic-strength extraction procedures

Biochemical Journal ◽

10.1042/bj1310541 ◽

1973 ◽

Vol 131 (3) ◽

pp. 541-553 ◽

Cited By ~ 35

Author(s):

Robert W. Mayes ◽

Roger M. Mason ◽

David C. Griffin

Keyword(s):

Amino Acid ◽

Ionic Strength ◽

Density Gradient ◽

Amino Acid Analysis ◽

Chondroitin Sulphate ◽

High Ionic Strength ◽

Guanidinium Chloride ◽

Equilibrium Conditions ◽

Chondroitin Sulphate Proteoglycans ◽

Low Ionic Strength

1. A proteoglycan fraction (the proteoglycan subunit fraction) was prepared from extracts, with 0.15m-KCl (low-ionic-strength) and 0.5m-LaCl3, 2.0m-CaCl2 and 4.0m-guanidinium chloride (high-ionic-strength), of bovine nasal cartilage by equilibrium-density-gradient centrifugation, essentially as described by Hascall & Sajdera (1969). 2. The use of different centrifugation times showed that near-equilibrium conditions were reached by 48h for the fractions prepared from the high-ionic-strength extracts. The fraction isolated from the low-ionic-strength extract required a longer centrifugation time to reach equilibrium conditions. 3. The composition of the proteoglycan fractions from the various extracts was compared by analyses of their carbohydrate and amino acid contents. Difference indices were calculated from the amino acid analysis to compare the degree of compositional relationship between the protein components of the proteoglycans. 4. Small compositional differences were found between the proteoglycans isolated from the various high-ionic-strength extracts. The protein content of the fractions from the CaCl2 extract and the guanidinium chloride extract showed the greatest difference in this respect, although their amino acid analysis was similar. 5. The proteoglycan fraction isolated from the low-ionic-strength extract shows marked differences in composition from the fractions isolated from the high-ionic-strength extracts. Its protein and glucosamine contents were lower whereas its hexuronic acid and galactosamine contents were higher than those of the latter. It also exhibits major differences in its amino acid composition. The glucosamine:galactosamine ratio of the fraction from the low-ionic-strength extract indicates that it may be an almost exclusively chondroitin sulphate–proteoglycan. Its analysis correlates closely with that of a low-molecular-weight proteoglycan isolated from pig laryngeal cartilage by Tsiganos & Muir (1969). 6. The proteoglycan fractions from both the low- and high-ionic-strength extracts migrate as a single band in zone electrophoresis carried out in a sucrose-density gradient at both pH3.0 and pH7.0, although each showed evidence of band widening during the electrophoresis. All the proteoglycan fractions migrated with the same electrophoretic mobility at pH3.0, irrespective of the differences in composition between them. 7. The differences between the proteoglycans from the low- and high-ionic-strength extracts are discussed and the view is advanced that they may be due to association between predominantly chondroitin sulphate–proteoglycans and a keratan sulphate-enriched proteoglycan species.

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Breakdown and reassociation of bacterial spinae

Canadian Journal of Microbiology ◽

10.1139/m82-121 ◽

1982 ◽

Vol 28 (7) ◽

pp. 795-808

Author(s):

K. B. Easterbrook ◽

R. W. Coombs

Keyword(s):

Ionic Strength ◽

Protein Conformation ◽

High Ionic Strength ◽

Random Coil ◽

Temperature Dependent ◽

Calcium Effect ◽

Α Helix ◽

Low Ionic Strength ◽

Β Sheet ◽

Polymeric Structures

The tubular appendage, spina (Easterbrook and Coombs. 1976. Can. J. Microbiol. 22: 438–440), dissociates most efficiently under conditions of low ionic strength (0.01 M), high pH (10), and high temperature (95 °C). The protomer, spinin, thus produced is stable under these conditions and reassociates on cooling to give two distinct filamentous polymeric structures that differ in their stability, protein conformation, and reassociation characteristics. Under conditions of low ionic strength (0.01 M), reassociation is relatively slow and leads to a product that has significant amounts of α-helix in addition to the high β-sheet component; under conditions of high ionic strength (1 M), reassociation is rapid and the non-β-sheet component is in the random coil configuration. Since polymerization of the latter structure is "seeded" by either endogenous or exogenously supplied spina fragments, the protomers comprising it are assumed to be in the same conformation as in the spinae. High ionic strength induces folding of the protomer, multimeric association, and finally, elongation by a temperature-dependent process. Reassociation appears to be pH (6–10) independent and, apart from a possible minor calcium effect, cation nonspecific.

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Subunit composition and structure of subcomponent C1q of the first component of human complement

Biochemical Journal ◽

10.1042/bj1550019 ◽

1976 ◽

Vol 155 (1) ◽

pp. 19-23 ◽

Cited By ~ 234

Author(s):

K B M Reid ◽

R R Porter

Keyword(s):

Ionic Strength ◽

Sodium Dodecyl ◽

Gel Filtration ◽

Helical Structure ◽

Guanidinium Chloride ◽

Molecular Weights ◽

Composition And Structure ◽

Covalently Linked ◽

Low Ionic Strength ◽

Expected Position

1. Unreduced human subcomponent C1q was shown by electrophoresis on polyacrylamide gels run in the presence of sodium dodecyl sulphate to be composed of two types of non-covalently linked subunits of apparent mol.wts. 69 000 and 54 000. The ratio of the two subunits was markedly affected by the ionic strength of the applied sample. At a low ionic strength of applied sample, which gave the optimum value for the 54 000-apparent mol.wt. subunit, a ratio of 1.99:1.00 was obtained for the ratio of the 69 000-apparent mol.wt. subunit to the 5400-apparent-mol.wt. subunit. The amount of the 54 000-apparent-mol.wt. subunit detected in the expected position on the gel was found to be inversely proportional to increases in the ionic strength of the applled sample. 2. Human subcomponent C1q on reduction and alkylation, or oxidation, yields equimolar amounts of three chains designated A, B and C [Reid et al. (1972) Biochem. J. 130, 749-763]. The results obtained by Yonemasu & Stroud [(1972) Immunochemistry 9, 545-554], which showed that the 69 000-apparent-mol.wt. subunit was a disulphide-linked dimer of the A and B chains and that the 54 000-apparent-mol.wt. subunit was a disulphide-linked dimer of the C chain, were confirmed. 3. Gel filtration on Sephadex G-200 in 6.0M-guanidinium chloride showed that both types of unreduced subunit were eluted together as a single symmetrical peak of apparent mol.wt. 49 000-50 000 when globular proteins were used as markers. The molecular weights of the oxidized or reduced A, B and C chains have been shown previously to be very similar all being in the range 23 000-24 000 [Reid et al. (1972) Biochem. J. 130, 749-763; Reid (1974) Biochem. J. 141, 189-203]. 4. It is proposed that subcomponent C1q (mol.wt. 410000) is composed of nine non-covalently linked subunits, i.e. six A-B dimers and three C-C dimers. 5. A structure for subcomponent C1q is proposed and is based on the assumption that the collagen-like regions of 78 residues in each of the A, B and C chains are combined to form a triple-helical structure of the same type as is found in collagens.

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Helix Formation in Preorganized β/γ-Peptide Foldamers: Hydrogen-Bond Analogy to the α-Helix without α-Amino Acid Residues

Journal of the American Chemical Society ◽

10.1021/ja103233a ◽

2010 ◽

Vol 132 (23) ◽

pp. 7868-7869 ◽

Cited By ~ 77

Author(s):

Li Guo ◽

Aaron M. Almeida ◽

Weicheng Zhang ◽

Andrew G. Reidenbach ◽

Soo Hyuk Choi ◽

...

Keyword(s):

Hydrogen Bond ◽

Amino Acid ◽

Amino Acid Residues ◽

Helix Formation ◽

Α Helix

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Circular Dichroism, Self Interaction and Side Chain Conformation of Riboflavin and Riboflavin Analogues

Zeitschrift für Naturforschung B ◽

10.1515/znb-1972-0911 ◽

1972 ◽

Vol 27 (9) ◽

pp. 1044-1046 ◽

Cited By ~ 12

Author(s):

G. Scola-Nagelschneider ◽

P. Hemmerich

Keyword(s):

Circular Dichroism ◽

Ionic Strength ◽

Aqueous Solutions ◽

Chain Conformation ◽

Side Chain ◽

Cd Spectra ◽

Polar Solvents ◽

Side Chain Conformation ◽

Vibronic Transitions ◽

Circular Dichroïsm

The CD-spectra of riboflavin and riboflavin analogues in aqueous solutions differ very little depending on pH and ionic strength, but are extremely sensitive upon solvent changes. The two bands in the region of 300 —500 nm seen in aqueous solutions are split into seven bands in less polar solvents, which can be assigned to seven vibronic transitions. The spectra may be interpreted by “through space” and “through chain” interactions of the sidechain centers of chirality with the flavin chromophore, which influence the two first π —π* transitions in different manner.

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