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Risso VA, Ermácora MR. Equilibrium partially folded states of B. licheniformis
β
-lactamase. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2019; 48:341-348. [PMID: 30929094 DOI: 10.1007/s00249-019-01361-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 02/14/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
Abstract
β -Lactamases (penicillinases) facilitate bacterial resistance to antibiotics and are excellent theoretical and experimental models in protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class Aβ -lactamase with three tryptophan residues located one in each of its two domains and one in the interface between domains. The conformational landscape of three well-characterized ESP Trp→ Phe mutants was characterized in equilibrium unfolding experiments by measuring tryptophan fluorescence, far-UV CD, activity, hydrodynamic radius, and limited proteolysis. The Trp→ Phe substitutions had little impact on the native conformation, but changed the properties of the partially folded states populated at equilibrium. The results were interpreted in the framework of modern theories of protein folding.
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Affiliation(s)
- Valeria A Risso
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071, Granada, Spain
| | - Mario R Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.
- Instituto Multidisciplinario de Biología Celular, Conicet-CIC-UNLP, Calle 526 y Camino General Belgrano, B1906APO, La Plata, Buenos Aires, Argentina.
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2
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Human Chitotriosidase: Catalytic Domain or Carbohydrate Binding Module, Who's Leading HCHT's Biological Function. Sci Rep 2017; 7:2768. [PMID: 28584264 PMCID: PMC5459812 DOI: 10.1038/s41598-017-02382-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 04/10/2017] [Indexed: 01/07/2023] Open
Abstract
Chitin is an important structural component of numerous fungal pathogens and parasitic nematodes. The human macrophage chitotriosidase (HCHT) is a chitinase that hydrolyses glycosidic bonds between the N-acetyl-D-glucosamine units of this biopolymer. HCHT belongs to the Glycoside Hydrolase (GH) superfamily and contains a well-characterized catalytic domain appended to a chitin-binding domain (ChBDCHIT1). Although its precise biological function remains unclear, HCHT has been described to be involved in innate immunity. In this study, the molecular basis for interaction with insoluble chitin as well as with soluble chito-oligosaccharides has been determined. The results suggest a new mechanism as a common binding mode for many Carbohydrate Binding Modules (CBMs). Furthermore, using a phylogenetic approach, we have analysed the modularity of HCHT and investigated the evolutionary paths of its catalytic and chitin binding domains. The phylogenetic analyses indicate that the ChBDCHIT1 domain dictates the biological function of HCHT and not its appended catalytic domain. This observation may also be a general feature of GHs. Altogether, our data have led us to postulate and discuss that HCHT acts as an immune catalyser.
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Risso VA, Acierno JP, Capaldi S, Monaco HL, Ermácora MR. X-ray evidence of a native state with increased compactness populated by tryptophan-less B. licheniformis β-lactamase. Protein Sci 2012; 21:964-76. [PMID: 22496053 DOI: 10.1002/pro.2076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 03/25/2012] [Accepted: 03/29/2012] [Indexed: 11/12/2022]
Abstract
β-lactamases confer antibiotic resistance, one of the most serious world-wide health problems, and are an excellent theoretical and experimental model in the study of protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class-A β-lactamase with three tryptophan residues located in the protein core. Here, we report the 1.7-Å resolution X-ray structure, catalytic parameters, and thermodynamic stability of ESP(ΔW), an engineered mutant of ESP in which phenylalanine replaces the wild-type tryptophan residues. The structure revealed no qualitative conformational changes compared with thirteen previously reported structures of B. licheniformis β-lactamases (RMSD = 0.4-1.2 Å). However, a closer scrutiny showed that the mutations result in an overall more compact structure, with most atoms shifted toward the geometric center of the molecule. Thus, ESP(ΔW) has a significantly smaller radius of gyration (R(g)) than the other B. licheniformis β-lactamases characterized so far. Indeed, ESP(ΔW) has the smallest R(g) among 126 Class-A β-lactamases in the Protein Data Bank (PDB). Other measures of compactness, like the number of atoms in fixed volumes and the number and average of noncovalent distances, confirmed the effect. ESP(ΔW) proves that the compactness of the native state can be enhanced by protein engineering and establishes a new lower limit to the compactness of the Class-A β-lactamase fold. As the condensation achieved by the native state is a paramount notion in protein folding, this result may contribute to a better understanding of how the sequence determines the conformational variability and thermodynamic stability of a given fold.
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Affiliation(s)
- Valeria A Risso
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 325, 1876 Bernal, Buenos Aires, Argentina
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4
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Scotto-Lavino E, Bai M, Zhang YB, Freimuth P. Export is the default pathway for soluble unfolded polypeptides that accumulate during expression in Escherichia coli. Protein Expr Purif 2011; 79:137-41. [PMID: 21443953 DOI: 10.1016/j.pep.2011.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 03/18/2011] [Accepted: 03/21/2011] [Indexed: 01/31/2023]
Abstract
Several E. coli endogenous, cytoplasmic proteins that are known clients of the chaperonin GroEL were overexpressed to examine the fate of accumulated unfolded polypeptides. Substantial fractions of about half of the proteins formed insoluble aggregates, consistent with the hypothesis that these proteins were produced at rates or in amounts that exceeded the protein-folding capacity of GroEL. In addition, large fractions of three overexpressed GroEL client proteins were localized in an extra-cytoplasmic, osmotically-sensitive compartment, suggesting they had initially accumulated in the cytoplasm as soluble unfolded polypeptides and thus were able to access a protein export pathway. Consistent with this model, an intrinsically unfoldable, hydrophilic, non-secretory polypeptide was quantitatively exported from the E. coli cytoplasm into an osmotically-sensitive compartment. Our results support the conclusion that a soluble, unfolded conformation alone may be sufficient to direct non-secretory polypeptides into a protein export pathway for signal peptide-independent translocation across the inner membrane, and that export rather than degradation by cytoplasmic proteases is the preferred fate for newly-synthesized, soluble, unfolded polypeptides that accumulate in the cytoplasm. The stable folded conformation of exported GroEL client proteins further suggests that the requirement for GroEL may be conditional on protein folding in the molecularly-crowded environment of the cytoplasm.
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5
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Risso VA, Primo ME, Brunet JE, Sotomayor CP, Ermácora MR. Optical studies of single-tryptophan B. licheniformis beta-lactamase variants. Biophys Chem 2010; 151:111-8. [PMID: 20561743 DOI: 10.1016/j.bpc.2010.05.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 05/27/2010] [Accepted: 05/27/2010] [Indexed: 11/30/2022]
Abstract
beta-lactamases (penicillinases) are important complicating factors in bacterial infections and excellent theoretical and experimental models in protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase (ESP) is a Class A beta-lactamase with three tryptophan residues, one located in each of the two protein domains and one located in the interface between domains. To determine the tryptophan contribution to the ESP UV-absorption, circular dichroism, and steady-state and time-resolved fluorescence, four Trp-->Phe mutants were prepared and characterized. The residue substitutions had little impact on the native conformation. UV-absorption and CD features were identified and ascribed to specific aromatic residues. Time-resolved fluorescence showed that most of the fluorescence decay of ESP tryptophans is due to a discrete exponential component with a lifetime of 5-6ns. Fluorescence polarization measurements indicated that fluorescence of Trp 210 is nearly independent of the fluorescence of Trp 229 and Trp 251, whereas a substantial energy homotransfer between the latter pair takes place. The spectroscopic information was rationalized on the basis of structural considerations and should help in the interpretation and monitoring of the changes at the sub domain level during the conformational transitions and fluctuations of ESP and other Class A beta-lactamases.
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Affiliation(s)
- Valeria A Risso
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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6
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Beassoni PR, Berti FPD, Otero LH, Risso VA, Ferreyra RG, Lisa AT, Domenech CE, Ermácora MR. Preparation and biophysical characterization of recombinant Pseudomonas aeruginosa phosphorylcholine phosphatase. Protein Expr Purif 2010; 71:153-9. [PMID: 20064618 DOI: 10.1016/j.pep.2010.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 01/03/2010] [Accepted: 01/05/2010] [Indexed: 12/01/2022]
Abstract
Pseudomonas aeruginosa infections constitute a widespread health problem with high economical and social impact, and the phosphorylcholine phosphatase (PchP) of this bacterium is a potential target for antimicrobial treatment. However, drug design requires high-resolution structural information and detailed biophysical knowledge not available for PchP. An obstacle in the study of PchP is that current methods for its expression and purification are suboptimal and allowed only a preliminary kinetic characterization of the enzyme. Herein, we describe a new procedure for the efficient preparation of recombinant PchP overexpressed in Escherichia coli. The enzyme is purified from urea solubilized inclusion bodies and refolded by dialysis. The product of PchP refolding is a mixture of native PchP and a kinetically-trapped, alternatively-folded aggregate that is very slowly converted into the native state. The properly folded and fully active enzyme is isolated from the refolding mixture by size-exclusion chromatography. PchP prepared by the new procedure was subjected to chemical and biophysical characterization, and its basic optical, hydrodynamic, metal-binding, and catalytic properties are reported. The unfolding of the enzyme was also investigated, and its thermal stability was determined. The obtained information should help to compare PchP with other phosphatases and to obtain a better understanding of its catalytic mechanism. In addition, preliminary trials showed that PchP prepared by the new protocol is suitable for crystallization, opening the way for high-resolution studies of the enzyme structure.
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Affiliation(s)
- Paola R Beassoni
- Departamento de Biología Molecular, Universidad Nacional de Río Cuarto, Río Cuarto, Córdoba, Argentina
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7
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Tian P, Bernstein HD. Identification of a post-targeting step required for efficient cotranslational translocation of proteins across the Escherichia coli inner membrane. J Biol Chem 2009; 284:11396-404. [PMID: 19211555 PMCID: PMC2670145 DOI: 10.1074/jbc.m900375200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Indexed: 11/06/2022] Open
Abstract
Recent studies have shown that cytoplasmic proteins are exported efficiently in Escherichia coli only if they are attached to signal peptides that are recognized by the signal recognition particle and are thereby targeted to the SecYEG complex cotranslationally. The evidence suggests that the entry of these proteins into the secretory pathway at an early stage of translation is necessary to prevent them from folding into a translocation-incompetent conformation. We found, however, that several glycolytic enzymes attached to signal peptides that are recognized by the signal recognition particle were exported inefficiently. Based on previous studies of post-translational export, we hypothesized that the export block was due to the presence of basic residues at the extreme N terminus of each enzyme. Consistent with our hypothesis, we found that the introduction of negatively charged residues into this segment increased the efficiency of export. Export efficiency was sensitive to the number, position, and sequence context of charged residues. The importance of charge for efficient export was underscored by an in silico analysis that revealed a conserved negative charge bias at the N terminus of the mature region of bacterial presecretory proteins. Our results demonstrate that cotranslational targeting of a protein to the E. coli SecYEG complex does not ensure its export but that export also depends on a subsequent event (most likely the initiation of translocation) that involves sequences both within and just beyond the signal peptide.
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Affiliation(s)
- Pu Tian
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0538, USA
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8
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Risso VA, Primo ME, Ermácora MR. Re-engineering a β-lactamase using prototype peptides from a library of local structural motifs. Protein Sci 2009; 18:440-9. [PMID: 19165724 DOI: 10.1002/pro.47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Valeria A Risso
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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9
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Influence of N-Terminal Truncations on the Functional Expression of Bacillus licheniformis γ-Glutamyltranspeptidase in Recombinant Escherichia coli. Curr Microbiol 2008; 57:603-8. [DOI: 10.1007/s00284-008-9250-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 07/24/2008] [Accepted: 08/11/2008] [Indexed: 11/24/2022]
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10
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Vandevenne M, Gaspard G, Yilmaz N, Giannotta F, Frère JM, Galleni M, Filée P. Rapid and easy development of versatile tools to study protein/ligand interactions. Protein Eng Des Sel 2008; 21:443-51. [PMID: 18456870 DOI: 10.1093/protein/gzn021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The system described here allows the expression of protein fragments into a solvent-exposed loop of a carrier protein, the beta-lactamase BlaP. When using Escherichia coli constitutive expression vectors, a positive selection of antibioresistant bacteria expressing functional hybrid beta-lactamases is achieved in the presence of beta-lactams making further screening of correctly folded and secreted hybrid beta-lactamases easier. Protease-specific recognition sites have been engineered on both sides of the beta-lactamase permissive loop in order to cleave off the exogenous protein fragment from the carrier protein by an original two-step procedure. According to our data, this approach constitutes a suitable alternative for production of difficult to express protein domains. This work demonstrates that the use of BlaP as a carrier protein does not alter the biochemical activity and the native disulphide bridge formation of the inserted chitin binding domain of the human macrophage chitotriosidase. We also report that the beta-lactamase activity of the hybrid protein can be used to monitor interactions between the inserted protein fragments and its ligands and to screen neutralizing molecules.
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Affiliation(s)
- M Vandevenne
- Macromolécules biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Sart-Tilman, Liège, Belgium
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11
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Vandevenne M, Filee P, Scarafone N, Cloes B, Gaspard G, Yilmaz N, Dumoulin M, François JM, Frère JM, Galleni M. The Bacillus licheniformis BlaP beta-lactamase as a model protein scaffold to study the insertion of protein fragments. Protein Sci 2007; 16:2260-71. [PMID: 17893363 PMCID: PMC2204133 DOI: 10.1110/ps.072912407] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Using genetic engineering technologies, the chitin-binding domain (ChBD) of the human macrophage chitotriosidase has been inserted into the host protein BlaP, a class A beta-lactamase produced by Bacillus licheniformis. The product of this construction behaved as a soluble chimeric protein that conserves both the capacity to bind chitin and to hydrolyze beta-lactam moiety. Here we describe the biochemical and biophysical properties of this protein (BlaPChBD). This work contributes to a better understanding of the reciprocal structural and functional effects of the insertion on the host protein scaffold and the heterologous structured protein fragments. The use of BlaP as a protein carrier represents an efficient approach to the functional study of heterologous protein fragments.
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Affiliation(s)
- Marylène Vandevenne
- Macromolécules Biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Liège, Belgium
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12
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Santos J, Risso VA, Sica MP, Ermácora MR. Effects of serine-to-cysteine mutations on beta-lactamase folding. Biophys J 2007; 93:1707-18. [PMID: 17496026 PMCID: PMC1948053 DOI: 10.1529/biophysj.106.103804] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
B. licheniformis exo-small beta-lactamase (ESBL) has two nonsequential domains and a complex architecture. We replaced ESBL serine residues 126 and 265 with cysteine to probe the conformation of buried regions in each domain. Spectroscopic, hydrodynamic, and chemical methods revealed that the mutations do not alter the native fold but distinctly change stability (S-126C > wild-type > S-126/265C > S-265C ESBL) and the features of partially folded states. The observed wild-type ESBL equilibrium intermediate has decreased fluorescence but full secondary structure. S-126C ESBL intermediate has the fluorescence of the unfolded state, no thiol reactivity, and partial secondary structure. S-265C and S-126/265C ESBL populate intermediate states unfolded by fluorescence and thiol reactivity but with full secondary structure. Mass analysis of S-126/265C ESBL in the partially folded state proved that both thiol groups become exposed simultaneously. None of the intermediates is compatible with sequential domain unfolding. Molecular dynamics simulation suggests that the stabilizing effect of the S-126C substitution is due to optimization of van der Waals interactions and packing. On the other hand, destabilization induced by the S-265C mutation results from alteration of the hydrogen-bond network. The results illustrate the large impact that seemingly conservative serine-to-cysteine changes can have on the energy landscape of proteins.
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Affiliation(s)
- Javier Santos
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876XD Bernal, Buenos Aires, Argentina
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13
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Ferreyra RG, Burgardt NI, Milikowski D, Melen G, Kornblihtt AR, Dell' Angelica EC, Santomé JA, Ermácora MR. A yeast sterol carrier protein with fatty-acid and fatty-acyl-CoA binding activity. Arch Biochem Biophys 2006; 453:197-206. [PMID: 16890184 DOI: 10.1016/j.abb.2006.06.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 06/29/2006] [Accepted: 06/30/2006] [Indexed: 11/22/2022]
Abstract
The 14-kDa sterol carrier protein 2 (SCP2) domain is present in Eukaria, Bacteria and Archaea, and has been implicated in the transport and metabolism of lipids. We report the cloning, expression, purification and physicochemical characterization of a SCP2 from the yeast Yarrowia lipolytica (YLSCP2). Analytical size-exclusion chromatography, circular dichroism and fluorescence spectra, indicate that recombinant YLSCP2 is a well-folded monomer. Thermal unfolding experiments show that SCP2 maximal stability is at pH 7.0-9.0. YLSCP2 binds cis-parinaric acid and palmitoyl-CoA with KD values of 81+/-40 nM and 73+/-33 nM, respectively, sustaining for the first time the binding of fatty acids and their CoA esters to a nonanimal SCP2. The role of yeast SCP2 and other lipid binding proteins in transport, storage and peroxisomal oxidation of fatty acids is discussed.
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Affiliation(s)
- Raúl G Ferreyra
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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14
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Gebhard LG, Risso VA, Santos J, Ferreyra RG, Noguera ME, Ermácora MR. Mapping the Distribution of Conformational Information Throughout a Protein Sequence. J Mol Biol 2006; 358:280-8. [PMID: 16510154 DOI: 10.1016/j.jmb.2006.01.095] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 01/26/2006] [Accepted: 01/27/2006] [Indexed: 12/01/2022]
Abstract
The three-dimensional structure of protein is encoded in the sequence, but many amino acid residues carry no essential conformational information, and the identity of those that are structure-determining is elusive. By circular permutation and terminal deletion, we produced and purified 25 Bacillus licheniformis beta-lactamase (ESBL) variants that lack 5-21 contiguous residues each, and collectively have 82% of the sequence and 92% of the non-local atom-atom contacts eliminated. Circular dichroism and size-exclusion chromatography showed that most of the variants form conformationally heterogeneous mixtures, but by measuring catalytic constants, we found that all populate, to a greater or lesser extent, conformations with the essential features of the native fold. This suggests that no segment of the ESBL sequence is essential to the structure as a whole, which is congruent with the notion that local information and modular organization can impart most of the tertiary fold specificity and cooperativity.
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Affiliation(s)
- Leopoldo G Gebhard
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 180, (1876) Bernal, Buenos Aires, Argentina
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15
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Primo ME, Sica MP, Risso VA, Poskus E, Ermácora MR. Expression and physicochemical characterization of an extracellular segment of the receptor protein tyrosine phosphatase IA-2. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1764:174-81. [PMID: 16413232 DOI: 10.1016/j.bbapap.2005.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 11/14/2005] [Accepted: 11/23/2005] [Indexed: 10/25/2022]
Abstract
The receptor protein tyrosine phosphatase superfamily (RPTP) includes proteins with a single transmembrane, one or more intracellular phosphatase, and a variety of extracellular domains. The 106-kDa insulinoma-associated protein (IA-2, ICA512) receptor is unique among RPTP members because: (a) it has a single, phosphatase-like intracellular domain identified as one of the most prominent self antigens in autoimmune diabetes; (b) its extracellular region bears no sequence similarity to known domains; (c) it is present in the membrane of secretory granules in neurons and pancreatic beta-cells where it suffers a complex processing; and (d) it has very poorly understood biological properties. In this work, we describe the expression, purification, and physicochemical characterization of residues 449-576 of IA-2 (IA-2ec(449-576)). Judging from CD, fluorescence, hydrodynamic, and thermal unfolding analyses, this fragment forms an autonomously folding unit with tight packing and well-defined secondary and tertiary structure. CD analysis suggests that about 25% of IA-2ec(449-576) residues are alpha-helical, whereas about the same amount are in beta-sheet structure. The availability of soluble and folded IA-2ec(449-576) is a step forward toward the characterization of a part of IA-2 at atomic detail, which may provide new insight in the biology of diabetes, the neurotransmission process, and the dynamic of secretory granules.
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Affiliation(s)
- María E Primo
- Cátedra de Inmunología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA) and IDEHU (CONICET-UBA), Argentina
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16
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Santos J, Gebhard LG, Risso VA, Ferreyra RG, Rossi JPFC, Ermácora MR. Folding of an abridged beta-lactamase. Biochemistry 2004; 43:1715-23. [PMID: 14769049 DOI: 10.1021/bi0358162] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of C-terminal truncation on the equilibrium folding transitions and folding kinetics of B. licheniformis exo small beta-lactamase (ES-betaL) have been measured. ES-betaL lacking 19 residues (ES-betaL(C)(Delta)(19)) has no enzymic activity. Deletion of the last 14 residues produces ES-betaL(C)(Delta)(14), which is 0.1% active. The enzyme lacking nine residues (ES-betaL(C)(Delta)(9)) is nearly fully active, has native optical and hydrodynamic properties, and is protease resistant, a distinguishing feature of the wild-type enzyme. Although ES-betaL(C)(Delta)(9) folds properly, it does so 4 orders of magnitude slower than ES-betaL, making possible the isolation and characterization of a compact intermediate state (I(P) ES-betaL(C)(Delta)(9)). Based on the analysis of folding rates and equilibrium constants, we propose that equilibrium between I(P) ES-betaL(C)(Delta)(9) and other intermediate slow folding. Residues removed in ES-betaL(C)(Delta)(9) and ES-betaL(C)(Delta)(14) are helical and firmly integrated into the enzyme body through many van der Waals interactions involving residues distant in sequence. The results suggest that the deleted residues play a key role in the folding process and also the existence of a modular organization of the protein matrix, at the subdomain level. The results are compared with other examples of this kind in the folding literature.
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Affiliation(s)
- Javier Santos
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 180, (1876) Bernal, Buenos Aires, Argentina
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17
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Avrahami D, Shai Y. Bestowing antifungal and antibacterial activities by lipophilic acid conjugation to D,L-amino acid-containing antimicrobial peptides: a plausible mode of action. Biochemistry 2004; 42:14946-56. [PMID: 14674771 DOI: 10.1021/bi035142v] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dramatically increased frequency of opportunistic fungal infections has prompted research to diversify the arsenal of antifungal agents. Antimicrobial peptides constitute a promising family for future antibiotics with a new mode of action. However, only a few are effective against fungal pathogens because of their ability to self-assemble. Recently, we showed that the conjugation of fatty acids to the potent antibacterial peptide magainin endowed it with antifungal activity concomitant with an increase in its oligomeric state in solution. To investigate whether a high potency of the parental peptide is prerequisite for antifungal activity, we conjugated undecanoic acid (UA) and palmitic acid (PA) to inactive diastereomers of magainin containing four d-amino acids ([D]-4-magainin), as well as to a weakly active diastereomeric lytic peptide containing Lys and Leu ([D]-K(5)L(7)). All lipopeptides gained potent activity toward Cryptococcus neoformans. Most importantly, [D]-K(5)L(7)-UA was highly potent against all microorganisms tested, including bacteria, yeast, and opportunistic fungi. All lipopeptides increased the permeability of Escherichia coli spheroplasts and intact C. neoformans, as well as their corresponding membranes, phosphatidylethanol (PE)/phosphatidylglycerol (PG) and phosphatidylcholine (PC)/PE/phosphatidylinositol (PI)/ergosterol, respectively. The extent of membrane-permeating activity correlated with their biological function, suggesting that the plasma membrane was one of their major targets. Circular dichroism (CD) and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy revealed that their mode of oligomerization in solution, structure, and organization in membranes have important roles regarding their antibacterial and antifungal activities. Together with the advantage of using diastereomers versus all l-amino acid peptides, this study paves the way to the design of a new group of potent antifungal peptides urgently needed to combat opportunistic fungal infection.
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Affiliation(s)
- Dorit Avrahami
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, 76100 Israel
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Avrahami D, Shai Y. A new group of antifungal and antibacterial lipopeptides derived from non-membrane active peptides conjugated to palmitic acid. J Biol Chem 2004; 279:12277-85. [PMID: 14709550 DOI: 10.1074/jbc.m312260200] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report on the synthesis, biological function, and a plausible mode of action of a new group of lipopeptides with potent antifungal and antibacterial activities. These lipopeptides are derived from positively charged peptides containing d- and l-amino acids (diastereomers) that are palmitoylated (PA) at their N terminus. The peptides investigated have the sequence K(4)X(7)W, where X designates Gly, Ala, Val, or Leu (designated d-X peptides). The data revealed that PA-d-G and PA-d-A gained potent antibacterial and antifungal activity despite the fact that both parental peptides were completely devoid of any activity toward microorganisms and model phospholipid membranes. In contrast, PA-d-L lost the potent antibacterial activity of the parental peptide but gained and preserved partial antifungal activity. Interestingly, both d-V and its palmitoylated analog were inactive toward bacteria, and only the palmitoylated peptide was highly potent toward yeast. Both PA-d-L and PA-d-V lipopeptides were also endowed with hemolytic activity. Mode of action studies were performed by using tryptophan fluorescence and attenuated total reflectance Fourier transform infrared and circular dichroism spectroscopy as well as transmembrane depolarization assays with bacteria and fungi. The data suggest that the lipopeptides act by increasing the permeability of the cell membrane and that differences in their potency and target specificity are the result of differences in their oligomeric state and ability to dissociate and insert into the cytoplasmic membrane. These results provide insight regarding a new approach of modulating hydrophobicity and the self-assembly of non-membrane interacting peptides in order to endow them with both antibacterial and antifungal activities urgently needed to combat bacterial and fungal infections.
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Affiliation(s)
- Dorit Avrahami
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
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Tsang JSH, Sze J. Sec-dependent and Sec-independent translocation of haloacid dehalogenase Chd1 of Burkholderia cepacia MBA4 in Escherichia coli. FEMS Microbiol Lett 2002; 211:259-64. [PMID: 12076822 DOI: 10.1111/j.1574-6968.2002.tb11234.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
2-Haloacid dehalogenases are hydrolytic enzymes that cleave the halogen-carbon bond(s) in haloalkanoic acids. We have previously isolated a cryptic haloacid dehalogenase gene from Burkholderia cepacia MBA4 and expressed it in Escherichia coli. This recombinant protein is unusual in having a long leader sequence, a property of periplasmic enzymes. In this paper, we report the functional role of this leader sequence. Western blot analyses showed that Chd1 is translocated to the periplasm. The results on the expression of Chd1 in the presence of sodium azide suggested the cleavage of the leader to be Sec-dependent. Chimeras of Chd1 and green fluorescent protein demonstrated that the leader sequence is fully functional in translocating the fusion protein to the periplasm. The expression of the chimeras in Sec mutants supported the Sec-dependent translocation. Surprisingly, recombinant Chd1 and a chimera with no leader sequence were also found in the periplasm.
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Affiliation(s)
- Jimmy S H Tsang
- Molecular Microbiology Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, PR China.
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