1
|
Hossain M, Huda N, Bhuyan AK. A three-state mechanism for trifluoroethanol denaturation of an intrinsically disordered protein (IDP). J Biochem 2023; 174:519-531. [PMID: 37709541 DOI: 10.1093/jb/mvad067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023] Open
Abstract
Relating the amino acid composition and sequence to chain folding and binding preferences of intrinsically disordered proteins (IDPs) has emerged as a huge challenge. While globular proteins have respective 3D structures that are unique to their individual functions, IDPs violate this structure-function paradigm because rather than having a well-defined structure an ensemble of rapidly interconverting disordered structures characterize an IDP. This work measures 2,2,2-trifluoroethanol (TFE)-induced equilibrium transitions of an IDP called AtPP16-1 (Arabidopsis thaliana phloem protein type 16-1) by using fluorescence, circular dichroism, infrared and nuclear magnetic resonance (NMR) methods at pH 4, 298 K. Low TFE reversibly removes the tertiary structure to produce an ensemble of obligate intermediate ($\mathrm{I}$) retaining the native-state ($\mathrm{N}$) secondary structure. The intermediate $\mathrm{I}$ is preceded by a non-obligate tryptophan-specific intermediate ${\mathrm{I}}_{\mathrm{w}}$ whose population is detectable for AtPP16-1 specifically. Accumulation of such non-obligate intermediates is discriminated according to the sequence composition of the protein. In all cases, however, a tertiary structure-unfolded general obligate intermediate $\mathrm{I}$ is indispensable. The $\mathrm{I}$ ensemble has higher helical propensity conducive to the acquisition of an exceedingly large level of α-helices by a reversible denaturation transition of $\mathrm{I}$ to the denatured state $\mathrm{D}$ as the TFE level is increased. Strikingly, it is the same $\mathrm{N}\rightleftharpoons \mathrm{I}\rightleftharpoons \mathrm{D}$ scheme typifying the TFE transitions of globular proteins. The high-energy state $\mathrm{I}$ characterized by increased helical propensity is called a universal intermediate encountered in both genera of globular and disordered proteins. Neither $\mathrm{I}$ nor $\mathrm{D}$ strictly show molten globule (MG)-like properties, dismissing the belief that TFE promotes MGs.
Collapse
Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| |
Collapse
|
2
|
Hossain M, Huda N, Bhuyan AK. A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol. Biophys Chem 2022; 291:106895. [PMID: 36182744 DOI: 10.1016/j.bpc.2022.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.
Collapse
Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
| |
Collapse
|
3
|
Mandal P, Molla AR. Solvent Perturbation of Protein Structures - A Review Study with Lectins. Protein Pept Lett 2020; 27:538-550. [PMID: 31682206 DOI: 10.2174/0929866526666191104145511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 01/07/2023]
Abstract
Use of organic molecules as co-solvent with water, the ubiquitous biological solvent, to perturb the structure of proteins is popular in the research area of protein structure and folding. These organic co-solvents are believed to somehow mimic the environment near the cell membrane. Apart from that they induce non-native states which can be present in the protein folding pathway or those states also may be representative of the off pathway structures leading to amyloid formation, responsible for various fatal diseases. In this review, we shall focus on organic co-solvent induced structure perturbation of various members of lectin family. Lectins are excellent model systems for protein folding study because of its wide occurrence, diverse structure and versatile biological functions. Lectins were mainly perturbed by two fluoroalcohols - 2,2,2- trifluoroethanol and 1,1,1,3,3,3-hexafluoroisopropanol whereas glycerol, ethylene glycol and polyethylene glycols were used in some cases. Overall, all native lectins were denatured by alcohols and most of the denatured lectins have predominant helical secondary structure. But characterization of the helical states and the transition pathway for various lectins revealed diverse result.
Collapse
Affiliation(s)
- Pritha Mandal
- Department of Chemistry, Krishnagar Government College, Krishnagar, West Bengal-741101, India
| | - Anisur R Molla
- Department of Chemistry, Bidhannagar College, Salt Lake, Kolkata -700 064, India
| |
Collapse
|
4
|
Abstract
Investigations of protein folding have largely involved studies using disulfide-containing proteins, as disulfide-coupled folding of proteins permits the folding intermediates to be trapped and their conformations determined. Over the last decade, a combination of new biotechnical and chemical methodology has resulted in a remarkable acceleration in our understanding of the mechanism of disulfide-coupled protein folding. In particular, expressed protein ligation, a combination of native chemical ligation and an intein-based approach, permits specifically labeled proteins to be easily produced for studies of protein folding using biophysical methods, such as NMR spectroscopy and X-ray crystallography. A method for regio-selective formation of disulfide bonds using chemical procedures has also been established. This strategy is particularly relevant for the study of disulfide-coupled protein folding, and provides us not only with the native conformation, but also the kinetically trapped topological isomer with native disulfide bonds. Here we review recent developments and applications of biotechnical and chemical methods to investigations of disulfide-coupled peptide and protein folding. Chemical additives designed to accelerate correct protein folding and to avoid non-specific aggregation are also discussed.
Collapse
Affiliation(s)
- Masaki Okumura
- Faculty of Science and Engineering, Kinki University, Higashi-osaka, Osaka, Japan
| | | | | |
Collapse
|
5
|
SILIGARDI GIULIANO, DRAKE ALEXF, MASCAGNI PAOLO, ROWLANDS DAVIDJ, BROWN FRED, GIBBONS WILLIAMA. A CD strategy for the study of polypeptide folding/unfolding. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1991.tb01535.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Abstract
The solution conformation of human calcitonin in a mixture of 60% water and 40% trifluoroethanol has been determined by the combined use of 1H NMR spectroscopy and distance geometry calculations with a distributed computing technique. 1H NMR spectroscopy provided 195 distance constraints and 13 hydrogen bond constraints. The 20 best converged structures exhibit atomic rmsd of 0.43 A for the backbone atoms from the averaged coordinate position in the region of Asn3-Phe22. The conformation is characterized by a nearly amphiphilic alpha-helix domain that extends from Leu4 in the cyclic region to His20. There are no significant differences observed among the overall structures of a series of calcitonins obtained from ultimobranchial bodies, including those that possess 20- to 50-fold greater activity. Three aromatic amino acid residues, Tyr12, Phe16 and Phe19, form a hydrophobic surface of human calcitonin. Bulky side chains on the surface could interfere with the ligand-receptor interaction thereby causing its low activity, relative to those of other species.
Collapse
Affiliation(s)
- Kiyoshi Ogawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871 Japan
| | | | | | | | | | | | | | | |
Collapse
|
7
|
Fossati G, Izzo G, Rizzi E, Gancia E, Modena D, Moras ML, Niccolai N, Giannozzi E, Spiga O, Bono L, Marone P, Leone E, Mangili F, Harding S, Errington N, Walters C, Henderson B, Roberts MM, Coates ARM, Casetta B, Mascagni P. Mycobacterium tuberculosis chaperonin 10 is secreted in the macrophage phagosome: is secretion due to dissociation and adoption of a partially helical structure at the membrane? J Bacteriol 2003; 185:4256-67. [PMID: 12837802 PMCID: PMC164881 DOI: 10.1128/jb.185.14.4256-4267.2003] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2003] [Accepted: 04/28/2003] [Indexed: 11/20/2022] Open
Abstract
To confirm that Mycobacterium tuberculosis chaperonin 10 (Cpn10) is secreted outside the live bacillus, infected macrophages were examined by electron microscopy. This revealed that the mycobacterial protein accumulates both in the wall of the bacterium and in the matrix of the phagosomes in which ingested mycobacteria survive within infected macrophages. To understand the structural implications underlying this secretion, a structural study of M. tuberculosis Cpn10 was performed under conditions that are generally believed to mimic the membrane environment. It was found that in buffer-organic solvent mixtures, the mycobacterial protein forms two main species, namely, a partially helical monomer that prevails in dilute solutions at room temperature and a dimer that folds into a beta-sheet-dominated structure and prevails in either concentrated protein solutions at room temperature or in dilute solutions at low temperature. A partially helical monomer was also found and was completely associated with negatively charged detergents in a micelle-bound state. Remarkably, zwitterionic lipids had no effect on the protein structure. By using N- and C-truncated forms of the protein, the C- and N-terminal sequences were identified as possessing an amphiphilic helical character and as selectively associating with acidic detergent micelles. When the study was extended to other chaperonins, it was found that human Cpn10 is also monomeric and partially helical in dilute organic solvent-buffer mixtures. In contrast, Escherichia coli Cpn10 is mostly dimeric and predominately beta-sheet in both dilute and concentrated solutions. Interestingly, human Cpn10 also crosses biological membranes, whereas the E. coli homologue is strictly cytosolic. These results suggest that dissociation to partially helical monomers and interaction with acidic lipids may be two important steps in the mechanism of secretion of M. tuberculosis Cpn10 to the external environment.
Collapse
Affiliation(s)
- Gianluca Fossati
- Italfarmaco Research Centre, Cinisello Balsamo 20092, Milan, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Jaseja M, Copié V, Starkey J. Conformational studies of antimetastatic laminin-1 derived peptides in different solvent systems, using solution NMR spectroscopy. J Pept Res 2003; 61:24-39. [PMID: 12472846 DOI: 10.1034/j.1399-3011.2003.21040.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Due to its critical role in cancer progression, interactions between laminin-1 and the 67 kDa Laminin-Binding Protein (the 67 kDa LBP) have been the focus of a number of structural and biological studies. As laminin-1 is such a large and complex molecule, research interests have turned to the investigation of bioactive peptides derived from binding domains of laminin-1. Two peptides of interest, CDPGYIGSR (peptide 11) and YIGSR, both derived from the beta1 chain of laminin-1, have been shown to block invasion of basement membranes by tumor cells. Substituting the C-terminal arginine to lysine, a conservative substitution, results in a loss of peptide antimetastatic activity. This difference in bioactivity has been attributed, based on numerous modeling studies of free peptide conformations, to structural differences between YIGSR and YIGSK. Yet the nature of the 'active' free peptide backbone conformation has been a matter of debate and controversy. In order to test the validity of the structural modeling claims, we have undertaken detailed conformational studies of the two laminin-1 derived peptides YIGSR and CDPGYIGSR along with the biologically inactive YIGSK analog by two-dimensional solution 1H NMR spectroscopy in three different solvent systems. Herein we report that although both the active (YIGSR, CDPGYIGSR) and the inactive (YIGSK) peptides can adopt several closely related conformations in solution, the two peptides share similar conformational preferences, and there are no significant structural differences between the active and inactive peptides, contrary to previously reported modeling data. We conclude that the basis of the peptide biological activity, in contrast to published models, cannot be attributed to well-defined structural preferences of the free peptides. We infer that the difference in bioactivity observed between YIGSR and YIGSK originates primarily from the chemical nature of the arginine versus lysine sidechain substitution, rather than being due to a structural change in the free peptide conformations.
Collapse
Affiliation(s)
- M Jaseja
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Massachusetts 59717, USA
| | | | | |
Collapse
|
9
|
Abstract
Leuprolide acetate (pGlu-His-Trp-Ser-Tyr-d-Leu-Leu-Arg-Pro-NHEt), a potent LHRH agonist in wide clinical use, was characterized conformationally by NMR and circular dichroism. It displayed quite different preferred conformations under different solution conditions: two low population beta-turns in water, a nascent helix in TFE/water at low pH, and a high population beta-turn in TFE/water at slightly acidic pH. The pH-related conformational change in TFE/water is attributed to the pK(a) of the acetate counterion, not to ionizable groups on the peptide. None of these conformations are in exact agreement with previous computational predictions.
Collapse
Affiliation(s)
- J D Meyer
- Center for Pharmaceutical Biotechnology, University of Colorado Health Sciences Center, Denver, USA
| | | | | |
Collapse
|
10
|
Alexander McNamara LM, Andrews MJ, Mitzel F, Siligardi G, Tabor AB. Peptides constrained by an aliphatic linkage between two C(alpha) sites: design, synthesis, and unexpected conformational properties of an i,(i + 4)-linked peptide. J Org Chem 2001; 66:4585-94. [PMID: 11421778 DOI: 10.1021/jo015508e] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel route for the synthesis of cyclic peptides constrained by an aliphatic bridge between two C(alpha)sites, using a triply orthogonal protecting group strategy, is described. The synthesis of the orthogonally protected bis-amino acid 1, via an enantioselective route utilizing the Schöllkopf and Evans methodologies, is first described. This is then incorporated into a short, alanine-rich peptide 13, using a novel triply orthogonal protecting group strategy to couple first one, then the other, amino acid moiety in such a way that an aliphatic bridge is formed between the i and i + 4 positions. Unexpectedly, the resulting constrained peptide does not adopt a helical conformation: instead, it is shown by CD at low temperature to adopt a left-handed type II beta-turn conformation in aqueous media and a right-handed type I beta-turn conformation in TFE.
Collapse
Affiliation(s)
- L M Alexander McNamara
- Department of Chemistry, University College London, Christoper Ingold Laboratories, 20 Gordon Street, London WC1H 0AJ, U.K
| | | | | | | | | |
Collapse
|
11
|
Abstract
The structural stabilizing property of 2,2,2-trifluoroethanol (TFE) in peptides has been widely demonstrated. More recently, TFE has been shown to enhance secondary structure content in globular proteins, and to influence quaternary interactions in protein multimers. The molecular mechanisms by which TFE exerts its influence on peptide and protein structures remain poorly understood. The present analysis integrates the known physical properties of TFE with a variety of experimental observations on the interaction of TFE with peptides and proteins and on the properties of fluorocarbons. Two features of TFE, namely the hydrophobicity of the trifluoromethyl group and the hydrogen bonding character (strong donor and poor acceptor), emerge as the most important factors for rationalising the observed effects of TFE. A model is proposed for TFE interaction with peptides which involves an initial replacement of the hydration shell by fluoroalcohol molecules, a process driven by apolar interactions and favourable entropy of dehydration. Subsequent bifurcated hydrogen-bond formation with peptide carbonyl groups, which leave intramolecular interactions unaffected, promotes secondary structure formations.
Collapse
Affiliation(s)
- R Rajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
| | | |
Collapse
|
12
|
Abstract
The conformation of the repeating heptapeptide unit of the carboxyl-terminal domain of RNA Polymerase II, Y1S2P3T4S5P6S7 has been examined using nuclear magnetic resonance spectroscopy and circular dichroism. Nuclear Overhauser effects and CD spectra for the synthetic 56-residue peptide H2N-(S2P3T4S5P6S7Y1)8-COOH in water indicate that the peptide is largely unordered. A small population of folded molecules is observed to contain beta-turns located at Ser2-Pro3-Thr4-Ser5 (SPTS) and Ser5-Pro6-Ser7-Tyr1 (SPSY). CD and NMR results in 90% TFE also indicate an equilibrium population of structures, but the fraction of turns is higher. Similarities of nuclear Overhauser effects in water and in 90% TFE suggest that the structures in TFE are biologically relevant. Based on these observations, the average structure of a single conformer of the heptapeptide repeat in 90% TFE was obtained by a distance geometry-simulated annealing method, using distance restraints extracted from nuclear Overhauser data. NMR spectra of the 56-mer show signals corresponding to only one repeat indicating that each repeat is in an identical environment. Thus it is possible to obtain an average structure of the heptapeptide repeat from NOE data on the 56-mer. Twenty-seven final structures were calculated and the root mean square deviations between the 27 structures and the mean coordinates was 1.52 A for the backbone and 2.2 A for all nonhydrogen atoms. The heptapeptide repeat consists of two overlapping beta-turns which are potentially stabilized by hydrogen bonds. The hydroxyl side chains of Ser2, Ser5, Thr4, and Ser7 all appear to be equally exposed for potential phosphorylation. The tyrosyl side chain of each repeat is folded inwards to the backbone and can potentially hydrogen bond to the carbonyl oxygen of the tyrosine in the preceding repeat. Interation of the average structure of the heptapeptide repeat results in a model of the carboxyl-terminal domain with a regular but unusual secondary structure consisting of a series of staggered beta-turns.
Collapse
Affiliation(s)
- P M Cagas
- Howard Hughes Medical Institute, Johns Hopkins Medical School, Baltimore, Maryland 21205, USA
| | | |
Collapse
|
13
|
Siedler F, Quarzago D, Rudolph-Böhner S, Moroder L. Redox-active bis-cysteinyl peptides. II. Comparative study on the sequence-dependent tendency for disulfide loop formation. Biopolymers 1994; 34:1563-72. [PMID: 7827267 DOI: 10.1002/bip.360341114] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Bis(cysteinyl)octapeptides related to the active sites of the oxidoreductases protein disulfide isomerase (PDI), thioredoxin reductase (trr), glutaredoxin (grx), and thioredoxin (trx) were analyzed for their propensity to form the intramolecular 14-membered disulfide ring in oxidation experiments. The rank order of percentage of cyclic monomer formed in aqueous buffer (pH 7.0) at 10(-3) M concentration was found to be very similar, but opposite to that of the Kox and, correspondingly, of the redox potentials of the native enzymes. Attempts to induce intrinsic conformational preferences of the peptides by addition of trifluoroethanol led to enhancements of beta-turn structures as reflected by the CD and Fourier transform ir spectra. The induced secondary structure, instead of aligning the tendencies of the excised fragments for loop formation with those of the intact proteins, was found to suppress the differences by significantly increasing the preference for cyclic monomers (approximately 90%). Similarly, operating under denaturing conditions, i.e., in 6 M guanidinium hydrochloride, only for the trx peptide was the statistical product distribution obtained. For the remaining peptides, again a strong increase of cyclic monomer contents was observed that could not be correlated with dissolution of beta-sheet type aggregates. The CD spectra are more consistent with the presence of ordered structure to some extent, possibly resulting from an hydrophobic collapse of the sparingly soluble peptides. The results of the oxidation experiments further support previous findings from thiol disulfide interchange equilibria, which clearly revealed a decisive role of the characteristic thioredoxin structural motif in dictating the redox properties of the enzymes. Point mutations in the active sites of the oxidoreductases allowed us to affect their redox potentials strongly, but apparently only in the constraint form of the three-dimensional structure as similar exchanges in the excised fragments did not produce the expected effect. This observation contrasts with numerous reports that the conformation of short disulfide loops is mainly dictated by the amino acid sequence.
Collapse
Affiliation(s)
- F Siedler
- Max-Planck Institute of Biochemistry, Martinsried, Germany
| | | | | | | |
Collapse
|
14
|
Roig X, Novella IS, Giralt E, Andreu D. Examining the relationship between secondary structure and antibody recognition in immunopeptides from foot-and-mouth disease virus. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf00132761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
15
|
Abstract
NMR spectroscopic experiments were performed to study the structure of synthetic peptides identical to two extracellular regions of the human thrombin receptor. The smaller molecule, comprising 14 amino acids, was biologically active and was equivalent to the "tethered ligand" exposed after cleavage of the receptor by thrombin. The principal structural elements were two overlapping turns (amino acids 5-8 and 6-9), the second of which was stabilized by a hydrogen bond, 6CO-9NH. The five N-terminal residues, considered to be responsible for biological activity, were essentially unstructured. A second version of this peptide, biologically inactive due to the reversal of the two N-terminal amino acids, had a very similar structure. A longer peptide (23 amino acids) covering the proposed thrombin cleavage site was found to be more highly structured. The seven residues from Pro-2 to Arg5 (the N-terminal amino acid exposed after cleavage is taken as residue 1) formed a 3(10) helix which is not present in the shorter tethered ligand peptide. The structure is partially stabilized by a charged hydrogen bond between the side chains of Arg-1 and Asp-3. The overlapping turns observed in the shorter peptides could also be distinguished in the longer molecule. On the basis of the structure determined for the peptide which encompasses the cleavage site and the determined structure of thrombin, a model is postulated for the interaction of the thrombin receptor and the protease during activation.
Collapse
Affiliation(s)
- K J Smith
- School of Biochemistry, University of Birmingham, Edgbaston, U.K
| | | | | |
Collapse
|
16
|
Shin HC, Merutka G, Waltho JP, Wright PE, Dyson HJ. Peptide models of protein folding initiation sites. 2. The G-H turn region of myoglobin acts as a helix stop signal. Biochemistry 1993; 32:6348-55. [PMID: 8518280 DOI: 10.1021/bi00076a007] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A series of peptide fragments of sperm whale myoglobin, corresponding to segments of the region between the G- and H-helices of the protein, have been synthesized and their conformational preferences investigated using circular dichroism and nuclear magnetic resonance spectroscopy in aqueous solution and in solvent mixtures containing water and trifluoroethanol. The smallest fragment, Mb-GH5, a five-residue peptide with the sequence HPGDF corresponding to the connecting loop between the two helices in the folded protein, adopts highly populated turn conformations in aqueous solution. A 25-residue peptide, Mb-GH25, containing the same sequence flanked by contiguous segments of the G- and H-helix sequences, was also found to contain a high proportion of conformers with a turn in this region. No helix formation was observed in the flanking sequences in water solution, either in Mb-GH25 or in control 10-residue peptides (Mb-G10 and Mb-H10) with sequences corresponding to the G- and H-helix segments. No additional helicity above that of the sum of the components was observed for Mb-GH25, indicating that a helical hairpin structure is not formed in the monomeric peptide in aqueous solution. In the presence of TFE, ordered helix is formed in Mb-GH25 according to the CD spectrum, and NMR spectra indicate that this is localized in the N-terminal portion of the peptide. NOESY spectra clearly show that the turn conformation is retained under these conditions.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- H C Shin
- Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037
| | | | | | | | | |
Collapse
|
17
|
Siligardi G, Campbell MM, Gibbons WA, Drake AF. Conformational analysis of the melanin-concentrating hormone core by circular dichroic spectroscopy. Disulphide bridge and tyrosine contributions. Eur J Biochem 1992; 206:23-9. [PMID: 1587273 DOI: 10.1111/j.1432-1033.1992.tb16897.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A detailed circular dichroic (CD) study of the conformational flexibility of the melanin-concentrating hormone core [MCH(5-14)] is reported. Variable pH (2-10) and temperature (-80 degrees to +80 degrees C) in aqueous media reveal that CD contributions from tyrosine, disulphide bridge and the amide backbone can be discriminated. Only below -10 degrees C does a preferred -S-S-conformation (P chirality, dihedral angle phi = 90 +/- 10 degrees) dominate. The amide backbone CD contribution varies over all temperatures (-80 degrees to +80 degrees C) providing evidence for a type-II beta-turn at low temperatures, with the emergence of a type-I beta-turn at higher temperatures. Tyrosine exhibits a special behaviour at pH 7. These conclusions are in broad agreement with published NMR studies. Nevertheless, the MCH(5-14) core is seen to be conformationally flexible in aqueous solution at ambient temperatures. Conformation differences are observed in a non-aqueous environment.
Collapse
Affiliation(s)
- G Siligardi
- Department of Chemistry, University of Calabria, Arcavacata di Rende (CS), Italy
| | | | | | | |
Collapse
|
18
|
Siligardi G, Drake AF, Mascagni P, Rowlands D, Brown F, Gibbons WA. Correlations between the conformations elucidated by CD spectroscopy and the antigenic properties of four peptides of the foot-and-mouth disease virus. Eur J Biochem 1991; 199:545-51. [PMID: 1651235 DOI: 10.1111/j.1432-1033.1991.tb16153.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational features of four related antigenic peptides (A, B, C and USA) from the foot-and-mouth disease virus (FMDV) (VP1; 141-160 of serotype A, subtype 12), assessed by CD, were found to correlate with the serological properties of these peptides. The CD spectra of the four peptides, obtained under cryogenic and solvent titration conditions, were consistent with three conformational components (a left-handed extended helix, an alpha-helix and a 3(10) helix) for peptides A and C and four components (a beta-turn of type II, an alpha-helix, a gamma-turn and a 3(10) helix) for peptides B and USA. The amino acid substitutions at positions 148 and 153, which distinguish the peptides, are therefore responsible for both their conformational and antigenic differences.
Collapse
Affiliation(s)
- G Siligardi
- School of Pharmacy, Department of Pharmaceutical Chemistry, London, England
| | | | | | | | | | | |
Collapse
|
19
|
Bracci L, Antoni G, Cusi MG, Lozzi L, Niccolai N, Petreni S, Rustici M, Santucci A, Soldani P, Valensin PE. Antipeptide monoclonal antibodies inhibit the binding of rabies virus glycoprotein and alpha-bungarotoxin to the nicotinic acetylcholine receptor. Mol Immunol 1988; 25:881-8. [PMID: 3062388 DOI: 10.1016/0161-5890(88)90125-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
It has been reported that binding to muscle nicotinic acetylcholine receptor at the post-synaptic membrane is an important event of the rabies virus neurotropism. The binding site can be located within the 190-203 region of the virus glycoprotein sharing a high degree of homology with the "toxic loop" of the curare-mimetic snake neurotoxins. We have synthesized a tetradecapeptide corresponding to this glycoprotein region and used it, following conjugation with an immunogenic carrier to raise MAbs. We found that some MAbs raised against the peptide were able to recognize both the virus glycoprotein and the snake neurotoxin alpha-bungarotoxin; moreover, they can inhibit the binding of rabies virus glycoprotein and alpha-bungarotoxin to the nicotinic acetylcholine receptor extracted from the electric organs of Torpedo marmorata. On the basis of this cross-reactivity, we suggest that rabies virus glycoprotein and curare-mimetic snake neurotoxins share three-dimensionally similar structures in order to bind to the nicotinic cholinergic receptor. The potential use of the immunogenic properties of the peptide for the rational design of a synthetic vaccine against rabies is proposed.
Collapse
Affiliation(s)
- L Bracci
- Dipartimento di Biologia Evolutiva Via P. A. Mattioli, Università di Siena, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Lentz TL, Hawrot E, Wilson PT. Synthetic peptides corresponding to sequences of snake venom neurotoxins and rabies virus glycoprotein bind to the nicotinic acetylcholine receptor. Proteins 1987; 2:298-307. [PMID: 3448605 DOI: 10.1002/prot.340020406] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Peptides corresponding to portions of loop 2 of snake venom curare-mimetic neurotoxins and to a structurally similar region of rabies virus glycoprotein were synthesized. Interaction of these peptides with purified Torpedo electric organ acetylcholine receptor was tested by measuring their ability to block the binding of 125I-labeled alpha-bungarotoxin to the receptor. In addition, inhibition of alpha-bungarotoxin binding to a 32-residue synthetic peptide corresponding to positions 173-204 of the alpha-subunit was determined. Neurotoxin and glycoprotein peptides corresponding to toxin loop 2 inhibited labeled toxin binding to the receptor with IC50 values comparable to those of nicotine and the competitive antagonist d-tubocurarine and to the alpha-subunit peptides with apparent affinities between those of d-tubocurarine and alpha-cobratoxin. Substitution of neurotoxin residue Arg37, the proposed counterpart of the quaternary ammonium of acetylcholine, with a negatively charged Glu residue reduced the apparent affinity about 10-fold. Peptides containing the neurotoxin invariant residue Trp29 and 10- to 100-fold higher affinities than peptides lacking this residue. These results demonstrate that relatively short synthetic peptides retain some of the binding ability of the native protein from which they are derived, indicating that such peptides are useful in the study of protein-protein interactions. The ability of the peptides to compete alpha-bungarotoxin binding to the receptor with apparent affinities comparable to those of other cholinergic ligands indicates that loop 2 of the neurotoxins and the structurally similar segment of the rabies virus glycoprotein act as recognition sites for the acetylcholine receptor. Invariant toxin residues Arg37 and Trp29 and their viral homologs play important, although not essential, roles in binding, possibly by interaction with complementary anionic and hydrophobic subsites on the acetylcholine receptor. The alpha-subunit peptide most likely contains all of the determinants for binding of the toxin and glycoprotein peptides present on the alpha-subunit, because these peptides bind to the 32-residue alpha-subunit peptide with the same or greater affinity as to the intact subunit.
Collapse
Affiliation(s)
- T L Lentz
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510
| | | | | |
Collapse
|
21
|
Moroder L, Besse D, Musiol HJ, Rudolph-Böhner S, Siedler F. Oxidative folding of cystine-rich peptides vs regioselective cysteine pairing strategies. Biopolymers 1996; 40:207-34. [PMID: 8785364 DOI: 10.1002/(sici)1097-0282(1996)40:2<207::aid-bip2>3.0.co;2-#] [Citation(s) in RCA: 112] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The methodology of regioselective cysteine pairings in synthetic multiple-cystine peptides has progressed in the past years to an efficiency that allows for at least three specific inter- and intrachain disulfide bridgings. Conformational studies on various multiple-cystine peptides like hormones, protease inhibitors, and toxins revealed that these bioactive peptides, generated by posttranslational processing of precursor proteins, are folded into miniprotein-like compact globular structures of remarkable stability. This strongly suggests protein domain or subdomain properties of these families of peptides, and thus sufficient sequence-encoded information for correct oxidative refolding under appropriate experimental conditions. From intensive research on the mechanisms and pathways of oxidative refolding of proteins in vivo and in vitro, the efficient methods have emerged for simulating nature in the regeneration of native folds not only for intact proteins, but also for protein domains and subdomains. In fact, the results obtained in the oxidative folding of excised protein fragments and of relatively low mass products of posttranslational processings show that this procedure is indeed a simple way of preparing peptides with several disulfide bonds, if optimization of reaction conditions is performed in terms of redox buffer, temperature, and additives capable of disrupting aggregates and of stabilizing nascent secondary structures. Moreover, with increased knowledge about stable, small natural cystine frameworks, their use instead of artificial templates should facilitate engineering of synthetic miniproteins with specific conformation and tailored functions.
Collapse
Affiliation(s)
- L Moroder
- Max-Planck-Institut für Biochemie, Martinsried, Germany
| | | | | | | | | |
Collapse
|