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Dores-Silva PR, Barbosa LRS, Ramos CHI, Borges JC. Human mitochondrial Hsp70 (mortalin): shedding light on ATPase activity, interaction with adenosine nucleotides, solution structure and domain organization. PLoS One 2015; 10:e0117170. [PMID: 25615450 PMCID: PMC4304843 DOI: 10.1371/journal.pone.0117170] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 12/19/2014] [Indexed: 12/28/2022] Open
Abstract
The human mitochondrial Hsp70, also called mortalin, is of considerable importance for mitochondria biogenesis and the correct functioning of the cell machinery. In the mitochondrial matrix, mortalin acts in the importing and folding process of nucleus-encoded proteins. The in vivo deregulation of mortalin expression and/or function has been correlated with age-related diseases and certain cancers due to its interaction with the p53 protein. In spite of its critical biological roles, structural and functional studies on mortalin are limited by its insoluble recombinant production. This study provides the first report of the production of folded and soluble recombinant mortalin when co-expressed with the human Hsp70-escort protein 1, but it is still likely prone to self-association. The monomeric fraction of mortalin presented a slightly elongated shape and basal ATPase activity that is higher than that of its cytoplasmic counterpart Hsp70-1A, suggesting that it was obtained in the functional state. Through small angle X-ray scattering, we assessed the low-resolution structural model of monomeric mortalin that is characterized by an elongated shape. This model adequately accommodated high resolution structures of Hsp70 domains indicating its quality. We also observed that mortalin interacts with adenosine nucleotides with high affinity. Thermally induced unfolding experiments indicated that mortalin is formed by at least two domains and that the transition is sensitive to the presence of adenosine nucleotides and that this process is dependent on the presence of Mg2+ ions. Interestingly, the thermal-induced unfolding assays of mortalin suggested the presence of an aggregation/association event, which was not observed for human Hsp70-1A, and this finding may explain its natural tendency for in vivo aggregation. Our study may contribute to the structural understanding of mortalin as well as to contribute for its recombinant production for antitumor compound screenings.
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Affiliation(s)
- Paulo R Dores-Silva
- Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, P.O. Box 780, 13560-970, Brazil
| | - Leandro R S Barbosa
- Institute of Physics, University of Sao Paulo, Sao Paulo, SP, 05508-090, Brazil
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, 13083-970, Campinas, SP, Brazil
| | - Júlio C Borges
- Institute of Chemistry of Sao Carlos, University of Sao Paulo, Sao Carlos, SP, P.O. Box 780, 13560-970, Brazil
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202
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Razinkov VI, Treuheit MJ, Becker GW. Accelerated formulation development of monoclonal antibodies (mAbs) and mAb-based modalities: review of methods and tools. ACTA ACUST UNITED AC 2015; 20:468-83. [PMID: 25576149 DOI: 10.1177/1087057114565593] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More therapeutic monoclonal antibodies and antibody-based modalities are in development today than ever before, and a faster and more accurate drug discovery process will ensure that the number of candidates coming to the biopharmaceutical pipeline will increase in the future. The process of drug product development and, specifically, formulation development is a critical bottleneck on the way from candidate selection to fully commercialized medicines. This article reviews the latest advances in methods of formulation screening, which allow not only the high-throughput selection of the most suitable formulation but also the prediction of stability properties under manufacturing and long-term storage conditions. We describe how the combination of automation technologies and high-throughput assays creates the opportunity to streamline the formulation development process starting from early preformulation screening through to commercial formulation development. The application of quality by design (QbD) concepts and modern statistical tools are also shown here to be very effective in accelerated formulation development of both typical antibodies and complex modalities derived from them.
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203
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Liu J, Yadav S, Andya J, Demeule B, Shire SJ. Analytical Ultracentrifugation and Its Role in Development and Research of Therapeutical Proteins. Methods Enzymol 2015; 562:441-76. [DOI: 10.1016/bs.mie.2015.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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204
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Zhao H, Schuck P. Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:3-14. [PMID: 25615855 PMCID: PMC4304681 DOI: 10.1107/s1399004714010372] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/07/2014] [Indexed: 12/29/2022]
Abstract
Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysical techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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205
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206
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Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter. Nat Commun 2014; 5:5419. [PMID: 25377891 PMCID: PMC4242082 DOI: 10.1038/ncomms6419] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 09/29/2014] [Indexed: 11/09/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the conserved aspartate, which coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. Our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.
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207
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Impact of detergent on biophysical properties and immune response of the IpaDB fusion protein, a candidate subunit vaccine against Shigella species. Infect Immun 2014; 83:292-9. [PMID: 25368115 DOI: 10.1128/iai.02457-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Shigella spp. are causative agents of bacillary dysentery, a human illness with high global morbidity levels, particularly among elderly and infant populations. Shigella infects via the fecal-oral route, and its virulence is dependent upon a type III secretion system (T3SS). Two components of the exposed needle tip complex of the Shigella T3SS, invasion plasmid antigen D (IpaD) and IpaB, have been identified as broadly protective antigens in the mouse lethal pneumonia model. A recombinant fusion protein (DB fusion) was created by joining the coding sequences of IpaD and IpaB. The DB fusion is coexpressed with IpaB's cognate chaperone, IpgC, for proper recombinant expression. The chaperone can then be removed by using the mild detergents octyl oligooxyethelene (OPOE) or N,N-dimethyldodecylamine N-oxide (LDAO). The DB fusion in OPOE or LDAO was used for biophysical characterization and subsequent construction of an empirical phase diagram (EPD). The EPD showed that the DB fusion in OPOE is most stable at neutral pH below 55 °C. In contrast, the DB fusion in LDAO exhibited remarkable thermal plasticity, since this detergent prevents the loss of secondary and tertiary structures after thermal unfolding at 90 °C, as well as preventing thermally induced aggregation. Moreover, the DB fusion in LDAO induced higher interleukin-17 secretion and provided a higher protective efficacy in a mouse challenge model than did the DB fusion in OPOE. These data indicate that LDAO might introduce plasticity to the protein, promoting thermal resilience and enhanced protective efficacy, which may be important in its use as a subunit vaccine.
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208
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Ko SH, Vargas-Lara F, Patrone PN, Stavis SM, Starr FW, Douglas JF, Liddle JA. High-speed, high-purity separation of gold nanoparticle-DNA origami constructs using centrifugation. SOFT MATTER 2014; 10:7370-7378. [PMID: 25080973 DOI: 10.1039/c4sm01071j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions have yields of <100%, requiring the development of methods to purify the desired product. We study the performance of centrifugation as a separation approach by combining optical and hydrodynamic measurements and computations. We demonstrate that bench-top microcentrifugation is a simple and efficient method of separating the reaction products, readily achieving purities of >90%. The gold nanoparticles play a number of critical roles in our system, functioning not only as integral components of the purified products, but also as hydrodynamic separators and optical indicators of the reaction products during the purification process. We find that separation resolution is ultimately limited by the polydispersity in the mass of the gold nanoparticles and by structural distortions of DNA origami induced by the gold nanoparticles. Our study establishes a methodology for determining the design rules for nanomanufacturing DNA origami-nanoparticle constructs.
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Affiliation(s)
- Seung Hyeon Ko
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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209
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Olszowy P, Buszewski B. Urine sample preparation for proteomic analysis. J Sep Sci 2014; 37:2920-8. [PMID: 25132110 DOI: 10.1002/jssc.201400331] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/08/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022]
Abstract
Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery.
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Affiliation(s)
- Pawel Olszowy
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Torun, Poland; Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University, Torun, Poland
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210
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Lee CY, Liu YL, Lin CL, Liu GY, Hung HC. Functional roles of the dimer-interface residues in human ornithine decarboxylase. PLoS One 2014; 9:e104865. [PMID: 25140796 PMCID: PMC4139326 DOI: 10.1371/journal.pone.0104865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/13/2014] [Indexed: 01/06/2023] Open
Abstract
Ornithine decarboxylase (ODC) catalyzes the decarboxylation of ornithine to putrescine and is the rate-limiting enzyme in the polyamine biosynthesis pathway. ODC is a dimeric enzyme, and the active sites of this enzyme reside at the dimer interface. Once the enzyme dissociates, the enzyme activity is lost. In this paper, we investigated the roles of amino acid residues at the dimer interface regarding the dimerization, protein stability and/or enzyme activity of ODC. A multiple sequence alignment of ODC and its homologous protein antizyme inhibitor revealed that 5 of 9 residues (residues 165, 277, 331, 332 and 389) are divergent, whereas 4 (134, 169, 294 and 322) are conserved. Analytical ultracentrifugation analysis suggested that some dimer-interface amino acid residues contribute to formation of the dimer of ODC and that this dimerization results from the cooperativity of these interface residues. The quaternary structure of the sextuple mutant Y331S/Y389D/R277S/D332E/V322D/D134A was changed to a monomer rather than a dimer, and the Kd value of the mutant was 52.8 µM, which is over 500-fold greater than that of the wild-type ODC (ODC_WT). In addition, most interface mutants showed low but detectable or negligible enzyme activity. Therefore, the protein stability of these interface mutants was measured by differential scanning calorimetry. These results indicate that these dimer-interface residues are important for dimer formation and, as a consequence, are critical for enzyme catalysis.
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Affiliation(s)
- Chien-Yun Lee
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Institute of Microbiology and Immunology and Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University and Hospital, Taichung, Taiwan
| | - Chih-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology and Immunology and Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University and Hospital, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center (ABC), National Chung-Hsing University (NCHU), Taichung, Taiwan
- * E-mail: (HCH); (GYL)
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211
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Separation and quantification of monoclonal-antibody aggregates by hollow-fiber-flow field-flow fractionation. Anal Bioanal Chem 2014; 406:6257-64. [DOI: 10.1007/s00216-014-8065-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/16/2014] [Accepted: 07/24/2014] [Indexed: 10/24/2022]
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212
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Kamnesky G, Hirschhorn O, Shaked H, Chen J, Yao L, Chill JH. Molecular determinants of tetramerization in the KcsA cytoplasmic domain. Protein Sci 2014; 23:1403-16. [PMID: 25042120 DOI: 10.1002/pro.2525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 11/11/2022]
Abstract
The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels.
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Affiliation(s)
- Guy Kamnesky
- Department of Chemistry, Bar Ilan University, Ramat Gan, 52900, Israel
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213
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Purushotham S, Deivanayagam C. The calcium-induced conformation and glycosylation of scavenger-rich cysteine repeat (SRCR) domains of glycoprotein 340 influence the high affinity interaction with antigen I/II homologs. J Biol Chem 2014; 289:21877-87. [PMID: 24923446 PMCID: PMC4139206 DOI: 10.1074/jbc.m114.565507] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 06/10/2014] [Indexed: 01/17/2023] Open
Abstract
Oral streptococci adhere to tooth-immobilized glycoprotein 340 (GP340) via the surface protein antigen I/II (AgI/II) and its homologs as the first step in pathogenesis. Studying this interaction using recombinant proteins, we observed that calcium increases the conformational stability of the scavenger-rich cysteine repeat (SRCRs) domains of GP340. Our results also show that AgI/II adheres specifically with nanomolar affinity to the calcium-induced SRCR conformation in an immobilized state and not in solution. This interaction is significantly dependent on the O-linked carbohydrates present on the SRCRs. This study also establishes that a single SRCR domain of GP340 contains the two surfaces to which the apical and C-terminal regions of AgI/II noncompetitively adhere. Compared with the single SRCR domain, the three tandem SRCR domains displayed a collective/cooperative increase in their bacterial adherence and aggregation. The previously described SRCRP2 peptide that was shown to aggregate several oral streptococci displayed limited aggregation and also nonspecific adherence compared to SRCR domains. Finally, we show distinct species-specific adherence/aggregation between Streptococcus mutans AgI/II and Streptococcus gordonii SspB in their interaction with the SRCRs. This study concludes that identification of the metal ion and carbohydrate adherence motifs on both SRCRs and AgI/II homologs could lead to the development of anti-adhesive inhibitors that could deter the adherence of pathogenic oral streptococci and thereby prevent the onset of infections.
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Affiliation(s)
- Sangeetha Purushotham
- From the Department of Vision Sciences/Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400
| | - Champion Deivanayagam
- From the Department of Vision Sciences/Center for Structural Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294-4400
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214
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Sharma IM, Prakash S, Dhanaraman T, Chatterji D. Characterization of a dual-active enzyme, DcpA, involved in cyclic diguanosine monophosphate turnover in Mycobacterium smegmatis. MICROBIOLOGY-SGM 2014; 160:2304-2318. [PMID: 25037163 DOI: 10.1099/mic.0.080200-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have reported previously that the long-term survival of Mycobacterium smegmatis is facilitated by a dual-active enzyme MSDGC-1 (renamed DcpA), which controls the cellular turnover of cyclic diguanosine monophosphate (c-di-GMP). Most mycobacterial species possess at least a single copy of a DcpA orthologue that is highly conserved in terms of sequence similarity and domain architecture. Here, we show that DcpA exists in monomeric and dimeric forms. The dimerization of DcpA is due to non-covalent interactions between two protomers that are arranged in a parallel orientation. The dimer shows both synthesis and hydrolysis activities, whereas the monomer shows only hydrolysis activity. In addition, we have shown that DcpA is associated with the cytoplasmic membrane and exhibits heterogeneous cellular localization with a predominance at the cell poles. Finally, we have also shown that DcpA is involved in the change in cell length and colony morphology of M. smegmatis. Taken together, our study provides additional evidence about the role of the bifunctional protein involved in c-di-GMP signalling in M. smegmatis.
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Affiliation(s)
- Indra Mani Sharma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Thillaivillalan Dhanaraman
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal H3C 3J7, Québec, Canada
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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215
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Chandola H, Williamson TE, Craig BA, Friedman AM, Bailey-Kellogg C. Stoichiometries and affinities of interacting proteins from concentration series of solution scattering data: decomposition by least squares and quadratic optimization. J Appl Crystallogr 2014; 47:899-914. [PMID: 24904243 PMCID: PMC4038797 DOI: 10.1107/s1600576714005913] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 03/17/2014] [Indexed: 11/10/2022] Open
Abstract
In studying interacting proteins, complementary insights are provided by analyzing both the association model (the stoichiometry and affinity constants of the intermediate and final complexes) and the quaternary structure of the resulting complexes. Many current methods for analyzing protein interactions either give a binary answer to the question of association and no information about quaternary structure or at best provide only part of the complete picture. Presented here is a method to extract both types of information from X-ray or neutron scattering data for a series of equilibrium mixtures containing the initial components at different concentrations. The method determines the association pathway and constants, along with the scattering curves of the individual members of the mixture, so as to best explain the scattering data for the mixtures. The derived curves then enable reconstruction of the intermediate and final complexes. Using simulated solution scattering data for four hetero-oligomeric complexes with different structures, molecular weights and association models, it is demonstrated that this method accurately determines the simulated association model and scattering profiles for the initial components and complexes. Recognizing that experimental mixtures contain static contaminants and nonspecific complexes with the lowest affinities (inter-particle interference) as well as the desired specific complex(es), a new analytical method is also employed to extend this approach to evaluating the association models and scattering curves in the presence of static contaminants, testing both a nonparticipating monomer and a large homo-oligomeric aggregate. It is demonstrated that the method is robust to both random noise and systematic noise from such contaminants, and the treatment of nonspecific complexes is discussed. Finally, it is shown that this method is applicable over a large range of weak association constants typical of specific but transient protein-protein complexes.
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Affiliation(s)
- Himanshu Chandola
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | - Tim E. Williamson
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce A. Craig
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Alan M. Friedman
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Markey Center for Structural Biology, Purdue Cancer Center and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
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216
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Sammond DW, Yarbrough JM, Mansfield E, Bomble YJ, Hobdey SE, Decker SR, Taylor LE, Resch MG, Bozell JJ, Himmel ME, Vinzant TB, Crowley MF. Predicting enzyme adsorption to lignin films by calculating enzyme surface hydrophobicity. J Biol Chem 2014; 289:20960-9. [PMID: 24876380 DOI: 10.1074/jbc.m114.573642] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The inhibitory action of lignin on cellulase cocktails is a major challenge to the biological saccharification of plant cell wall polysaccharides. Although the mechanism remains unclear, hydrophobic interactions between enzymes and lignin are hypothesized to drive adsorption. Here we evaluate the role of hydrophobic interactions in enzyme-lignin binding. The hydrophobicity of the enzyme surface was quantified using an estimation of the clustering of nonpolar atoms, identifying potential interaction sites. The adsorption of enzymes to lignin surfaces, measured using the quartz crystal microbalance, correlates to the hydrophobic cluster scores. Further, these results suggest a minimum hydrophobic cluster size for a protein to preferentially adsorb to lignin. The impact of electrostatic contribution was ruled out by comparing the isoelectric point (pI) values to the adsorption of proteins to lignin surfaces. These results demonstrate the ability to predict enzyme-lignin adsorption and could potentially be used to design improved cellulase cocktails, thus lowering the overall cost of biofuel production.
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Affiliation(s)
| | | | - Elisabeth Mansfield
- the Applied Chemicals and Materials Division, National Institute for Standards and Technology, Boulder, Colorado 80305, and
| | | | | | | | | | - Michael G Resch
- From the Biosciences Center and National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Joseph J Bozell
- the Center for Renewable Carbon, Center for the Catalytic Conversion of Biomass (C3Bio), University of Tennessee, Knoxville, Tennessee 37917
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217
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Mehta SB, Bee JS, Randolph TW, Carpenter JF. Partial unfolding of a monoclonal antibody: role of a single domain in driving protein aggregation. Biochemistry 2014; 53:3367-77. [PMID: 24804773 DOI: 10.1021/bi5002163] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have examined the effect of incubating a monoclonal antibody (mAb) in low (0-2.0 M) concentrations of guanidine hydrochloride (GdnHCl) on the protein's conformation and aggregation during isothermal incubation. In GdnHCl solutions at concentrations from 1.2 to 1.6 M, the mAb was partially unfolded. As demonstrated by fluorescence and circular dichroism spectroscopy, the partially unfolded state of the antibody had perturbed tertiary structure but retained native secondary structure. Furthermore, partial unfolding of the antibody was documented by analytical ultracentrifugation, dynamic light scattering, and limited proteolysis. Subsequent aggregation of the antibody was characterized using size-exclusion chromatography, analytical ultracentrifugation, and dynamic light scattering. Over the entire concentration range (0-2.0 M) of GdnHCl, protein-protein interactions were attractive, as quantified by negative osmotic second virial coefficients measured with static light scattering. However, during isothermal incubation at 37 °C, the aggregation of the antibody was detected only in solutions that induced partial unfolding. Differential scanning calorimetry studies showed that the antibody's CH2 domains were unfolded in antibody molecules that had been incubated in 1.2 M and higher concentrations of GdnHCl. These results suggest that unfolding of the CH2 domains leads to aggregation.
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Affiliation(s)
- Shyam B Mehta
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , Aurora, Colorado 80045, United States
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218
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Arosio P, Müller T, Mahadevan L, Knowles TPJ. Density-gradient-free microfluidic centrifugation for analytical and preparative separation of nanoparticles. NANO LETTERS 2014; 14:2365-2371. [PMID: 24611748 DOI: 10.1021/nl404771g] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Sedimentation and centrifugation techniques are widely applied for the separation of biomolecules and colloids but require the presence of controlled density gradients for stable operation. Here we present an approach for separating nanoparticles in free solution without gradients. We use microfluidics to generate a convective flow perpendicular to the sedimentation direction. We show that the hydrodynamic Rayleigh-Taylor-like instability, which, in traditional methods, requires the presence of a density gradient, can be suppressed by the Poiseuille flow in the microchannel. We illustrate the power of this approach by demonstrating the separation of mixtures of particles on the nanometer scale, orders of magnitude smaller than the micrometer-sized objects separated by conventional inertial microfluidic approaches. This technique exhibits a series of favorable features including short analysis time, small sample volume, limited dilution of the analyte, limited interactions with surfaces as well as the possibility to tune easily the separation range by adjusting the geometry of the system. These features highlight the potential of gradient-free microfluidic centrifugation as an attractive route toward a broad range of nanoscale applications.
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Affiliation(s)
- Paolo Arosio
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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219
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Kuhle K, Krausze J, Curth U, Rössle M, Heuner K, Lang C, Flieger A. Oligomerization inhibits Legionella pneumophila PlaB phospholipase A activity. J Biol Chem 2014; 289:18657-66. [PMID: 24811180 DOI: 10.1074/jbc.m114.573196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The intracellularly replicating lung pathogen Legionella pneumophila consists of an extraordinary variety of phospholipases, including at least 15 different phospholipases A (PLA). Among them, PlaB, the first characterized member of a novel lipase family, is a hemolytic virulence factor that exhibits the most prominent PLA activity in L. pneumophila. We analyzed here protein oligomerization, the importance of oligomerization for activity, addressed further essential regions for activity within the PlaB C terminus, and the significance of PlaB-derived lipolytic activity for L. pneumophila intracellular replication. We determined by means of analytical ultracentrifugation and small angle x-ray scattering analysis that PlaB forms homodimers and homotetramers. The C-terminal 5, 10, or 15 amino acids, although the individual regions contributed to PLA activity, were not essential for protein tetramerization. Infection of mouse macrophages with L. pneumophila wild type, plaB knock-out mutant, and plaB complementing or various mutated plaB-harboring strains showed that catalytic activity of PlaB promotes intracellular replication. We observed that PlaB was most active in the lower nanomolar concentration range but not at or only at a low level at concentration above 0.1 μm where it exists in a dimer/tetramer equilibrium. We therefore conclude that PlaB is a virulence factor that, on the one hand, assembles in inactive tetramers at micromolar concentrations. On the other hand, oligomer dissociation at nanomolar concentrations activates PLA activity. Our data highlight the first example of concentration-dependent phospholipase inactivation by tetramerization, which may protect the bacterium from internal PLA activity, but enzyme dissociation may allow its activation after export.
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Affiliation(s)
- Katja Kuhle
- From the Robert Koch-Institut, 38855 Wernigerode
| | - Joern Krausze
- the Helmholtz Center for Infection Research, 38124 Braunschweig
| | - Ute Curth
- the Institute for Biophysical Chemistry, Hannover Medical School, 30625 Hannover
| | - Manfred Rössle
- the European Molecular Biology Laboratory, 22603 Hamburg Branch, c/o DESY, Hamburg, and the Lübeck University of Applied Sciences, 23562 Lübeck, Germany
| | - Klaus Heuner
- From the Robert Koch-Institut, 38855 Wernigerode
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220
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Piazza R. Settled and unsettled issues in particle settling. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2014; 77:056602. [PMID: 24801715 DOI: 10.1088/0034-4885/77/5/056602] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Colloid sedimentation has played a seminal role in the development of statistical physics thanks to the celebrated experiments by Perrin, which provided a concrete demonstration of molecular reality and gave strong support to Einstein's theory of Brownian motion. This review, which mostly focuses on settling at low Peclét number, where Brownian fluctuations are dominant, aims to show that a lot more can be learnt both from the sedimentation equilibrium and from the particle settling dynamics of a wide class of systems, ranging from simple colloids to mesogenic suspensions, from soft solids to active particles and living organisms. At the same time, the occurrence of unexpected and surprising effects brings about challenging questions in statistical and fluid mechanics that make sedimentation an exciting field of research.
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Affiliation(s)
- Roberto Piazza
- Department of Chemistry, Material Science, and Chemical Engineering Politecnico di Milano, via Ponzio 34/3, 20133 Milano, Italy
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221
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Yu X, Strub MP, Barnard TJ, Noinaj N, Piszczek G, Buchanan SK, Taraska JW. An engineered palette of metal ion quenchable fluorescent proteins. PLoS One 2014; 9:e95808. [PMID: 24752441 PMCID: PMC3994163 DOI: 10.1371/journal.pone.0095808] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/31/2014] [Indexed: 12/17/2022] Open
Abstract
Many fluorescent proteins have been created to act as genetically encoded biosensors. With these sensors, changes in fluorescence report on chemical states in living cells. Transition metal ions such as copper, nickel, and zinc are crucial in many physiological and pathophysiological pathways. Here, we engineered a spectral series of optimized transition metal ion-binding fluorescent proteins that respond to metals with large changes in fluorescence intensity. These proteins can act as metal biosensors or imaging probes whose fluorescence can be tuned by metals. Each protein is uniquely modulated by four different metals (Cu2+, Ni2+, Co2+, and Zn2+). Crystallography revealed the geometry and location of metal binding to the engineered sites. When attached to the extracellular terminal of a membrane protein VAMP2, dimeric pairs of the sensors could be used in cells as ratiometric probes for transition metal ions. Thus, these engineered fluorescent proteins act as sensitive transition metal ion-responsive genetically encoded probes that span the visible spectrum.
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Affiliation(s)
- Xiaozhen Yu
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Travis J. Barnard
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nicholas Noinaj
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Grzegorz Piszczek
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Susan K. Buchanan
- Laboratory of Molecular Biology, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Justin W. Taraska
- Laboratory of Molecular Biophysics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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222
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Bandi S, Singh SM, Mallela KMG. The C-terminal domain of the utrophin tandem calponin-homology domain appears to be thermodynamically and kinetically more stable than the full-length protein. Biochemistry 2014; 53:2209-11. [PMID: 24678640 DOI: 10.1021/bi500120e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Domains are in general less stable than the corresponding full-length proteins. Human utrophin tandem calponin-homology (CH) domain seems to be an exception. Reversible, equilibrium denaturant melts indicate that the isolated C-terminal domain (CH2) is thermodynamically more stable than the tandem CH domain. Thermal melts show that CH2 unfolds at a temperature higher than that at which the full-length protein unfolds. Stopped-flow kinetics indicates that CH2 unfolds slower than the full-length protein, indicating its higher kinetic stability. Thus, the utrophin tandem CH domain may be one of the few proteins in which an isolated domain is more stable than the corresponding full-length protein.
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Affiliation(s)
- Swati Bandi
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , 12850 East Montview Boulevard, C238, Aurora, Colorado 80045, United States
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223
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Utilization of a precolumn with size exclusion and reversed-phase modes for size-exclusion chromatographic analysis of polysorbate-containing protein aggregates. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 953-954:68-72. [PMID: 24576768 DOI: 10.1016/j.jchromb.2014.01.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 01/23/2014] [Accepted: 01/25/2014] [Indexed: 11/22/2022]
Abstract
Size-exclusion chromatography (SEC) is a useful method for quantification of protein aggregates because of its high throughput capacity and highly quantitative performance. One of the problems in this method concerns polysorbates, which are well-known additives for protein-containing products to prevent protein aggregation, but frequently interfere with the photometric detection of protein aggregates. We developed a new SEC method that can separate polysorbates from protein sample solutions in an on-line mode with a precolumn with size exclusion and reversed-phase mixed modes. The precolumn can effectively trap polysorbates in aqueous mobile phase, and the trapped polysorbates are easily eluted with acetonitrile-containing aqueous mobile phase to clean the precolumn. Small parts of protein aggregates may be also trapped on the precolumn depending on temperature and proteins. Setting appropriate column temperature can minimize such inconvenient trapping of aggregates.
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224
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Zhao H, Mayer ML, Schuck P. Analysis of protein interactions with picomolar binding affinity by fluorescence-detected sedimentation velocity. Anal Chem 2014; 86:3181-7. [PMID: 24552356 PMCID: PMC3988680 DOI: 10.1021/ac500093m] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
The study of high-affinity
protein interactions with equilibrium
dissociation constants (KD) in the picomolar
range is of significant interest in many fields, but the characterization
of stoichiometry and free energy of such high-affinity binding can
be far from trivial. Analytical ultracentrifugation has long been
considered a gold standard in the study of protein interactions but
is typically applied to systems with micromolar KD. Here we present a new approach for the study of high-affinity
interactions using fluorescence detected sedimentation velocity analytical
ultracentrifugation (FDS-SV). Taking full advantage of the large data
sets in FDS-SV by direct boundary modeling with sedimentation coefficient
distributions c(s), we demonstrate detection and
hydrodynamic resolution of protein complexes at low picomolar concentrations.
We show how this permits the characterization of the antibody–antigen
interactions with low picomolar binding constants, 2 orders of magnitude
lower than previously achieved. The strongly size-dependent separation
and quantitation by concentration, size, and shape of free and complex
species in free solution by FDS-SV has significant potential for studying
high-affinity multistep and multicomponent protein assemblies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health , Bethesda, Maryland 20892, United States
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225
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Niebel Y, Buschmann MD, Lavertu M, De Crescenzo G. Combined analysis of polycation/ODN polyplexes by analytical ultracentrifugation and dynamic light scattering reveals their size, refractive index increment, stoichiometry, porosity, and molecular weight. Biomacromolecules 2014; 15:940-7. [PMID: 24571262 DOI: 10.1021/bm4018148] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Analytical ultracentrifugation (AUC) and dynamic light scattering (DLS) were combined to characterize polyplexes formed with 10 kDa chitosan or 10 kDa PEI and oligodeoxynucleotides (ODN). Combined analysis revealed that both polyplexes were highly porous (over 80%) and that their weight average hydrodynamic diameters were of 46 and 55 nm for chitosan/ODN and PEI/ODN complexes, respectively. Transformation of the sedimentation coefficient distribution to a size and molecular weight distribution gave an average molecular weight of 19 and 29 MDa for chitosan and PEI polyplexes, respectively. Data from AUC also allowed for the calculation of the actual dn/dc and N/P ratios of each polyplex. Additional data from scanning electron microscopy and static light scattering confirmed the conclusions that were initially derived from AUC and DLS, thus validating that the combination of AUC and DLS is a powerful approach to characterize polyplexes in terms of refractive index increment, size, and molecular weight distributions, as well as porosity.
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Affiliation(s)
- Yves Niebel
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales, École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal Quebec, Canada H3C 3A7
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226
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Bastos IMD, Motta FN, Grellier P, Santana JM. Parasite prolyl oligopeptidases and the challenge of designing chemotherapeuticals for Chagas disease, leishmaniasis and African trypanosomiasis. Curr Med Chem 2014; 20:3103-15. [PMID: 23514419 PMCID: PMC3778648 DOI: 10.2174/0929867311320250006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/16/2012] [Indexed: 11/22/2022]
Abstract
The trypanosomatids Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp. cause Chagas disease, leishmaniasis and human African trypanosomiasis, respectively. It is estimated that over 10 million people worldwide suffer from these neglected diseases, posing enormous social and economic problems in endemic areas. There are no vaccines to prevent these infections and chemotherapies are not adequate. This picture indicates that new chemotherapeutic agents must be developed to treat these illnesses. For this purpose, understanding the biology of the pathogenic trypanosomatid-host cell interface is fundamental for molecular and functional characterization of virulence factors that may be used as targets for the development of inhibitors to be used for effective chemotherapy. In this context, it is well known that proteases have crucial functions for both metabolism and infectivity of pathogens and are thus potential drug targets. In this regard, prolyl oligopeptidase and oligopeptidase B, both members of the S9 serine protease family, have been shown to play important roles in the interactions of pathogenic protozoa with their mammalian hosts and may thus be considered targets for drug design. This review aims to discuss structural and functional properties of these intriguing enzymes and their potential as targets for the development of drugs against Chagas disease, leishmaniasis and African trypanosomiasis.
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Affiliation(s)
- I M D Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília, Brazil
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227
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Spruijt E, Biesheuvel PM. Sedimentation dynamics and equilibrium profiles in multicomponent mixtures of colloidal particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:075101. [PMID: 24451477 DOI: 10.1088/0953-8984/26/7/075101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper we give a general theoretical framework that describes the sedimentation of multicomponent mixtures of particles with sizes ranging from molecules to macroscopic bodies. Both equilibrium sedimentation profiles and the dynamic process of settling, or its converse, creaming, are modeled. Equilibrium profiles are found to be in perfect agreement with experiments. Our model reconciles two apparently contradicting points of view about buoyancy, thereby resolving a long-lived paradox about the correct choice of the buoyant density. On the one hand, the buoyancy force follows necessarily from the suspension density, as it relates to the hydrostatic pressure gradient. On the other hand, sedimentation profiles of colloidal suspensions can be calculated directly using the fluid density as apparent buoyant density in colloidal systems in sedimentation-diffusion equilibrium (SDE) as a result of balancing gravitational and thermodynamic forces. Surprisingly, this balance also holds in multicomponent mixtures. This analysis resolves the ongoing debate of the correct choice of buoyant density (fluid or suspension): both approaches can be used in their own domain. We present calculations of equilibrium sedimentation profiles and dynamic sedimentation that show the consequences of these insights. In bidisperse mixtures of colloids, particles with a lower mass density than the homogeneous suspension will first cream and then settle, whereas particles with a suspension-matched mass density form transient, bimodal particle distributions during sedimentation, which disappear when equilibrium is reached. In all these cases, the centers of the distributions of the particles with the lowest mass density of the two, regardless of their actual mass, will be located in equilibrium above the so-called isopycnic point, a natural consequence of their hard-sphere interactions. We include these interactions using the Boublik-Mansoori-Carnahan-Starling-Leland (BMCSL) equation of state. Finally, we demonstrate that our model is not limited to hard spheres, by extending it to charged spherical particles, and to dumbbells, trimers and short chains of connected beads.
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Affiliation(s)
- E Spruijt
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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228
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Nazmi AR, Schofield LR, Dobson RC, Jameson GB, Parker EJ. Destabilization of the Homotetrameric Assembly of 3-Deoxy-d-Arabino-Heptulosonate-7-Phosphate Synthase from the Hyperthermophile Pyrococcus furiosus Enhances Enzymatic Activity. J Mol Biol 2014; 426:656-73. [DOI: 10.1016/j.jmb.2013.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 11/05/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022]
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229
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Eves-van den Akker S, Lilley CJ, Ault JR, Ashcroft AE, Jones JT, Urwin PE. The feeding tube of cyst nematodes: characterisation of protein exclusion. PLoS One 2014; 9:e87289. [PMID: 24489891 PMCID: PMC3905015 DOI: 10.1371/journal.pone.0087289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/19/2013] [Indexed: 11/18/2022] Open
Abstract
Plant parasitic nematodes comprise several groups; the most economically damaging of these are the sedentary endoparasites. Sedentary endoparasitic nematodes are obligate biotrophs and modify host root tissue, using a suite of effector proteins, to create a feeding site that is their sole source of nutrition. They feed by withdrawing host cell assimilate from the feeding site though a structure known as the feeding tube. The function, composition and molecular characteristics of feeding tubes are poorly characterised. It is hypothesised that the feeding tube facilitates uptake of host cell assimilate by acting as a molecular sieve. Several studies, using molecular mass as the sole indicator of protein size, have given contradictory results about the exclusion limits of the cyst nematode feeding tube. In this study we propose a method to predict protein size, based on protein database coordinates in silico. We tested the validity of these predictions using travelling wave ion mobility spectrometry – mass spectrometry, where predictions and measured values were within approximately 6%. We used the predictions, coupled with mass spectrometry, analytical ultracentrifugation and protein electrophoresis, to resolve previous conflicts and define the exclusion characteristics of the cyst nematode feeding tube. Heterogeneity was tested in the liquid, solid and gas phase to provide a comprehensive evaluation of three proteins of particular interest to feeding tube size exclusion, GFP, mRFP and Dual PI. The data and procedures described here could be applied to the design of plant expressed defence compounds intended for uptake into cyst nematodes. We also highlight the need to assess protein heterogeneity when creating novel fusion proteins.
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Affiliation(s)
- Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | | | - James R. Ault
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Alison E. Ashcroft
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - John T. Jones
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Peter E. Urwin
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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230
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Sundriyal A, Massa C, Samoray D, Zehender F, Sharpe T, Jenal U, Schirmer T. Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP. J Biol Chem 2014; 289:6978-6990. [PMID: 24451384 DOI: 10.1074/jbc.m113.516195] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The universal second messenger cyclic di-GMP (cdG) is involved in the regulation of a diverse range of cellular processes in bacteria. The intracellular concentration of the dinucleotide is determined by the opposing actions of diguanylate cyclases and cdG-specific phosphodiesterases (PDEs). Whereas most PDEs have accessory domains that are involved in the regulation of their activity, the regulatory mechanism of this class of enzymes has remained unclear. Here, we use biophysical and functional analyses to show that the isolated EAL domain of a PDE from Escherichia coli (YahA) is in a fast thermodynamic monomer-dimer equilibrium, and that the domain is active only in its dimeric state. Furthermore, our data indicate thermodynamic coupling between substrate binding and EAL dimerization with the dimerization affinity being increased about 100-fold upon substrate binding. Crystal structures of the YahA-EAL domain determined under various conditions (apo, Mg(2+), cdG·Ca(2+) complex) confirm structural coupling between the dimer interface and the catalytic center. The built-in regulatory properties of the EAL domain probably facilitate its modular, functional combination with the diverse repertoire of accessory domains.
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Affiliation(s)
- Amit Sundriyal
- Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland
| | - Claudia Massa
- Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland
| | - Dietrich Samoray
- Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland
| | - Fabian Zehender
- Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Facility, University of Basel, CH-4056 Basel, Switzerland
| | - Urs Jenal
- Focal Area of Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Tilman Schirmer
- Focal Area of Structural Biology and Biophysics, University of Basel, CH-4056 Basel, Switzerland.
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231
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Khatter H, Myasnikov AG, Mastio L, Billas IML, Birck C, Stella S, Klaholz BP. Purification, characterization and crystallization of the human 80S ribosome. Nucleic Acids Res 2014; 42:e49. [PMID: 24452798 PMCID: PMC3973290 DOI: 10.1093/nar/gkt1404] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Ribosomes are key macromolecular protein synthesis machineries in the cell. Human ribosomes have so far not been studied to atomic resolution because of their particularly complex structure as compared with other eukaryotic or prokaryotic ribosomes, and they are difficult to prepare to high homogeneity, which is a key requisite for high-resolution structural work. We established a purification protocol for human 80S ribosomes isolated from HeLa cells that allows obtaining large quantities of homogenous samples as characterized by biophysical methods using analytical ultracentrifugation and multiangle laser light scattering. Samples prepared under different conditions were characterized by direct single particle imaging using cryo electron microscopy, which helped optimizing the preparation protocol. From a small data set, a 3D reconstruction at subnanometric resolution was obtained showing all prominent structural features of the human ribosome, and revealing a salt concentration dependence of the presence of the exit site tRNA, which we show is critical for obtaining crystals. With these well-characterized samples first human 80S ribosome crystals were obtained from several crystallization conditions in capillaries and sitting drops, which diffract to 26 Å resolution at cryo temperatures and for which the crystallographic parameters were determined, paving the way for future high-resolution work.
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Affiliation(s)
- Heena Khatter
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé de la Recherche Médicale (INSERM) U964/Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
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232
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Polling S, Mok YF, Ramdzan YM, Turner BJ, Yerbury JJ, Hill AF, Hatters DM. Misfolded polyglutamine, polyalanine, and superoxide dismutase 1 aggregate via distinct pathways in the cell. J Biol Chem 2014; 289:6669-6680. [PMID: 24425868 DOI: 10.1074/jbc.m113.520189] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Protein aggregation into intracellular inclusions is a key feature of many neurodegenerative disorders. A common theme has emerged that inappropriate self-aggregation of misfolded or mutant polypeptide sequences is detrimental to cell health. Yet protein quality control mechanisms may also deliberately cluster them together into distinct inclusion subtypes, including the insoluble protein deposit (IPOD) and the juxtanuclear quality control (JUNQ). Here we investigated how the intrinsic oligomeric state of three model systems of disease-relevant mutant protein and peptide sequences relates to the IPOD and JUNQ patterns of aggregation using sedimentation velocity analysis. Two of the models (polyalanine (37A) and superoxide dismutase 1 (SOD1) mutants A4V and G85R) accumulated into the same JUNQ-like inclusion whereas the other, polyglutamine (72Q), formed spatially distinct IPOD-like inclusions. Using flow cytometry pulse shape analysis (PulSA) to separate cells with inclusions from those without revealed the SOD1 mutants and 37A to have abruptly altered oligomeric states with respect to the nonaggregating forms, regardless of whether cells had inclusions or not, whereas 72Q was almost exclusively monomeric until inclusions formed. We propose that mutations leading to JUNQ inclusions induce a constitutively "misfolded" state exposing hydrophobic side chains that attract and ultimately overextend protein quality capacity, which leads to aggregation into JUNQ inclusions. Poly(Q) is not misfolded in this same sense due to universal polar side chains, but is highly prone to forming amyloid fibrils that we propose invoke a different engagement mechanism with quality control.
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Affiliation(s)
- Saskia Polling
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Yasmin M Ramdzan
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Bradley J Turner
- Florey Institute of Neuroscience and Mental Health and Centre for Neuroscience, The University of Melbourne, Victoria 3010, Australia
| | - Justin J Yerbury
- School of Biological Sciences, Faculty of Science and Illawarra Health and Medical Institute, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Andrew F Hill
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.
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233
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Abstract
A new native protein gel system was recently developed that enables the rapid and convenient analysis of virtually all soluble proteins, in particular including basic proteins, in their native oligomeric states. This gel system combines the addition of negative charges to the proteins by the dye SERVA Blue G with a Tris-histidine discontinuous buffer system and the use of polyacrylamide gradient gels. The use of histidine for sample focusing rather than glycine as a slow dipolar ion following from the cathode buffer serves to improve migration of basic proteins. In this review, the principle of function as well as the advantages and disadvantages of the new gel system are discussed in the context of other native protein gel systems and further methods for the analysis of the oligomeric state of a protein.
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Affiliation(s)
- Michael Niepmann
- Justus-Liebig-University Giessen, Institute of Biochemistry, Faculty of Medicine, Giessen, Germany.
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234
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Characterization of Rhinodrilus alatus hemoglobin (HbRa) and its subunits: Evidence for strong interaction with cationic surfactants DTAB and CTAC. Comp Biochem Physiol B Biochem Mol Biol 2014; 167:23-9. [DOI: 10.1016/j.cbpb.2013.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/23/2013] [Accepted: 09/23/2013] [Indexed: 11/15/2022]
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235
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Panigrahi R, Adina-Zada A, Whelan J, Vrielink A. Ligand recognition by the TPR domain of the import factor Toc64 from Arabidopsis thaliana. PLoS One 2013; 8:e83461. [PMID: 24391770 PMCID: PMC3877065 DOI: 10.1371/journal.pone.0083461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 11/04/2013] [Indexed: 01/21/2023] Open
Abstract
The specific targeting of protein to organelles is achieved by targeting signals being recognised by their cognate receptors. Cytosolic chaperones, bound to precursor proteins, are recognized by specific receptors of the import machinery enabling transport into the specific organelle. The aim of this study was to gain greater insight into the mode of recognition of the C-termini of Hsp70 and Hsp90 chaperones by the Tetratricopeptide Repeat (TPR) domain of the chloroplast import receptor Toc64 from Arabidopsis thaliana (At). The monomeric TPR domain binds with 1∶1 stoichiometry in similar micromolar affinity to both Hsp70 and Hsp90 as determined by isothermal titration calorimetry (ITC). Mutations of the terminal EEVD motif caused a profound decrease in affinity. Additionally, this study considered the contributions of residues upstream as alanine scanning experiments of these residues showed reduced binding affinity. Molecular dynamics simulations of the TPR domain helices upon peptide binding predicted that two helices within the TPR domain move backwards, exposing the cradle surface for interaction with the peptide. Our findings from ITC and molecular dynamics studies suggest that AtToc64_TPR does not discriminate between C-termini peptides of Hsp70 and Hsp90.
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Affiliation(s)
- Rashmi Panigrahi
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| | - Abdussalam Adina-Zada
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Western Australia, Australia
- Department of Botany, School of Life Science, La Trobe University, Bundoora, Victoria, Australia
| | - Alice Vrielink
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia, Australia
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236
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Zhao H, Lomash S, Glasser C, Mayer ML, Schuck P. Analysis of high affinity self-association by fluorescence optical sedimentation velocity analytical ultracentrifugation of labeled proteins: opportunities and limitations. PLoS One 2013; 8:e83439. [PMID: 24358283 PMCID: PMC3866193 DOI: 10.1371/journal.pone.0083439] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 11/12/2013] [Indexed: 12/22/2022] Open
Abstract
Sedimentation velocity analytical ultracentrifugation (SV) is a powerful first-principle technique for the study of protein interactions, and allows a rigorous characterization of binding stoichiometry and affinities. A recently introduced commercial fluorescence optical detection system (FDS) permits analysis of high-affinity interactions by SV. However, for most proteins the attachment of an extrinsic fluorophore is an essential prerequisite for analysis by FDS-SV. Using the glutamate receptor GluA2 amino terminal domain as a model system for high-affinity homo-dimerization, we demonstrate how the experimental design and choice of fluorescent label can impact both the observed binding constants as well as the derived hydrodynamic parameter estimates for the monomer and dimer species. Specifically, FAM (5,6-carboxyfluorescein) was found to create different populations of artificially high-affinity and low-affinity dimers, as indicated by both FDS-SV and the kinetics of dimer dissociation studied using a bench-top fluorescence spectrometer and Förster Resonance Energy Transfer. By contrast, Dylight488 labeled GluA2, as well as GluA2 expressed as an EGFP fusion protein, yielded results consistent with estimates for unlabeled GluA2. Our study suggests considerations for the choice of labeling strategies, and highlights experimental designs that exploit specific opportunities of FDS-SV for improving the reliability of the binding isotherm analysis of interacting systems.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
| | - Suvendu Lomash
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
| | - Carla Glasser
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
| | - Mark L. Mayer
- Laboratory of Cellular and Molecular Neurophysiology, Porter Neuroscience Research Center, National Institute of Child Health and Human Development; National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (PS); (MLM)
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (PS); (MLM)
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237
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Iwura T, Fukuda J, Yamazaki K, Kanamaru S, Arisaka F. Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals. J Biochem 2013; 155:63-71. [PMID: 24155259 DOI: 10.1093/jb/mvt095] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Intermolecular interactions and conformation in dimer species of Palivizumab, a monoclonal antibody (IgG1), were investigated to elucidate the physical and chemical properties of the dimerized antibody. Palivizumab solution contains ∼1% dimer and 99% monomer. The dimer species was isolated by size-exclusion chromatography and analysed by a number of methods including analytical ultracentrifugation-sedimantetion velocity (AUC-SV). AUC-SV in the presence of sodium dodecyl sulphate indicated that approximately half of the dimer fraction was non-covalently associated, whereas the other half was dimerized by covalent bond. Disulphide bond and dityrosine formation were likely to be involved in the covalent dimerization. Limited proteolysis of the isolated dimer by Lys-C and mass spectrometry for the resultant products indicated that the dimer species were formed by Fab-Fc or Fab-Fab interactions, whereas Fc-Fc interactions were not found. It is thus likely that the dimerization occurs mainly via the Fab region. With regard to the conformation of the dimer species, the secondary and tertiary structures were shown to be almost identical to those of the monomer. Furthermore, the thermal stability turned out also to be very similar between the dimer and monomer.
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Affiliation(s)
- Takafumi Iwura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 B-9 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501; and Bio Process Research and Development Laboratories, Production Division, Kyowa Hakko Kirin Co., Ltd.; 100-1 Hagiwara-machi, Takasaki, Gunma 370-0013, Japan
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238
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Wu S, Wang X, Ye X, Zhang G. pH-Induced conformational change and dimerization of DNA chains investigated by analytical ultracentrifugation. J Phys Chem B 2013; 117:11541-7. [PMID: 24010411 DOI: 10.1021/jp405561f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
pH-induced conformational change of i-motif DNA has been studied by analytical ultracentrifugation. As pH increases, the hydrodynamic radius of individual DNA chains in aqueous solutions prepared by being heat-treated suddenly increases while the molar mass is constant, indicating that the conformation changes from an i-motif to a random coil. When DNA concentrations are higher than 1.0 μM, relatively stable dimers are formed as pH sharply decreases from 7.5 to 4.5. Moreover, the weight percentage of the dimers increases with the initial DNA concentration. The study can help to understand the functions of the telomeres containing repeated cytosine-rich sequences and to develop DNA-based devices.
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Affiliation(s)
- Sha Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
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239
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Khavrutskii L, Yeh J, Timofeeva O, Tarasov SG, Pritt S, Stefanisko K, Tarasova N. Protein purification-free method of binding affinity determination by microscale thermophoresis. J Vis Exp 2013. [PMID: 23979559 DOI: 10.3791/50541] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantitative characterization of protein interactions is essential in practically any field of life sciences, particularly drug discovery. Most of currently available methods of KD determination require access to purified protein of interest, generation of which can be time-consuming and expensive. We have developed a protocol that allows for determination of binding affinity by microscale thermophoresis (MST) without purification of the target protein from cell lysates. The method involves overexpression of the GFP-fused protein and cell lysis in non-denaturing conditions. Application of the method to STAT3-GFP transiently expressed in HEK293 cells allowed to determine for the first time the affinity of the well-studied transcription factor to oligonucleotides with different sequences. The protocol is straightforward and can have a variety of application for studying interactions of proteins with small molecules, peptides, DNA, RNA, and proteins.
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240
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Nefedova VV, Sudnitsyna MV, Strelkov SV, Gusev NB. Structure and properties of G84R and L99M mutants of human small heat shock protein HspB1 correlating with motor neuropathy. Arch Biochem Biophys 2013; 538:16-24. [PMID: 23948568 DOI: 10.1016/j.abb.2013.07.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/26/2013] [Accepted: 07/31/2013] [Indexed: 11/26/2022]
Abstract
Some properties of G84R and L99M mutants of HspB1 associated with peripheral distal neuropathies were investigated. Homooligomers formed by these mutants are larger than those of the wild type HspB1. Large oligomers of G84R and L99M mutants have compromised stability and tend to dissociate at low protein concentration. G84R and L99M mutations promote phosphorylation-dependent dissociation of HspB1 oligomers without affecting kinetics of HspB1 phosphorylation by MAPKAP2 kinase. Both mutants weakly interact with HspB6 forming small heterooligomers and being unable to form large heterooligomers characteristic for the wild type HspB1. G84R and L99M mutants possess lower chaperone-like activity than the wild type HspB1 with several model substrates. We suggest that G84R mutation affects mobility and accessibility of the N-terminal domain thus modifying interdimer contacts in HspB1 oligomers. The L99M mutation is located within the hydrophobic core of the α-crystallin domain close to the key R140 residue, and could affect the dimer stability.
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Affiliation(s)
- Victoria V Nefedova
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russian Federation
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241
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Dynamics of forward and backward translocation of mRNA in the ribosome. PLoS One 2013; 8:e70789. [PMID: 23951009 PMCID: PMC3739767 DOI: 10.1371/journal.pone.0070789] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/24/2013] [Indexed: 11/19/2022] Open
Abstract
Translocation of the mRNA-tRNA complex in the ribosome, which is catalyzed by elongation factor EF-G, is one of critical steps in the elongation cycle of protein synthesis. Besides this conventional forward translocation, the backward translocation can also occur, which can be catalyzed by elongation factor LepA. However, the molecular mechanism of the translocation remains elusive. To understand the mechanism, here we study theoretically the dynamics of the forward translocation under various nucleotide states of EF-G and the backward translocation in the absence of and in the presence of LepA. We present a consistent explanation of spontaneous forward translocations in the absence of EF-G, the EF-G-catalyzed forward translocations in the presence of a non-hydrolysable GTP analogue and in the presence of GTP, and the spontaneous and LepA-catalyzed backward translocation. The theoretical results provide quantitative explanations of a lot of different, independent experimental data, and also provide testable predictions.
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242
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Merkley ED, Cort JR, Adkins JN. Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze. ACTA ACUST UNITED AC 2013; 14:77-90. [PMID: 23917845 DOI: 10.1007/s10969-013-9160-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022]
Abstract
Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes.
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Affiliation(s)
- Eric D Merkley
- MS K8-98, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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243
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Piazza R, Buzzaccaro S, Secchi E, Parola A. On the general concept of buoyancy in sedimentation and ultracentrifugation. Phys Biol 2013; 10:045005. [DOI: 10.1088/1478-3975/10/4/045005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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244
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Carvalho FAO, Carvalho JWP, Alves FR, Tabak M. pH effect upon HbGp oligomeric stability: characterization of the dissociated species by AUC and DLS studies. Int J Biol Macromol 2013; 59:333-41. [DOI: 10.1016/j.ijbiomac.2013.04.070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 10/26/2022]
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245
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Encinar M, Kralicek AV, Martos A, Krupka M, Cid S, Alonso A, Rico AI, Jiménez M, Vélez M. Polymorphism of FtsZ filaments on lipid surfaces: role of monomer orientation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9436-9446. [PMID: 23837832 DOI: 10.1021/la401673z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
FtsZ is a bacterial cytoskeletal protein involved in cell division. It forms a ringlike structure that attaches to the membrane to complete bacterial division. It binds and hydrolyzes GTP, assembling into polymers in a GTP-dependent manner. To test how the orientation of the monomers affects the curvature of the filaments on a surface, we performed site-directed mutagenesis on the E. coli FtsZ protein to insert cysteine residues at lateral locations to orient FtsZ on planar lipid bilayers. The E93C and S255C mutants were overproduced, purified, and found to be functionally active in solution, as well as being capable of sustaining cell division in vivo in complementation assays. Atomic force microscopy was used to observe the shape of the filament fibers formed on the surface. The FtsZ mutants were covalently linked to the lipids and could be polymerized on the bilayer surface in the presence of GTP. Unexpectedly, both mutants assembled into straight structures. E93C formed a well-defined lattice with monomers interacting at 60° and 120° angles, whereas S255C formed a more open array of straight thicker filament aggregates. These results indicate that filament curvature and bending are not fixed and that they can be modulated by the orientation of the monomers with respect to the membrane surface. As filament curvature has been associated with the force generation mechanism, these results point to a possible role of filament membrane attachment in lateral association and curvature, elements currently identified as relevant for force generation.
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Affiliation(s)
- Mario Encinar
- Instituto de Catálisis y Petroleoquímica, CSIC, Marie Curie, 2, Cantoblanco, 28049 Madrid, Spain
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246
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Mitra S, Traughber CA, Brannon MK, Gomez S, Capelluto DGS. Ubiquitin interacts with the Tollip C2 and CUE domains and inhibits binding of Tollip to phosphoinositides. J Biol Chem 2013; 288:25780-25791. [PMID: 23880770 DOI: 10.1074/jbc.m113.484170] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A large number of cellular signaling processes are directed through internalization, via endocytosis, of polyubiquitinated cargo proteins. Tollip is an adaptor protein that facilitates endosomal cargo sorting for lysosomal degradation. Tollip preferentially binds phosphatidylinositol 3-phosphate (PtdIns(3)P) via its C2 domain, an association that may be required for endosomal membrane targeting. Here, we show that Tollip binds ubiquitin through its C2 and CUE domains and that its association with the C2 domain inhibits PtdIns(3)P binding. NMR analysis demonstrates that the C2 and CUE domains bind to overlapping sites on ubiquitin, suggesting that two ubiquitin molecules associate with Tollip simultaneously. Hydrodynamic studies reveal that ubiquitin forms heterodimers with the CUE domain, indicating that the association disrupts the dimeric state of the CUE domain. We propose that, in the absence of polyubiquitinated cargo, the dual binding of ubiquitin partitions Tollip into membrane-bound and membrane-free states, a function that contributes to the engagement of Tollip in both membrane trafficking and cytosolic pathways.
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Affiliation(s)
- Sharmistha Mitra
- From the Department of Biological Sciences, Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia 24061
| | - C Alicia Traughber
- From the Department of Biological Sciences, Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia 24061
| | - Mary K Brannon
- From the Department of Biological Sciences, Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia 24061
| | - Stephanie Gomez
- From the Department of Biological Sciences, Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia 24061
| | - Daniel G S Capelluto
- From the Department of Biological Sciences, Protein Signaling Domains Laboratory, Virginia Tech, Blacksburg, Virginia 24061.
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247
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Mu Q, Hu T, Yu J. Molecular insight into the steric shielding effect of PEG on the conjugated staphylokinase: biochemical characterization and molecular dynamics simulation. PLoS One 2013; 8:e68559. [PMID: 23874671 PMCID: PMC3715476 DOI: 10.1371/journal.pone.0068559] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022] Open
Abstract
PEGylation is a successful approach to improve potency of a therapeutic protein. The improved therapeutic potency is mainly due to the steric shielding effect of PEG. However, the underlying mechanism of this effect on the protein is not well understood, especially on the protein interaction with its high molecular weight substrate or receptor. Here, experimental study and molecular dynamics simulation were used to provide molecular insight into the interaction between the PEGylated protein and its receptor. Staphylokinase (Sak), a therapeutic protein for coronary thrombolysis, was used as a model protein. Four PEGylated Saks were prepared by site-specific conjugation of 5 kDa/20 kDa PEG to N-terminus and C-terminus of Sak, respectively. Experimental study suggests that the native conformation of Sak is essentially not altered by PEGylation. In contrast, the bioactivity, the hydrodynamic volume and the molecular symmetric shape of the PEGylated Sak are altered and dependent on the PEG chain length and the PEGylation site. Molecular modeling of the PEGylated Saks suggests that the PEG chain remains highly flexible and can form a distinctive hydrated layer, thereby resulting in the steric shielding effect of PEG. Docking analyses indicate that the binding affinity of Sak to its receptor is dependent on the PEG chain length and the PEGylation site. Computational simulation results explain experimental data well. Our present study clarifies molecular details of PEG chain on protein surface and may be essential to the rational design, fabrication and clinical application of PEGylated proteins.
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Affiliation(s)
- Qimeng Mu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
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248
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Soper MT, DeToma AS, Hyung SJ, Lim MH, Ruotolo BT. Amyloid-β-neuropeptide interactions assessed by ion mobility-mass spectrometry. Phys Chem Chem Phys 2013; 15:8952-61. [PMID: 23612608 PMCID: PMC3664942 DOI: 10.1039/c3cp50721a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recently, small peptides have been shown to modulate aggregation and toxicity of the amyloid-β protein (Aβ). As such, these new scaffolds may help discover a new class of biotherapeutics useful in the treatment of Alzheimer's disease. Many of these inhibitory peptide sequences have been derived from natural sources or from Aβ itself (e.g., C-terminal Aβ fragments). In addition, much earlier work indicates that tachykinins, a broad class of neuropeptides, display neurotrophic properties, presumably through direct interactions with either Aβ or its receptors. Based on this work, we undertook a limited screen of neuropeptides using ion mobility-mass spectrometry to search for similar such peptides with direct Aβ binding properties. Our results reveal that the neuropeptides leucine enkephalin (LE) and galanin interact with both the monomeric and small oligomeric forms of Aβ(1-40) to create a range of complexes having diverse stoichiometries, while some tachyknins (i.e., substance P) do not. LE interacts with Aβ more strongly than galanin, and we utilized ion mobility-mass spectrometry, molecular dynamics simulations, gel electrophoresis/Western blot, and transmission electron microscopy to study the influence of this peptide on the structure of Aβ monomer, small Aβ oligomers, as well as the eventual formation of Aβ fibrils. We find that LE binds selectively within a region of Aβ between its N-terminal tail and hydrophobic core. Furthermore, our data indicate that LE modulates fibril generation, producing shorter fibrillar aggregates when added in stoichiometric excess relative to Aβ.
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Affiliation(s)
- Molly T. Soper
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Alaina S. DeToma
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Mi Hee Lim
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109
- Life Science Institute, University of Michigan, Ann Arbor, MI 48109
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249
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Fernandez TF, Samal AB, Bedwell GJ, Chen Y, Saad JS. Structural and biophysical characterization of the interactions between the death domain of Fas receptor and calmodulin. J Biol Chem 2013; 288:21898-908. [PMID: 23760276 DOI: 10.1074/jbc.m113.471821] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The extrinsic apoptotic pathway is initiated by cell surface death receptors such as Fas. Engagement of Fas by Fas ligand triggers a conformational change that allows Fas to interact with adaptor protein Fas-associated death domain (FADD) via the death domain, which recruits downstream signaling proteins to form the death-inducing signaling complex (DISC). Previous studies have shown that calmodulin (CaM) is recruited into the DISC in cholangiocarcinoma cells, suggesting a novel role of CaM in Fas-mediated signaling. CaM antagonists induce apoptosis through a Fas-related mechanism in cholangiocarcinoma and other cancer cell lines possibly by inhibiting Fas-CaM interactions. The structural determinants of Fas-CaM interaction and the underlying molecular mechanisms of inhibition, however, are unknown. Here we employed NMR and biophysical techniques to elucidate these mechanisms. Our data show that CaM binds to the death domain of Fas (FasDD) with an apparent dissociation constant (Kd) of ~2 μM and 2:1 CaM:FasDD stoichiometry. The interactions between FasDD and CaM are endothermic and entropically driven, suggesting that hydrophobic contacts are critical for binding. We also show that both the N- and C-terminal lobes of CaM are important for binding. NMR and surface plasmon resonance data show that three CaM antagonists (N-(6-aminohexyl)-5-chloro-1-naphthalene sulfonamide, tamoxifen, and trifluoperazine) greatly inhibit Fas-CaM interactions by blocking the Fas-binding site on CaM. Our findings provide the first structural evidence for Fas-CaM interactions and mechanism of inhibition and provide new insight into the molecular basis for a novel role of CaM in regulating Fas-mediated apoptosis.
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Affiliation(s)
- Timothy F Fernandez
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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250
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High-resolution structures of the IgM Fc domains reveal principles of its hexamer formation. Proc Natl Acad Sci U S A 2013; 110:10183-8. [PMID: 23733956 DOI: 10.1073/pnas.1300547110] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
IgM is the first antibody produced during the humoral immune response. Despite its fundamental role in the immune system, IgM is structurally only poorly described. In this work we used X-ray crystallography and NMR spectroscopy to determine the atomic structures of the constant IgM Fc domains (Cµ2, Cµ3, and Cµ4) and to address their roles in IgM oligomerization. Although the isolated domains share the typical Ig fold, they differ substantially in dimerization properties and quaternary contacts. Unexpectedly, the Cµ4 domain and its C-terminal tail piece are responsible and sufficient for the specific polymerization of Cµ4 dimers into covalently linked hexamers of dimers. Based on small angle X-ray scattering data, we present a model of the ring-shaped Cµ4 structure, which reveals the principles of IgM oligomerization.
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