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Alemasov NA, Ivanisenko NV, Ivanisenko VA. Learning the changes of barnase mutants thermostability from structural fluctuations obtained using anisotropic network modeling. J Mol Graph Model 2020; 97:107572. [PMID: 32114079 DOI: 10.1016/j.jmgm.2020.107572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/29/2020] [Accepted: 02/19/2020] [Indexed: 11/17/2022]
Abstract
In biotechnology applications, rational design of new proteins with improved physico-chemical properties includes a number of important tasks. One of the greatest practical and fundamental challenges is the design of highly thermostable protein enzymes that maintain catalytic activity at high temperatures. This problem may be solved by introducing mutations into the wild-type enzyme protein. In this work, to predict the impact of such mutations in barnase protein we applied the anisotropic network modeling approach, revealing atomic fluctuations in structural regions that are changed in mutants compared to the wild-type protein. A regression model was constructed based on these structural features that can allow one to predict the thermal stability of new barnase mutants. Moreover, the analysis of regression model provides a mechanistic explanation of how the structural features can contribute to the thermal stability of barnase mutants.
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Affiliation(s)
- Nikolay A Alemasov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia.
| | - Nikita V Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia; The Kurchatov's Genomics Center of the Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Prospekt Lavrentyeva 10, Novosibirsk, Russia
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2
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Liu F, Fitzgerald MC. Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using Limited Proteolysis. J Proteome Res 2016; 15:4666-4674. [PMID: 27794609 DOI: 10.1021/acs.jproteome.6b00755] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational changes in proteins can lead to disease. Thus, methods for identifying conformational changes in proteins can further improve our understanding and facilitate detection of disease states. Here we combine limited proteolysis (LiP) with Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) to characterize breast cancer-related conformational changes in proteins on the proteomic scale. Studied here are the conformational properties of proteins in two cell culture models of breast cancer, including the MCF-10A and MCF-7 cell lines. The SILAC-LiP approach described here identified ∼200 proteins with cell-line-dependent conformational changes, as determined by their differential susceptibility to proteolytic digestion using the nonspecific protease, proteinase K. The protease susceptibility profiles of the proteins in these cell lines were compared to thermodynamic stability and expression level profiles previously generated for proteins in these same breast cancer cell lines. The comparisons revealed that there was little overlap between the proteins with protease susceptibility changes and the proteins with thermodynamic stability and/or expression level changes. Thus, the large-scale conformational analysis described here provides unique insight into the molecular basis of the breast cancer phenotypes in this study.
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Affiliation(s)
- Fang Liu
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
| | - Michael C Fitzgerald
- Department of Chemistry, Duke University , Durham, North Carolina 27708, United States
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3
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Pershad K, Kay BK. Generating thermal stable variants of protein domains through phage display. Methods 2012; 60:38-45. [PMID: 23276752 DOI: 10.1016/j.ymeth.2012.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 12/13/2022] Open
Abstract
Often in protein design research, one desires to generate thermally stable variants of a protein or domain. One route to identifying mutations that yield domains that remain folded and active at a higher temperature is through the use of directed evolution. A library of protein domain variants can be generated by mutagenic PCR, expressed on the surface of bacteriophage M13, and subjected to heat, such that the unfolded forms of the domain, showing reduced or no binding activity, are lost during subsequent affinity selection, whereas variants that still retain binding to their target are selected and enriched with each subsequent round of affinity selection. This approach takes advantage of the fact that bacteriophage M13 particles are heat stable and resistant to many proteases and protein denaturants. We present the application of this general approach to generating thermally stable variants of a eukaryotic peptide-binding domain. The benefits of producing such variants are that they typically express at high levels in Escherichia coli (30-60 mg/L shake flask) and remain soluble in solution at higher concentrations for longer periods of time than the wild-type form of the domain. The process of library generation and screening generally requires about one month of effort, and yields variants with >10 °C increase in thermal stability, as measured in a simple fluorescence-based thermal shift assay. It is anticipated that thermally stable variants will serve as excellent scaffolds for generating affinity reagents to a variety of targets of interest.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, 845 W. Taylor St., 3240 SES-MC 066, Chicago, IL 60607-7060, USA
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4
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Fomin ES, Alemasov NA. A study of the thermal stability of mutant barnase protein variants with MOLKERN software. ACTA ACUST UNITED AC 2012. [DOI: 10.1134/s2079059712060068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Baeriswyl V, Heinis C. Phage selection of cyclic peptide antagonists with increased stability toward intestinal proteases. Protein Eng Des Sel 2012; 26:81-9. [DOI: 10.1093/protein/gzs085] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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6
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Ahmad S, Kumar V, Ramanand KB, Rao NM. Probing protein stability and proteolytic resistance by loop scanning: a comprehensive mutational analysis. Protein Sci 2012; 21:433-46. [PMID: 22246996 DOI: 10.1002/pro.2029] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/23/2011] [Accepted: 01/06/2012] [Indexed: 11/07/2022]
Abstract
Improvement in protein thermostability was often found to be associated with increase in its proteolytic resistance as revealed by comparative studies of homologous proteins from extremophiles or mutational studies. Structural elements of protein responsible for this association are not firmly established although loops are implicated indirectly due to their structural role in protein stability. To get a better insight, a detailed study of protein wide mutants and their influence on stability and proteolytic resistance would be helpful. To generate such a data set, a model protein, Bacillus subtilis lipase was subjected to loop scanning site-saturation mutagenesis on 86 positions spanning all loops including termini. Upon screening of ~16,000 clones, 17 single mutants with improved thermostability were identified with increment in apparent melting temperature (Tm(app) ) by 1-6°C resulting in an increase in free energy of unfolding (ΔG(unf) ) by 0.04-1.16 kcal/mol. Proteolytic resistance of all single mutants upon incubation with nonspecific protease, Subtilisin A, was determined. Upon comparison, post-proteolysis residual activities as well as kinetics of proteolysis of mutants showed excellent correlation with ΔG(unf) , (r > 0.9), suggesting that proteolysis was strongly correlated with the global stability of this protein. This significant correlation in this set, with least possible sequence changes (single aa substitution), while covering >60% of protein surface strongly argues for the covariance of these two variables. Compared to studies from extremophiles, with large sequence heterogeneity, the observed correlation in such a narrow sequence space (ΔΔG(unf) = 1.57 kcal⁻¹) justifies the robustness of this relation.
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Affiliation(s)
- Shoeb Ahmad
- Centre for Cellular and Molecular Biology (Council of Scientific and Industrial Research), Uppal Road, Hyderabad 500007, India
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7
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Whitehead TA, Bergeron LM, Clark DS. Tying up the loose ends: circular permutation decreases the proteolytic susceptibility of recombinant proteins. Protein Eng Des Sel 2009; 22:607-13. [DOI: 10.1093/protein/gzp034] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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8
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Random exchanges of non-conserved amino acid residues among four parental termite cellulases by family shuffling improved thermostability. Protein Eng Des Sel 2007; 20:535-42. [DOI: 10.1093/protein/gzm052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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9
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Reetz MT, Carballeira JD, Vogel A. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 2007; 45:7745-51. [PMID: 17075931 DOI: 10.1002/anie.200602795] [Citation(s) in RCA: 369] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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10
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Reetz MT, Carballeira JD, Vogel A. Iterative Saturation Mutagenesis on the Basis of B Factors as a Strategy for Increasing Protein Thermostability. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602795] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Affiliation(s)
- John W Kehoe
- Biosciences Division, Argonne National Laboratory, Building 202, Argonne, Illinois 60439, USA
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12
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Pedersen JS, Dikov D, Flink JL, Hjuler HA, Christiansen G, Otzen DE. The changing face of glucagon fibrillation: structural polymorphism and conformational imprinting. J Mol Biol 2005; 355:501-23. [PMID: 16321400 DOI: 10.1016/j.jmb.2005.09.100] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2005] [Revised: 07/15/2005] [Accepted: 09/13/2005] [Indexed: 11/17/2022]
Abstract
We have established a time-resolved fluorescence assay to study fibrillation of the 29 residue peptide hormone glucagon under a variety of different conditions in a high-throughput format. Fibrils formed at pH 2.5 differ in fibrillation kinetics, morphology, thioflavin T staining and FTIR/CD spectra depending on salts, glucagon concentration and fibrillation temperature. Apparent fibrillar stability correlates with spectral and kinetic properties; generally, fibrils formed under conditions favourable for rapid fibrillation (ambient temperatures, high glucagon concentration or high salt concentration) appear less thermostable than those formed under more challenging conditions (high temperatures, low glucagon or low salt concentrations). Properties of preformed fibrils used for seeding are inherited in a prion-like manner. Thus, we conclude that the structure of fibrils formed by glucagon is not the result of the global energy minimization, but rather kinetically controlled by solvent conditions and seed-imprinting. Fibrillar polymorphism, which is being reported for an increasing number of proteins, probably reflects that fibrils have not been under evolutionary constraints to retain a single active conformation. Our results highlight the complexity of the fibrillation mechanism of glucagon, since even subtle changes in fibrillation conditions can alter the type of fibrils formed, or result in formation of mixtures of several types of fibrils.
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13
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Eijsink VGH, Gåseidnes S, Borchert TV, van den Burg B. Directed evolution of enzyme stability. ACTA ACUST UNITED AC 2005; 22:21-30. [PMID: 15857780 DOI: 10.1016/j.bioeng.2004.12.003] [Citation(s) in RCA: 300] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2004] [Revised: 11/29/2004] [Accepted: 12/02/2004] [Indexed: 11/16/2022]
Abstract
Modern enzyme development relies to an increasing extent on strategies based on diversity generation followed by screening for variants with optimised properties. In principle, these directed evolution strategies might be used for optimising any enzyme property, which can be screened for in an economically feasible way, even if the molecular basis of that property is not known. Stability is an interesting property of enzymes because (1) it is of great industrial importance, (2) it is relatively easy to screen for, and (3) the molecular basis of stability relates closely to contemporary issues in protein science such as the protein folding problem and protein folding diseases. Thus, engineering enzyme stability is of both commercial and scientific interest. Here, we review how directed evolution has contributed to the development of stable enzymes and to new insight into the principles of protein stability. Several recent examples are described. These examples show that directed evolution is an effective strategy to obtain stable enzymes, especially when used in combination with rational or semi-rational engineering strategies. With respect to the principles of protein stability, some important lessons to learn from recent efforts in directed evolution are (1) that there are many structural ways to stabilize a protein, which are not always easy to rationalize, (2) that proteins may very well be stabilized by optimizing their surfaces, and (3) that high thermal stability may be obtained without forfeiture of catalytic performance at low temperatures.
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Affiliation(s)
- Vincent G H Eijsink
- Department of Chemistry, Biotechnology and Food Science, Agricultural University of Norway, P.O. Box 5003, N-1432 As, Norway
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14
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Dutta S, Batori V, Koide A, Koide S. High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Sci 2005; 14:2838-48. [PMID: 16199661 PMCID: PMC2253215 DOI: 10.1110/ps.051603005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The tenth fibronectin type III (FN3) domain of human fibronectin (FNfn10), a prototype of the ubiquitous FN3 domain, is a small, monomeric beta-sandwich protein. In this study, we have bisected FNfn10 in each loop to generate a total of six fragment pairs. We found that fragment pairs bisected at multiple loops of FNfn10 show complementation in vivo as tested with a yeast two-hybrid system. The dissociation constant of these fragment pairs determined in vitro were as low as 3 nM, resulting in one of the tightest fragment complementation systems reported so far. Furthermore, we show that the affinity of fragment complementation is correlated with the stability of the uncut parent protein. Exploring this correlation, we screened a yeast two-hybrid library of one fragment and identified mutations that suppress the effect of a destabilizing mutation in the other fragment. One of the identified mutations significantly increased the stability of the uncut wild-type protein, proving that fragment complementation can be used as a novel strategy for the selection of proteins with enhanced stability.
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Affiliation(s)
- Sanjib Dutta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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15
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Parker MH, Chen Y, Danehy F, Dufu K, Ekstrom J, Getmanova E, Gokemeijer J, Xu L, Lipovsek D. Antibody mimics based on human fibronectin type three domain engineered for thermostability and high-affinity binding to vascular endothelial growth factor receptor two. Protein Eng Des Sel 2005; 18:435-44. [PMID: 16087651 DOI: 10.1093/protein/gzi050] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The tenth human fibronectin type three domain ((10)Fn3) is a small (10 kDa), extremely stable and soluble protein with an immunoglobulin-like fold, but without cysteine residues. Selections from (10)Fn3-based libraries of proteins with randomized loops have yielded high-affinity, target-specific antibody mimics. However, little is known about the biophysical properties of such antibody mimics, which will determine their suitability for in vitro and medical applications. We characterized target binding and biophysical properties of two related (10)Fn3-based antibody mimics that bind vascular endothelial growth factor receptor two (VEGF-R2). The first antibody mimic, which has a dissociation constant (K(d)) of 13 nM, is highly stable [melting temperature (T(m))=62 degrees C] and soluble, whereas the second, which binds VEGF-R2 with 40 x higher affinity, is less stable (T(m) < 40 degrees C) and relatively insoluble. We used our understanding of these two (10)Fn3 derivatives and of wild-type (10)Fn3 structure to engineer the next generation of antibody mimics, which have an improved combination of high affinity (K(d)=0.59 nM), stability (T(m)=53 degrees C) and solubility. Our findings illustrate that (10)Fn3-based antibody mimics can be engineered for favorable biophysical properties even when 20% of the wild-type (10)Fn3 sequence is mutated in order to satisfy target-binding requirements.
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Affiliation(s)
- M H Parker
- Phylos, Inc., succeeded by Compound Therapeutics, Waltham, MA 02453, USA
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16
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Park C, Marqusee S. Probing the high energy states in proteins by proteolysis. J Mol Biol 2004; 343:1467-76. [PMID: 15491624 DOI: 10.1016/j.jmb.2004.08.085] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 08/24/2004] [Accepted: 08/26/2004] [Indexed: 11/29/2022]
Abstract
Unless the native conformation has an unstructured region, proteases cannot effectively digest a protein under native conditions. Digestion must occur from a higher energy form, when at least some part of the protein is exposed to solvent and becomes accessible by proteases. Monitoring the kinetics and denaturant dependence of proteolysis under native conditions yields insight into the mechanism of proteolysis as well as these high-energy conformations. We propose here a generalized approach to exploit proteolysis as a tool to probe high-energy states in proteins. This "native state proteolysis" experiment was carried out on Escherichia coli ribonuclease HI. Mass spectrometry and N-terminal sequencing showed that thermolysin cleaves the peptide bond between Thr92 and Ala93 in an extended loop region of the protein. By comparing the proteolysis rate of the folded protein and a peptidic substrate mimicking the sequence at the cleavage site, the energy required to reach the susceptible state (Delta G(proteolysis)) was determined. From the denaturant dependence of Delta G(proteolysis), we determined that thermolysin digests this protein through a local fluctuation, i.e. localized unfolding with minimal change in solvent assessable surface area. Proteolytic susceptibilities of proteins are discussed based on the finding of this local fluctuation mechanism for proteolysis under native conditions.
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Affiliation(s)
- Chiwook Park
- Department of Molecular and Cell Biology, QB3 Institute, University of California, Berkeley, CA 94720, USA
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17
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Abstract
The use of so-called protein scaffolds for the generation of novel binding proteins via combinatorial engineering has recently emerged as a powerful alternative to natural or recombinant antibodies. This concept requires an extraordinary stable protein architecture tolerating multiple substitutions or insertions at the primary structural level. With respect to broader applicability it should involve a type of polypeptide fold which is observed in differing natural contexts and with distinct biochemical functions, so that it is likely to be adaptable to novel molecular recognition purposes. The quickly growing number of approaches can be classified into three groups: carrier proteins for the display of single variegated loops, scaffolds providing rigid elements of secondary structure, and protein frameworks supporting a group of conformationally variable loops in a fixed spatial arrangement. Generally, such artificial receptor proteins should be based on monomeric and small polypeptides that are robust, easily engineered, and efficiently produced in inexpensive prokaryotic expression systems. Today, progress in protein library technology allows for the parallel development of immunoglobulin (Ig) as well as scaffold-based affinity reagents. Both biomolecular tools have the potential to complement each other, thus expanding the possibility to find an affinity reagent suitable for a given application. The repertoire of protein scaffolds hitherto recruited for combinatorial protein engineering purposes will probably be further expanded in the future, including both additional natural proteins and de novo designed proteins, contributing to the collection of libraries available at present. In this review both the structural features and the practical use of scaffold proteins will be discussed and exemplified.
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Affiliation(s)
- Per-Ake Nygren
- Department of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden.
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18
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Ueda H, Kristensen P, Winter G. Stabilization of antibody VH-domains by proteolytic selection. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2003.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Abstract
Globular proteins are characterized by the specific and tight packing of hydrophobic side-chains in the so-called "hydrophobic core." Formation of the core is key in folding, stabilization, and conformational specificity. The critical role of hydrophobic cores in maintaining the highly ordered structures present in natural proteins justifies the tremendous efforts devoted to their redesign. Both experimental and computational combinatorial-based approaches have been reported in the last years as powerful protein design tools. These manage to explore large regions of the sequence/conformational space, allowing the search for alternative protein core arrangements displaying native-like properties. The overall results obtained from core design projects have contributed significantly to our present knowledge of protein folding and function. In addition, core design has worked as a benchmark for the development of ambitious protein design projects that nowadays are allowing the de novo design of novel protein structures and functions.
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Affiliation(s)
- Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autonoma de Barcelona, Barcelona, Spain.
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20
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Abstract
To facilitate the process of protein design and learn the basic rules that control the structure and stability of proteins, combinatorial methods have been developed to select or screen proteins with desired properties from libraries of mutants. One such method uses phage-display and proteolysis to select stably folded proteins. This method does not rely on specific properties of proteins for selection. Therefore, in principle it can be applied to any protein. Since its first demonstration in 1998, the method has been used to create hyperthermophilic proteins, to evolve novel folded domains from a library generated by combinatorial shuffling of polypeptide segments and to convert a partially unfolded structure to a fully folded protein.
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Affiliation(s)
- Yawen Bai
- Laboratory of Biochemistry, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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21
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Affiliation(s)
- Oliver J Miller
- The Advanced Centre for Biochemical Engineering, Department of Biochemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
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22
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Williams RS, Chasman DI, Hau DD, Hui B, Lau AY, Glover JNM. Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. J Biol Chem 2003; 278:53007-16. [PMID: 14534301 DOI: 10.1074/jbc.m310182200] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most cancer-associated BRCA1 mutations identified to date result in the premature translational termination of the protein, highlighting a crucial role for the C-terminal, BRCT repeat region in mediating BRCA1 tumor suppressor function. However, the molecular and genetic effects of missense mutations that map to the BRCT region remain largely unknown. Using a protease-based assay, we directly assessed the sensitivity of the folding of the BRCT domain to an extensive set of truncation and single amino acid substitutions derived from breast cancer screening programs. The protein can tolerate truncations of up to 8 amino acids, but further deletion results in drastic BRCT folding defects. This molecular phenotype can be correlated with an increased susceptibility to disease. A cross-validated computational assessment of the BRCT mutation data base suggests that as much as half of all BRCT missense mutations contribute to BRCA1 loss of function and disease through protein-destabilizing effects. The coupled use of proteolytic methods and computational predictive methods to detect mutant BRCA1 conformations at the protein level will augment the efficacy of current BRCA1 screening protocols, especially in the absence of clinical data that can be used to discriminate deleterious BRCT missense mutations from benign polymorphisms.
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Affiliation(s)
- R Scott Williams
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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23
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Radley TL, Markowska AI, Bettinger BT, Ha JH, Loh SN. Allosteric switching by mutually exclusive folding of protein domains. J Mol Biol 2003; 332:529-36. [PMID: 12963365 PMCID: PMC3145375 DOI: 10.1016/s0022-2836(03)00925-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Many proteins are built from structurally and functionally distinct domains. A major goal is to understand how conformational change transmits information between domains in order to achieve biological activity. A two-domain, bi-functional fusion protein has been designed so that the mechanical stress imposed by the folded structure of one subunit causes the other subunit to unfold, and vice versa. The construct consists of ubiquitin inserted into a surface loop of barnase. The distance between the amino and carboxyl ends of ubiquitin is much greater than the distance between the termini of the barnase loop. This topological constraint causes the two domains to engage in a thermodynamic tug-of-war in which only one can exist in its folded state at any given time. This conformational equilibrium, which is cooperative, reversible, and controllable by ligand binding, serves as a model for the coupled binding and folding mechanism widely used to mediate protein-protein interactions and cellular signaling processes. The position of the equilibrium can be adjusted by temperature or ligand binding and is monitored in vivo by cell death. This design forms the basis for a new class of cytotoxic proteins that can be activated by cell-specific effector molecules, and can thus target particular cell types for destruction.
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24
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Fernandez-Gacio A, Uguen M, Fastrez J. Phage display as a tool for the directed evolution of enzymes. Trends Biotechnol 2003; 21:408-14. [PMID: 12948674 DOI: 10.1016/s0167-7799(03)00194-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Since its introduction in 1985, phage display has had a tremendous impact on the discovery of peptides that bind to a variety of receptors, the generation of binding sites within predefined scaffolds, and the creation of high-affinity antibodies without immunization. Its application to enzymology has required the development of techniques that couple enzymatic activity to selection protocols based on affinity chromatography. Here, we describe both indirect methods, using transition-state analogues and suicide substrates, and direct methods, using the ability of active phage-enzymes to transform substrate into product. The methods have been applied to large libraries for mechanistic-based studies and to generate variants with new or improved properties. In addition, such techniques have been successfully used to select catalytic antibodies and improve their catalytic efficiency.
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Affiliation(s)
- Ana Fernandez-Gacio
- Laboratoire de Biochimie Physique et des Biopolymères, Institut des Sciences de la Vie, Université Catholique de Louvain, Place L. Pasteur, 1, B1348 Louvain-la-Neuve, Belgium
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25
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Lemaire SD, Collin V, Keryer E, Quesada A, Miginiac-Maslow M. Characterization of thioredoxin y, a new type of thioredoxin identified in the genome of Chlamydomonas reinhardtii. FEBS Lett 2003; 543:87-92. [PMID: 12753911 DOI: 10.1016/s0014-5793(03)00416-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The sequencing of the Arabidopsis genome revealed a multiplicity of thioredoxins (TRX), ubiquitous protein disulfide oxido-reductases. We have analyzed the TRX family in the genome of the unicellular green alga Chlamydomonas reinhardtii and identified eight different thioredoxins for which we have cloned and sequenced the corresponding cDNAs. One of these TRXs represents a new type that we named TRX y. This most probably chloroplastic TRX is highly conserved in photosynthetic organisms. The biochemical characterization of the recombinant protein shows that it exhibits a thermal stability profile and specificity toward target enzymes completely different from those of TRXs characterized so far.
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Affiliation(s)
- S D Lemaire
- Institut de Biotechnologie des Plantes, UMR 8618 CNRS, Université Paris-Sud, Bâtiment 630, 91405 Cedex, Orsay, France.
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