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Tian J, López CA, Derdeyn CA, Jones MS, Pinter A, Korber B, Gnanakaran S. Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein. PLoS Comput Biol 2016; 12:e1005094. [PMID: 27716795 PMCID: PMC5055340 DOI: 10.1371/journal.pcbi.1005094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/01/2016] [Indexed: 12/14/2022] Open
Abstract
Heavy glycosylation of the envelope (Env) surface subunit, gp120, is a key adaptation of HIV-1; however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. Here we explore the patterns of HIV-1 Env gp120 glycosylation, and particularly the enrichment in glycosylation sites proximal to the disulfide linkages at the base of the surface-exposed variable domains. To dissect the influence of glycans on the conformation these regions, we focused on an antigenic peptide fragment from a disulfide bridge-bounded region spanning the V1 and V2 hyper-variable domains of HIV-1 gp120. We used replica exchange molecular dynamics (MD) simulations to investigate how glycosylation influences its conformation and stability. Simulations were performed with and without N-linked glycosylation at two sites that are highly conserved across HIV-1 isolates (N156 and N160); both are contacts for recognition by V1V2-targeted broadly neutralizing antibodies against HIV-1. Glycosylation stabilized the pre-existing conformations of this peptide construct, reduced its propensity to adopt other secondary structures, and provided resistance against thermal unfolding. Simulations performed in the context of the Env trimer also indicated that glycosylation reduces flexibility of the V1V2 region, and provided insight into glycan-glycan interactions in this region. These stabilizing effects were influenced by a combination of factors, including the presence of a disulfide bond between the Cysteines at 131 and 157, which increased the formation of beta-strands. Together, these results provide a mechanism for conservation of disulfide linkage proximal glycosylation adjacent to the variable domains of gp120 and begin to explain how this could be exploited to enhance the immunogenicity of those regions. These studies suggest that glycopeptide immunogens can be designed to stabilize the most relevant Env conformations to focus the immune response on key neutralizing epitopes. Heavy glycosylation of the envelope surface subunit, gp120, is a key adaptation of HIV-1, however, the precise effects of glycosylation on the folding, conformation and dynamics of this protein are poorly understood. The network of glycans on gp120 is of particular interest with regards to vaccine design, because the glycans both serve as targets for many classes of broadly neutralizing antibodies, and contribute to patterns of immune evasion and escape during HIV-1 infection. In this manuscript, we report on how glycosylation influences an immunogenic but disordered region of gp120. Glycosylation stabilizes the pre-existing conformation, and reduces its propensity to form other secondary structures. It also stabilizes preformed conformation against thermal unfolding. These complementary effects originate from a combination of multiple factors, including the observation that having a glycosylation site adjacent to the disulfide bond further promotes the formation of beta-strand structure in this peptide.
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Affiliation(s)
- Jianhui Tian
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Center for Biomolecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Cesar A. López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Cynthia A. Derdeyn
- Department of Pathology and Laboratory Medicine and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Morris S. Jones
- University of California Berkeley, School of Public Health, Berkeley, California, United States of America
| | - Abraham Pinter
- New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Bette Korber
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - S. Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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2
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Chiodi CG, Verli H. Structural characterization of NETNES glycopeptide from Trypanosoma cruzi. Carbohydr Res 2013; 373:28-34. [PMID: 23578542 DOI: 10.1016/j.carres.2013.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 11/26/2022]
Abstract
Trypanosoma cruzi is a protozoan, responsible for Chagas disease, that parasites triatomines and some vertebrates, mainly Homo sapiens. In 2010, nearly 10 million people in whole world, most from Latin America, had Chagas disease, which is an illness of high morbidity, low mortality, and serious problems of quality of life. The available treatment has high toxicity and low efficacy at chronic phase. Some of the protozoan antigenic or virulence factors include complex carbohydrate structures that, due to their uniqueness, may constitute potential selective targets for the development of new treatments. One example of such structures is NETNES, a low abundance T. cruzi glycopeptide, comprising 13 amino acid residues, one or two N-glycosylation chains, a GPI anchor and two P-glycosylations. In this context, the current work aims to obtain an atomic model for NETNES, including its glycan chains and membrane attachment, in order to contribute in the characterization of its structure and dynamics. Based on POPC and GPI models built in agreement with experimental data, our results indicate that, in the first third of the simulation, NETNES peptide is very flexible in solution, bending itself between asparagine residues and lying down on some carbohydrates and membrane, exposing amino acid residues and some other glycans, mainly terminal mannoses, to the extracellular medium, remaining in this position until the end of simulations.
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Affiliation(s)
- Carla G Chiodi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre 91500-970, RS, Brazil.
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3
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Sandhu N, Duus K, Jørgensen CS, Hansen PR, Bruun SW, Pedersen LØ, Højrup P, Houen G. Peptide binding specificity of the chaperone calreticulin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:701-13. [PMID: 17499031 DOI: 10.1016/j.bbapap.2007.03.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 03/28/2007] [Accepted: 03/29/2007] [Indexed: 10/23/2022]
Abstract
Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composition. A large set of available synthetic peptides (n=127) was tested for binding to calreticulin and the results analysed by multivariate data analysis. The parameter that correlated best with binding was hydrophobicity while beta-turn potential disfavoured binding. Only hydrophobic peptides longer than 5 amino acids showed binding and a clear correlation with hydrophobicity was demonstrated for oligomers of different hydrophobic amino acids. Insertion of hydrophilic amino acids in a hydrophobic sequence diminished or abolished binding. In conclusion our results show that calreticulin has a peptide-binding specificity for hydrophobic sequences and delineate the fine specificity of calreticulin for hydrophobic amino acid residues.
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Affiliation(s)
- Noreen Sandhu
- Department of Autoimmunology, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
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4
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Abstract
This review describes the recent advances in the field of glycopeptide and small glycoprotein synthesis. The strategies covered include chemical and chemoenzymatic synthesis, native chemical ligation (NCL), and expressed chemical ligation. The importance of glycopeptide synthesis is exemplified by giving the reader an overview of how versatile and important these well-defined glycopeptides are as tools in glycobiology.
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Affiliation(s)
- Therese Buskas
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA
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5
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Fusetti F, Schröter KH, Steiner RA, van Noort PI, Pijning T, Rozeboom HJ, Kalk KH, Egmond MR, Dijkstra BW. Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Structure 2002; 10:259-68. [PMID: 11839311 DOI: 10.1016/s0969-2126(02)00704-9] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Quercetin 2,3-dioxygenase is a copper-containing enzyme that catalyzes the insertion of molecular oxygen into polyphenolic flavonols. Dioxygenation catalyzed by iron-containing enzymes has been studied extensively, but dioxygenases employing other metal cofactors are poorly understood. We determined the crystal structure of quercetin 2,3-dioxygenase at 1.6 A resolution. The enzyme forms homodimers, which are stabilized by an N-linked heptasaccharide at the dimer interface. The mononuclear type 2 copper center displays two distinct geometries: a distorted tetrahedral coordination, formed by His66, His68, His112, and a water molecule, and a distorted trigonal bipyramidal environment, which additionally comprises Glu73. Manual docking of the substrate quercetin into the active site showed that the different geometries of the copper site might be of catalytic importance.
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Affiliation(s)
- Fabrizia Fusetti
- Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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6
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Abstract
N-linked oligosaccharides arise when blocks of 14 sugars are added cotranslationally to newly synthesized polypeptides in the endoplasmic reticulum (ER). These glycans are then subjected to extensive modification as the glycoproteins mature and move through the ER via the Golgi complex to their final destinations inside and outside the cell. In the ER and in the early secretory pathway, where the repertoire of oligosaccharide structures is still rather small, the glycans play a pivotal role in protein folding, oligomerization, quality control, sorting, and transport. They are used as universal "tags" that allow specific lectins and modifying enzymes to establish order among the diversity of maturing glycoproteins. In the Golgi complex, the glycans acquire more complex structures and a new set of functions. The division of synthesis and processing between the ER and the Golgi complex represents an evolutionary adaptation that allows efficient exploitation of the potential of oligosaccharides.
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Affiliation(s)
- A Helenius
- Institute of Biochemistry, Eidgenössische Technische Hochschule Zürich, Universitätstrasse 16, CH-8092 Zürich, Switzerland
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7
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O'Conner SE, Imperiali B. A molecular basis for glycosylation-induced conformational switching. CHEMISTRY & BIOLOGY 1998; 5:427-37. [PMID: 9710565 DOI: 10.1016/s1074-5521(98)90159-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Asparagine-linked glycosylation has the capacity to greatly influence the structure and function of glycoproteins. In most cases, however, it is unclear specifically how the carbohydrate moiety interacts with the protein to influence its conformation. RESULTS A series of glycosylation based on the critical A285 glycosylation site of the hemagglutinin glycoprotein from influenza from influenza virus was used as a model system to study the effects of asparagine-linked glycosylation. Derivatization of this peptide with a family of short carbohydrates reveals that subtle changes in the structure of the carbohydrate have a dramatic impact on peptide conformation. Modification of the hemagglutinin glycopeptide with a truncated version of the native carbohydrate induces a beta-turn structure similar to the structure found in the native protein. Replacement of the C2 and C2' N-acetyl groups of the carbohydrates with hydroxyl moieties results in a less well-ordered peptide conformation. CONCLUSIONS It is likely that the N-acetyl groups of the carbohydrates have a critical role in promoting the more compact beta-turn conformation through steric interactions with the peptide. This study has demonstrated that relatively small changes in carbohydrate composition can have dramatic ramifications on glycopeptide conformation.
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Affiliation(s)
- S E O'Conner
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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8
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Yang J, Teplyakov A, Quail JW. Crystal structure of the aspartic proteinase from Rhizomucor miehei at 2.15 A resolution. J Mol Biol 1997; 268:449-59. [PMID: 9159482 DOI: 10.1006/jmbi.1997.0968] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The crystal structure of the aspartic proteinase from Rhizomucor miehei (RMP, EC 3. 4. 23. 23) has been refined to 2.15 A resolution to a crystallographic R-value of 0.215 and an Rfree of 0.281. The root-mean-square (r.m.s.) error for the atomic coordinates estimated from a Luzzati plot is 0.2 A. The r.m.s. deviations for the bond distances and bond angles from ideality are 0.01 A and 1.7 degrees, respectively. RMP contains two domains that consist predominantly of beta-sheets. A large substrate-binding cleft is clearly visible between the two domains, and the two catalytic residues Asp38 and Asp237 are located in the middle of the cleft with a water molecule bridging the carboxyl groups of Asp38 and Asp237. Due to crystal packing, the C-terminal domain is more mobile than the N-terminal domain. Most of the aspartic proteinases (except renin) reach their maximum activity at acidic pH. We propose that the optimum pH of each aspartic proteinase is determined by the electrostatic potential at the active site, which, in turn, is determined by the positions and orientations of all the residues near the active site. RMP is the most glycosylated among the aspartic proteinases. The carbohydrate moieties are linked to Asn79 and Asn188. Asn79 is in the middle of a beta-strand and Asn188 is on a surface loop in contrast to the previous hypothesis proposed by Brown and Yada that they are both on surface beta-turns. RMP has a very high thermal stability. The high thermal stability is probably due to the high level of glycosylation. We propose that the highly flexible carbohydrates act as heat reservoirs to stabilize the conformation of RMP and therefore give the enzyme a high level of thermal stability. Three-dimensional structural and sequence alignments of RMP with other aspartic proteinases show that RMP is most structurally homologous to that of Mucor pusillus (MPP), and differs from other fungal enzymes as much as it does from the mammalian enzymes. This suggests that RMP and MPP diverged from the main stream of aspartic proteinases at an early stage of evolution. The present study adds a second member to this subfamily of aspartic proteinases.
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Affiliation(s)
- J Yang
- Department of Chemistry, University of Saskatchewan, Saskatoon, Canada
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9
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O'Connor SE, Imperiali B. Modulation of protein structure and function by asparagine-linked glycosylation. CHEMISTRY & BIOLOGY 1996; 3:803-12. [PMID: 8939697 DOI: 10.1016/s1074-5521(96)90064-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
In eukaryotic cells, many enzymes are devoted to the construction of the complex glycan structures that decorate secreted and cell-surface proteins. Recent studies have begun to elucidate the effects of asparagine-linked glycosylation on protein folding and on the structure and function of mature glycoproteins.
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Affiliation(s)
- S E O'Connor
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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10
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Imperiali B, Rickert KW. Conformational implications of asparagine-linked glycosylation. Proc Natl Acad Sci U S A 1995; 92:97-101. [PMID: 7816856 PMCID: PMC42824 DOI: 10.1073/pnas.92.1.97] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The effects of cotranslational protein modification on the process of protein folding are poorly understood. Time-resolved fluorescence energy transfer has been used to assess the impact of glycosylation on the conformational dynamics of flexible oligopeptides. The peptide sequences examined are selected from glycoproteins of known three-dimensional structure. The energy transfer modulation associated with N-linked glycosylation is consistent with the glycopeptides sampling different conformational profiles in water. Results show that glycosylation causes the modified peptides to adopt a different ensemble of conformations, and for some peptides this change may lead to conformations that are more compact and better approximate the conformation of these peptides in the final folded protein. This result further implies that cotranslational glycosylation can trigger the timely formation of structural nucleation elements and thus assist in the complex process of protein folding.
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Affiliation(s)
- B Imperiali
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125
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11
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Bell AF, Ford SJ, Hecht L, Wilson G, Barron LD. Vibrational Raman optical activity of glycoproteins. Int J Biol Macromol 1994; 16:277-8. [PMID: 7893631 DOI: 10.1016/0141-8130(94)90033-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This paper reports the first vibrational Raman optical activity (ROA) spectrum of a glycoprotein. The sample, orosomucoid (alpha 1-acid glycoprotein), shows ROA bands characteristic of a high beta-sheet content together with new bands which could be specific for the carbohydrate and its association with the protein. Our results suggest that ROA spectra of intact glycoproteins may contain information about both protein and carbohydrate conformation and the mutual influence on each other's stability and conformation.
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Affiliation(s)
- A F Bell
- Chemistry Department, The University, Glasgow, UK
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12
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Davis J, Hirani S, Bartlett C, Reid B. 1H NMR studies on an Asn-linked glycopeptide. GlcNAc-1 C2-N2 bond is rigid in H2O. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(17)41867-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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13
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Kern G, Kern D, Jaenicke R, Seckler R. Kinetics of folding and association of differently glycosylated variants of invertase from Saccharomyces cerevisiae. Protein Sci 1993; 2:1862-8. [PMID: 8268797 PMCID: PMC2142293 DOI: 10.1002/pro.5560021108] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A core-glycosylated form of the dimeric enzyme invertase has been isolated from secretion mutants of Saccharomyces cerevisiae blocked in transport to the Golgi apparatus. This glycosylation variant corresponds to the form that folds and associates during biosynthesis of the protein in vivo. In the present work, its largely homogeneous subunit size and well-defined quaternary structure were utilized to characterize the folding and association pathway of this highly glycosylated protein in comparison with the nonglycosylated cytoplasmic and the high-mannose-glycosylated periplasmic forms of the same enzyme encoded by the suc2 gene. Renaturation of core-glycosylated invertase upon dilution from guanidinium-chloride solutions follows a unibimolecular reaction scheme with consecutive first-order subunit folding and second-order association reactions. The rate constant of the rate-limiting step of subunit folding, as detected by fluorescence increase, is k1 = 1.6 +/- 0.4 x 10(-3) s-1 at 20 degrees C; it is characterized by an activation enthalpy of delta H++ = 65 kJ/mol. The reaction is not catalyzed by peptidyl-prolyl cis-trans isomerase of the cyclophilin type. Reactivation of the enzyme depends on protein concentration and coincides with subunit association, as monitored by size-exclusion high-pressure liquid chromatography. The association rate constant, estimated by numerical simulation of reactivation kinetics, increases from 5 x 10(3) M-1 s-1 to 7 x 10(4) M-1 s-1 between 5 and 30 degrees C.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- G Kern
- Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Germany
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14
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Brown ED, Yada RY. A kinetic and equilibrium study of the denaturation of aspartic proteinases from the fungi, Endothia parasitica and Mucor miehei. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1076:406-15. [PMID: 2001389 DOI: 10.1016/0167-4838(91)90484-h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Kinetic and equilibrium analyses of the denaturation of Endothia parasitica and Mucor miehei aspartic proteinases were performed using enzyme activity and ultraviolet absorption as indices of denaturation. Denaturation of these proteinases was shown to be irreversible, suggesting that the conformations of these aspartic proteinases may be predetermined in their zymogens. Thermal and guanidine hydrochloride denaturation of these proteinases produced first-order, two-state, kinetic behaviour. Equilibrium unfolding transitions of these proteinases were highly cooperative but not entirely coincident in the two indices employed, suggesting some deviation from two-state character. Oxidation to remove 37.8% of the carbohydrate of M. miehei glycoproteinase with sodium metaperiodate resulted in a substantial decrease in both kinetic and equilibrium stabilities without modification of the amino acid composition or specific activity. In addition, gel filtration subsequent to equilibrium studies indicated that partial removal of the carbohydrate from M. miehei proteinase promoted autolysis under denaturing conditions.
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Affiliation(s)
- E D Brown
- Department of Food Science, University of Guelph, Canada
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15
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Ball JB, Andrews PR, Alewood PF, Hughes RA. A one-variable topographical descriptor for the beta-turns of peptides and proteins. FEBS Lett 1990; 273:15-8. [PMID: 2226846 DOI: 10.1016/0014-5793(90)81040-u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The beta-turn is a common secondary structure in biologically active peptides and globular proteins, where it is widely thought to serve as a molecular recognition site for many biological processes. Although the primary beta-turn recognition requirements are thought to be straightforward, relating mainly to the relative positions of the peptide sidechains, current classifications of beta-turns are complex and are based solely upon the very variable geometry of the peptide backbone. We demonstrate here that beta-turns can be described in terms of a single dihedral angle, which we have called beta, which provides a complete description of the spatial relationship between the entry and exit peptide bonds as well as the relative orientations of the intervening sidechains for any beta-turn. This description should prove particularly useful in the development and application of novel peptide mimetic drugs, compounds for which a classification based on a peptide backbone geometry may be entirely irrelevant.
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Affiliation(s)
- J B Ball
- School of Pharmaceutical Chemistry, Victorian College of Pharmacy Ltd., Parkville, Australia
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16
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Schülke N, Schmid FX. Effect of glycosylation on the mechanism of renaturation of invertase from yeast. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68382-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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