201
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Mallik S, Kundu S. Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins. Genome Biol Evol 2017; 9:916-931. [PMID: 28338825 PMCID: PMC5388290 DOI: 10.1093/gbe/evx036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
Understanding the molecular evolution of macromolecular complexes in the light of their structure, assembly, and stability is of central importance. Here, we address how the modular organization of native molecular contacts shapes the selection pressure on individual residue sites of ribosomal complexes. The bacterial ribosomal complex is represented as a residue contact network where nodes represent amino acid/nucleotide residues and edges represent their van der Waals interactions. We find statistically overrepresented native amino acid-nucleotide contacts (OaantC, one amino acid contacts one or multiple nucleotides, internucleotide contacts are disregarded). Contact number is defined as the number of nucleotides contacted. Involvement of individual amino acids in OaantCs with smaller contact numbers is more random, whereas only a few amino acids significantly contribute to OaantCs with higher contact numbers. An investigation of structure, stability, and assembly of bacterial ribosome depicts the involvement of these OaantCs in diverse biophysical interactions stabilizing the complex, including high-affinity protein-RNA contacts, interprotein cooperativity, intersubunit bridge, packing of multiple ribosomal RNA domains, etc. Amino acid-nucleotide constituents of OaantCs with higher contact numbers are generally associated with significantly slower substitution rates compared with that of OaantCs with smaller contact numbers. This evolutionary rate heterogeneity emerges from the strong purifying selection pressure that conserves the respective amino acid physicochemical properties relevant to the stabilizing interaction with OaantC nucleotides. An analysis of relative molecular orientations of OaantC residues and their interaction energetics provides the biophysical ground of purifying selection conserving OaantC amino acid physicochemical properties.
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Affiliation(s)
- Saurav Mallik
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
- Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
- Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-II), University of Calcutta, Kolkata, India
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202
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Scheiblhofer S, Laimer J, Machado Y, Weiss R, Thalhamer J. Influence of protein fold stability on immunogenicity and its implications for vaccine design. Expert Rev Vaccines 2017; 16:479-489. [PMID: 28290225 PMCID: PMC5490637 DOI: 10.1080/14760584.2017.1306441] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION In modern vaccinology and immunotherapy, recombinant proteins more and more replace whole organisms to induce protective or curative immune responses. Structural stability of proteins is of crucial importance for efficient presentation of antigenic peptides on MHC, which plays a decisive role for triggering strong immune reactions. Areas covered: In this review, we discuss structural stability as a key factor for modulating the potency of recombinant vaccines and its importance for antigen proteolysis, presentation, and stimulation of B and T cells. Moreover, the impact of fold stability on downstream events determining the differentiation of T cells into effector cells is reviewed. We summarize studies investigating the impact of protein fold stability on the outcome of the immune response and provide an overview on computational methods to estimate the effects of point mutations on protein stability. Expert commentary: Based on this information, the rational design of up-to-date vaccines is discussed. A model for predicting immunogenicity of proteins based on their conformational stability at different pH values is proposed.
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Affiliation(s)
- Sandra Scheiblhofer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Laimer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Yoan Machado
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Richard Weiss
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
| | - Josef Thalhamer
- a Department of Molecular Biology , University of Salzburg , Salzburg , Austria
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203
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Djimsa BA, Abraham A, Mafi GG, VanOverbeke DL, Ramanathan R. Effects of Metmyoglobin Reducing Activity and Thermal Stability of NADH-Dependent Reductase and Lactate Dehydrogenase on Premature Browning in Ground Beef. J Food Sci 2017; 82:304-313. [PMID: 28099768 DOI: 10.1111/1750-3841.13606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/28/2016] [Accepted: 12/04/2016] [Indexed: 11/27/2022]
Abstract
Premature browning is a condition wherein ground beef exhibits a well-done appearance before reaching the USDA recommended internal cooked meat temperature of 71.1 °C; however, the mechanism is unclear. The objectives of this study were: (1) to determine the effects of packaging and temperature on metmyoglobin reducing activity (MRA) of cooked ground beef patties and (2) to assess the effects of temperature and pH on thermal stability of NADH-dependent reductase, lactate dehydrogenase (LDH), and oxymyoglobin (OxyMb) in-vitro. Beef patties (lean: fat = 85:15) were packaged in high-oxygen modified atmosphere (HiOX-MAP) or vacuum (VP) and cooked to either 65 or 71 °C. Internal meat color and MRA of both raw and cooked patties were determined. Purified NADH-dependent reductase and LDH were used to determine the effects of pH and temperature on enzyme activity. MRA of cooked patties was temperature and packaging dependent (P < 0.05). Vacuum packaged patties cooked to 71 °C had greater (P < 0.05) MRA than HiOX-MAP counterparts. Thermal stability of OxyMb, NADH-dependent reductase, and LDH were different and pH-dependent. LDH was able to generate NADH at 84 °C; whereas NADH-dependent reductase was least stable to heat. The results suggest that patties have MRA at cooking temperatures, which can influence cooked meat color.
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Affiliation(s)
| | - Anupam Abraham
- Dept. of Animal Science, Oklahoma State Univ., Stillwater, OK, 74078, U.S.A
| | - Gretchen G Mafi
- Dept. of Animal Science, Oklahoma State Univ., Stillwater, OK, 74078, U.S.A
| | | | - Ranjith Ramanathan
- Dept. of Animal Science, Oklahoma State Univ., Stillwater, OK, 74078, U.S.A
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204
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Liptrot DJ, Power PP. London dispersion forces in sterically crowded inorganic and organometallic molecules. Nat Rev Chem 2017. [DOI: 10.1038/s41570-016-0004] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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205
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Lonardi A, Oborský P, Hünenberger PH. Solvent-Modulated Influence of Intramolecular Hydrogen-Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study. Helv Chim Acta 2016. [DOI: 10.1002/hlca.201600158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alice Lonardi
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
| | - Pavel Oborský
- Laboratory of Physical Chemistry; ETH Hönggerberg; HCI; CH-8093 Zürich Switzerland
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206
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Corrêa F, Key J, Kuhlman B, Gardner K. Computational Repacking of HIF-2α Cavity Replaces Water-Based Stabilized Core. Structure 2016; 24:1918-1927. [DOI: 10.1016/j.str.2016.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/18/2016] [Accepted: 08/19/2016] [Indexed: 12/25/2022]
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207
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Idrees D, Prakash A, Haque MA, Islam A, Hassan MI, Ahmad F. GdnHCl-induced unfolding intermediate in the mitochondrial carbonic anhydrase VA. Int J Biol Macromol 2016; 91:1151-60. [DOI: 10.1016/j.ijbiomac.2016.06.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/24/2016] [Accepted: 06/26/2016] [Indexed: 10/21/2022]
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208
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Protein stability: computation, sequence statistics, and new experimental methods. Curr Opin Struct Biol 2016; 33:161-8. [PMID: 26497286 DOI: 10.1016/j.sbi.2015.09.002] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 11/22/2022]
Abstract
Calculating protein stability and predicting stabilizing mutations remain exceedingly difficult tasks, largely due to the inadequacy of potential functions, the difficulty of modeling entropy and the unfolded state, and challenges of sampling, particularly of backbone conformations. Yet, computational design has produced some remarkably stable proteins in recent years, apparently owing to near ideality in structure and sequence features. With caveats, computational prediction of stability can be used to guide mutation, and mutations derived from consensus sequence analysis, especially improved by recent co-variation filters, are very likely to stabilize without sacrificing function. The combination of computational and statistical approaches with library approaches, including new technologies such as deep sequencing and high throughput stability measurements, point to a very exciting near term future for stability engineering, even with difficult computational issues remaining.
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209
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Ireta J. Polyalanine α-helix microsolvation: assessing the energy of the peptide desolvation penalty with density functional theory. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1981-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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210
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Batra J, Tjong H, Zhou HX. Electrostatic effects on the folding stability of FKBP12. Protein Eng Des Sel 2016; 29:301-308. [PMID: 27381026 PMCID: PMC4955870 DOI: 10.1093/protein/gzw014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 03/28/2016] [Accepted: 04/15/2016] [Indexed: 01/17/2023] Open
Abstract
The roles of electrostatic interactions in protein folding stability have been a matter of debate, largely due to the complexity in the theoretical treatment of these interactions. We have developed computational methods for calculating electrostatic effects on protein folding stability. To rigorously test and further refine these methods, here we carried out experimental studies into electrostatic effects on the folding stability of the human 12-kD FK506 binding protein (FKBP12). This protein has a close homologue, FKBP12.6, with amino acid substitutions in only 18 of their 107 residues. Of the 18 substitutions, 8 involve charged residues. Upon mutating FKBP12 residues at these 8 positions individually into the counterparts in FKBP12.6, the unfolding free energy (ΔGu) of FKBP12 changed by -0.3 to 0.7 kcal/mol. Accumulating stabilizing substitutions resulted in a mutant with a 0.9 kcal/mol increase in stability. Additional charge mutations were grafted from a thermophilic homologue, MtFKBP17, which aligns to FKBP12 with 31% sequence identity over 89 positions. Eleven such charge mutations were studied, with ΔΔGu varying from -2.9 to 0.1 kcal/mol. The predicted electrostatic effects by our computational methods with refinements herein had a root-mean-square deviation of 0.9 kcal/mol from the experimental ΔΔGu values on 16 single mutations of FKBP12. The difference in ΔΔGu between mutations grafted from FKBP12.6 and those from MtFKBP17 suggests that more distant homologues are less able to provide guidance for enhancing folding stability.
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Affiliation(s)
- Jyotica Batra
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Department of Chemistry and Physics, Bellarmine University, 2001 Newburg Road, Louisville, KY40205, USA
| | - Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
- Present address: Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Huan-Xiang Zhou
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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211
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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212
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Hsu CH, Park S, Mortenson DE, Foley BL, Wang X, Woods RJ, Case DA, Powers ET, Wong CH, Dyson HJ, Kelly JW. The Dependence of Carbohydrate-Aromatic Interaction Strengths on the Structure of the Carbohydrate. J Am Chem Soc 2016; 138:7636-48. [PMID: 27249581 DOI: 10.1021/jacs.6b02879] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interactions between proteins and carbohydrates are ubiquitous in biology. Therefore, understanding the factors that determine their affinity and selectivity are correspondingly important. Herein, we have determined the relative strengths of intramolecular interactions between a series of monosaccharides and an aromatic ring close to the glycosylation site in an N-glycoprotein host. We employed the enhanced aromatic sequon, a structural motif found in the reverse turns of some N-glycoproteins, to facilitate face-to-face monosaccharide-aromatic interactions. A protein host was used because the dependence of the folding energetics on the identity of the monosaccharide can be accurately measured to assess the strength of the carbohydrate-aromatic interaction. Our data demonstrate that the carbohydrate-aromatic interaction strengths are moderately affected by changes in the stereochemistry and identity of the substituents on the pyranose rings of the sugars. Galactose seems to make the weakest and allose the strongest sugar-aromatic interactions, with glucose, N-acetylglucosamine (GlcNAc) and mannose in between. The NMR solution structures of several of the monosaccharide-containing N-glycoproteins were solved to further understand the origins of the similarities and differences between the monosaccharide-aromatic interaction energies. Peracetylation of the monosaccharides substantially increases the strength of the sugar-aromatic interaction in the context of our N-glycoprotein host. Finally, we discuss our results in light of recent literature regarding the contribution of electrostatics to CH-π interactions and speculate on what our observations imply about the absolute conservation of GlcNAc as the monosaccharide through which N-linked glycans are attached to glycoproteins in eukaryotes.
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Affiliation(s)
- Che-Hsiung Hsu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Sangho Park
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - David E Mortenson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - B Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Xiaocong Wang
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia , 315 Riverbend Road, Athens, Georgia 30602, United States
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University , Piscataway, New Jersey 08854, United States
| | - Evan T Powers
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,Genomics Research Center, Academia Sinica , Taipei 115, Taiwan.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Jeffery W Kelly
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States.,Department of Chemistry, The Scripps Research Institute , La Jolla, California 92037, United States.,The Skaggs Institute for Chemical Biology , La Jolla, California 92037, United States
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213
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Using natural sequences and modularity to design common and novel protein topologies. Curr Opin Struct Biol 2016; 38:26-36. [PMID: 27270240 DOI: 10.1016/j.sbi.2016.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 02/07/2023]
Abstract
Protein design is still a challenging undertaking, often requiring multiple attempts or iterations for success. Typically, the source of failure is unclear, and scoring metrics appear similar between successful and failed cases. Nevertheless, the use of sequence statistics, modularity and symmetry from natural proteins, combined with computational design both at the coarse-grained and atomistic levels is propelling a new wave of design efforts to success. Here we highlight recent examples of design, showing how the wealth of natural protein sequence and topology data may be leveraged to reduce the search space and increase the likelihood of achieving desired outcomes.
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214
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Analysis of the Structural Stability Among Cyclotide Members Through Cystine Knot Fold that Underpins Its Potential Use as a Drug Scaffold. Int J Pept Res Ther 2016. [DOI: 10.1007/s10989-016-9537-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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215
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Piovesan D, Minervini G, Tosatto SCE. The RING 2.0 web server for high quality residue interaction networks. Nucleic Acids Res 2016; 44:W367-74. [PMID: 27198219 PMCID: PMC4987896 DOI: 10.1093/nar/gkw315] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/13/2016] [Indexed: 01/06/2023] Open
Abstract
Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico–chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain–domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π–π stacking and π–cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring.
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Affiliation(s)
- Damiano Piovesan
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padua, Padua 35121, Italy CNR Institute of Neuroscience, Padua 35121, Italy
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216
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Bartlett GJ, Woolfson DN. On the satisfaction of backbone-carbonyl lone pairs of electrons in protein structures. Protein Sci 2016; 25:887-97. [PMID: 26833776 PMCID: PMC4941217 DOI: 10.1002/pro.2896] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/29/2016] [Indexed: 11/11/2022]
Abstract
Protein structures are stabilized by a variety of noncovalent interactions (NCIs), including the hydrophobic effect, hydrogen bonds, electrostatic forces and van der Waals’ interactions. Our knowledge of the contributions of NCIs, and the interplay between them remains incomplete. This has implications for computational modeling of NCIs, and our ability to understand and predict protein structure, stability, and function. One consideration is the satisfaction of the full potential for NCIs made by backbone atoms. Most commonly, backbone‐carbonyl oxygen atoms located within α‐helices and β‐sheets are depicted as making a single hydrogen bond. However, there are two lone pairs of electrons to be satisfied for each of these atoms. To explore this, we used operational geometric definitions to generate an inventory of NCIs for backbone‐carbonyl oxygen atoms from a set of high‐resolution protein structures and associated molecular‐dynamics simulations in water. We included more‐recently appreciated, but weaker NCIs in our analysis, such as n→π* interactions, Cα‐H bonds and methyl‐H bonds. The data demonstrate balanced, dynamic systems for all proteins, with most backbone‐carbonyl oxygen atoms being satisfied by two NCIs most of the time. Combinations of NCIs made may correlate with secondary structure type, though in subtly different ways from traditional models of α‐ and β‐structure. In addition, we find examples of under‐ and over‐satisfied carbonyl‐oxygen atoms, and we identify both sequence‐dependent and sequence‐independent secondary‐structural motifs in which these reside. Our analysis provides a more‐detailed understanding of these contributors to protein structure and stability, which will be of use in protein modeling, engineering and design.
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Affiliation(s)
- Gail J Bartlett
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom.,School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol, BS8 1TD, United Kingdom.,BrisSynBio, a BBSRC/EPSRC-Funded Synthetic Biology Research Centre, Life Sciences Building, Bristol, BS8 1TQ, United Kingdom
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217
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Deller MC, Kong L, Rupp B. Protein stability: a crystallographer's perspective. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:72-95. [PMID: 26841758 PMCID: PMC4741188 DOI: 10.1107/s2053230x15024619] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 12/18/2022]
Abstract
Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.
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Affiliation(s)
- Marc C Deller
- Stanford ChEM-H, Macromolecular Structure Knowledge Center, Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125, USA
| | - Leopold Kong
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084, USA
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218
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Makwana KM, Mahalakshmi R. Nature of aryl-tyrosine interactions contribute to β-hairpin scaffold stability: NMR evidence for alternate ring geometry. Phys Chem Chem Phys 2016; 17:4220-30. [PMID: 25569770 DOI: 10.1039/c4cp04991h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The specific contribution of the acidic-aromatic β-sheet favouring amino acid tyrosine to the stability of short octapeptide β-hairpin structures is presented here. Solution NMR analysis in near-apolar environments suggests the energetically favourable mode of interaction to be T-shaped face-to-edge (FtE) and that a Trp-Tyr interacting pair is the most stabilizing. Alternate aryl geometries also exist in solution, which readily equilibrate between a preferred π···π conformation to an aromatic-amide conformation, without any change in the backbone structure. While the phenolic ring is readily accommodated at the "edge" of FtE aryl interactions, it exhibits an overall lowered contribution to scaffold stability in the "face" orientation. Such differential tyrosine interactions are key to its dual nature in proteins.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal-462023, India.
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219
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Stadler AM, Demmel F, Ollivier J, Seydel T. Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding. Phys Chem Chem Phys 2016; 18:21527-38. [DOI: 10.1039/c6cp04146a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions.
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Affiliation(s)
- Andreas M. Stadler
- Jülich Centre for Neutron Science JCNS and Institute for Complex Systems ICS
- Forschungszentrum Jülich GmbH
- 52425 Jülich
- Germany
| | | | | | - Tilo Seydel
- Institut Laue-Langevin
- 38042 Grenoble Cedex 9
- France
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220
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Dorh N, Zhu S, Dhungana KB, Pati R, Luo FT, Liu H, Tiwari A. BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity. Sci Rep 2015; 5:18337. [PMID: 26679512 PMCID: PMC4683377 DOI: 10.1038/srep18337] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/19/2015] [Indexed: 02/07/2023] Open
Abstract
Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors can be used as a sensitive indicator of protein surface hydrophobicity. A first principle approach is used to identify the molecular level mechanism for the substantial increase in the fluorescence signal strength. Our results show that conformational change and increased molecular rigidity of the dye due to its hydrophobic interaction with protein lead to fluorescence enhancement.
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Affiliation(s)
- Nethaniah Dorh
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | - Shilei Zhu
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | - Kamal B. Dhungana
- Department of Physics, Michigan Technological University, Houghton, MI 49931, USA
| | - Ranjit Pati
- Department of Physics, Michigan Technological University, Houghton, MI 49931, USA
| | - Fen-Tair Luo
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Haiying Liu
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | - Ashutosh Tiwari
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
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221
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Senthilkumar B, Kumar P, Rajasekaran R. In-Silico Template Selection of In-Vitro Evolved Kalata B1 ofOldenlandia Affinisfor Scaffolding Peptide-Based Drug Design. J Cell Biochem 2015; 117:66-73. [DOI: 10.1002/jcb.25248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 05/29/2015] [Indexed: 12/20/2022]
Affiliation(s)
- B. Senthilkumar
- Bioinformatics Division; School of Bio Sciences and Technology; Vellore Institute of Technology University; Vellore 632014 Tamil Nadu India
| | - Prakash Kumar
- Bioinformatics Division; School of Bio Sciences and Technology; Vellore Institute of Technology University; Vellore 632014 Tamil Nadu India
| | - R. Rajasekaran
- Bioinformatics Division; School of Bio Sciences and Technology; Vellore Institute of Technology University; Vellore 632014 Tamil Nadu India
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222
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Thermodynamics of protein denaturation at temperatures over 100 °C: CutA1 mutant proteins substituted with hydrophobic and charged residues. Sci Rep 2015; 5:15545. [PMID: 26497062 PMCID: PMC4620440 DOI: 10.1038/srep15545] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/28/2015] [Indexed: 11/08/2022] Open
Abstract
Although the thermodynamics of protein denaturation at temperatures over 100 °C is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. We designed certain hydrophobic mutant proteins of CutA1 from Escherichia coli, which have denaturation temperatures (Td) ranging from 101 to 113 °C and show a reversible heat denaturation. Using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mutant protein (Td = 137 °C) by substituting six residues with charged ones. Thermodynamic analyses of these mutant proteins indicated that the hydrophobic mutants were stabilized by the accumulation of denaturation enthalpy (ΔH) with no entropic gain from hydrophobic solvation around 100 °C, and that the stabilization due to salt bridges resulted from both the increase in ΔH from ion-ion interactions and the entropic effect of the electrostatic solvation over 113 °C. This is the first experimental evidence that has successfully overcome the typical technical difficulties.
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223
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Howell DW, Tsai SP, Churion K, Patterson J, Abbey C, Atkinson JT, Porterpan D, You YH, Meissner KE, Bayless KJ, Bondos SE. Identification of multiple dityrosine bonds in materials composed of the Drosophila protein Ultrabithorax. ADVANCED FUNCTIONAL MATERIALS 2015; 25:5988-5998. [PMID: 28725173 PMCID: PMC5513195 DOI: 10.1002/adfm.201502852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The recombinant protein Ultrabithorax (Ubx), a Drosophila melanogaster Hox transcription factor, self-assembles into biocompatible materials in vitro that are remarkably extensible and strong. Here, we demonstrate that the strength of Ubx materials is due to intermolecular dityrosine bonds. Ubx materials auto-fluoresce blue, a characteristic of dityrosine, and bind dityrosine-specific antibodies. Monitoring the fluorescence of reduced Ubx fibers upon oxygen exposure reveals biphasic bond formation kinetics. Two dityrosine bonds in Ubx were identified by site-directed mutagenesis followed by measurements of fiber fluorescent intensity. One bond is located between the N-terminus and the homeodomain (Y4/Y296 or Y12/Y293), and another bond is formed by Y167 and Y240. Fiber fluorescence closely correlates with fiber strength, demonstrating that these bonds are intermolecular. To our knowledge, this is the first identification of specific residues that participate in dityrosine bonds in protein-based materials. The percentage of Ubx molecules harboring both bonds can be decreased or increased by mutagenesis, providing an additional mechanism to control the mechanical properties of Ubx materials. Duplication of tyrosine-containing motifs in Ubx increases dityrosine content in Ubx fibers, suggesting these motifs could be inserted in other self-assembling proteins to strengthen the corresponding materials.
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Affiliation(s)
- David W Howell
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Shang-Pu Tsai
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Kelly Churion
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Jan Patterson
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Colette Abbey
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Joshua T Atkinson
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX 77005, United States
| | - Dustin Porterpan
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Yil-Hwan You
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Kenith E Meissner
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Kayla J Bayless
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
| | - Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, United States
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224
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Miño-Galaz GA, Gutierrez G. Hydrogen bonds and asymmetrical heat diffusion in α-helices. A computational analysis. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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225
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Li GC, Srivastava AK, Kim J, Taylor SS, Veglia G. Mapping the Hydrogen Bond Networks in the Catalytic Subunit of Protein Kinase A Using H/D Fractionation Factors. Biochemistry 2015; 54:4042-9. [PMID: 26030372 PMCID: PMC4498444 DOI: 10.1021/acs.biochem.5b00387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein kinase A is a prototypical phosphoryl transferase, sharing its catalytic core (PKA-C) with the entire kinase family. PKA-C substrate recognition, active site organization, and product release depend on the enzyme's conformational transitions from the open to the closed state, which regulate its allosteric cooperativity. Here, we used equilibrium nuclear magnetic resonance hydrogen/deuterium (H/D) fractionation factors (φ) to probe the changes in the strength of hydrogen bonds within the kinase upon binding the nucleotide and a pseudosubstrate peptide (PKI5-24). We found that the φ values decrease upon binding both ligands, suggesting that the overall hydrogen bond networks in both the small and large lobes of PKA-C become stronger. However, we observed several important exceptions, with residues displaying higher φ values upon ligand binding. Notably, the changes in φ values are not localized near the ligand binding pockets; rather, they are radiated throughout the entire enzyme. We conclude that, upon ligand and pseudosubstrate binding, the hydrogen bond networks undergo extensive reorganization, revealing that the open-to-closed transitions require global rearrangements of the internal forces that stabilize the enzyme's fold.
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Affiliation(s)
- Geoffrey C Li
- †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Atul K Srivastava
- ‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jonggul Kim
- †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Susan S Taylor
- §Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, United States
| | - Gianluigi Veglia
- †Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States.,‡Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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226
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Miño-Galaz GA. Allosteric communication pathways and thermal rectification in PDZ-2 protein: a computational study. J Phys Chem B 2015; 119:6179-89. [PMID: 25933631 DOI: 10.1021/acs.jpcb.5b02228] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Allosteric communication in proteins is a fundamental and yet unresolved problem of structural biochemistry. Previous findings, from computational biology ( Ota, N.; Agard, D. A. J. Mol. Biol. 2005 , 351 , 345 - 354 ), have proposed that heat diffuses in a protein through cognate protein allosteric pathways. This work studied heat diffusion in the well-known PDZ-2 protein, and confirmed that this protein has two cognate allosteric pathways and that heat flows preferentially through these. Also, a new property was also observed for protein structures: heat diffuses asymmetrically through the structures. The underling structure of this asymmetrical heat flow was a normal length hydrogen bond (∼2.85 Å) that acted as a thermal rectifier. In contrast, thermal rectification was compromised in short hydrogen bonds (∼2.60 Å), giving rise to symmetrical thermal diffusion. Asymmetrical heat diffusion was due, on a higher scale, to the local, structural organization of residues that, in turn, was also mediated by hydrogen bonds. This asymmetrical/symmetrical energy flow may be relevant for allosteric signal communication directionality in proteins and for the control of heat flow in materials science.
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Affiliation(s)
- Germán A Miño-Galaz
- †Group of Nanomaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile.,‡Centro Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile.,§Universidad Andres Bello Center for Bioinformatics and Integrative Biology (CBIB), Facultad en Ciencias Biologicas, Santiago, Chile
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227
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Brüning A, Jückstock J. Misfolded proteins: from little villains to little helpers in the fight against cancer. Front Oncol 2015; 5:47. [PMID: 25759792 PMCID: PMC4338749 DOI: 10.3389/fonc.2015.00047] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/11/2015] [Indexed: 12/15/2022] Open
Abstract
The application of cytostatic drugs targeting the high proliferation rates of cancer cells is currently the most commonly used treatment option in cancer chemotherapy. However, severe side effects and resistance mechanisms may occur as a result of such treatment, possibly limiting the therapeutic efficacy of these agents. In recent years, several therapeutic strategies have been developed that aim at targeting not the genomic integrity and replication machinery of cancer cells but instead their protein homeostasis. During malignant transformation, the cancer cell proteome develops vast aberrations in the expression of mutated proteins, oncoproteins, drug- and apoptosis-resistance proteins, etc. A complex network of protein quality-control mechanisms, including chaperoning by heat shock proteins (HSPs), not only is essential for maintaining the extravagant proteomic lifestyle of cancer cells but also represents an ideal cancer-specific target to be tackled. Furthermore, the high rate of protein synthesis and turnover in certain types of cancer cells can be specifically directed by interfering with the proteasomal and autophagosomal protein recycling and degradation machinery, as evidenced by the clinical application of proteasome inhibitors. Since proteins with loss of their native conformation are prone to unspecific aggregations and have proved to be detrimental to normal cellular function, specific induction of misfolded proteins by HSP inhibitors, proteasome inhibitors, hyperthermia, or inducers of endoplasmic reticulum stress represents a new method of cancer cell killing exploitable for therapeutic purposes. This review describes drugs - approved, repurposed, or under investigation - that can be used to accumulate misfolded proteins in cancer cells, and particularly focuses on the molecular aspects that lead to the cytotoxicity of misfolded proteins in cancer cells.
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Affiliation(s)
- Ansgar Brüning
- Molecular Biology Laboratory, Ludwig-Maximilians-University , Munich , Germany
| | - Julia Jückstock
- Molecular Biology Laboratory, Ludwig-Maximilians-University , Munich , Germany
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228
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Guidez EB, Gordon MS. Dispersion Correction Derived from First Principles for Density Functional Theory and Hartree–Fock Theory. J Phys Chem A 2015; 119:2161-8. [DOI: 10.1021/acs.jpca.5b00379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilie B. Guidez
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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229
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Kister A. Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures. Biomolecules 2015; 5:41-59. [PMID: 25625198 PMCID: PMC4384110 DOI: 10.3390/biom5010041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/31/2014] [Indexed: 11/16/2022] Open
Abstract
We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of "favorable" residues, that are mainly responsible for a given fold formation, and "unfavorable" residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a "rule of amino acid distribution" for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design.
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Affiliation(s)
- Alexander Kister
- Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA.
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230
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Stadler AM, Koza MM, Fitter J. Determination of Conformational Entropy of Fully and Partially Folded Conformations of Holo- and Apomyoglobin. J Phys Chem B 2014; 119:72-82. [DOI: 10.1021/jp509732q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andreas M. Stadler
- Jülich
Centre for Neutron Science JCNS and Institute for Complex Systems
ICS, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | | | - Jörg Fitter
- Institute
of Complex Systems (ICS-5): Molecular Biophysics, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- I.
Physikalisches Institut (IA), AG Biophysik, RWTH Aachen, Sommerfeldstrasse
14, 52074 Aachen, Germany
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231
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Okano H, Ozaki M, Kanaya E, Kim JJ, Angkawidjaja C, Koga Y, Kanaya S. Structure and stability of metagenome-derived glycoside hydrolase family 12 cellulase (LC-CelA) a homolog of Cel12A from Rhodothermus marinus. FEBS Open Bio 2014; 4:936-46. [PMID: 25426413 PMCID: PMC4239480 DOI: 10.1016/j.fob.2014.10.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 10/27/2014] [Accepted: 10/27/2014] [Indexed: 11/24/2022] Open
Abstract
Ten novel cellulases, LC-CelA–J, were isolated from leaf–branch compost by a metagenomic approach. LC-CelA was characterized. The structure, activity, and stability of LC-CelA were similar to those of Cel12A from Rhodothermus marinus. Glu34-mediated hydrogen bonds and two disulfide bonds contribute to the stabilization of LC-CelA.
Ten genes encoding novel cellulases with putative signal peptides at the N-terminus, termed pre-LC-CelA–J, were isolated from a fosmid library of a leaf–branch compost metagenome by functional screening using agar plates containing carboxymethyl cellulose and trypan blue. All the cellulases except pre-LC-CelG have a 14–29 residue long flexible linker (FL) between the signal peptide and the catalytic domain. LC-CelA without a signal peptide (residues 20–261), which shows 76% amino acid sequence identity to Cel12A from Rhodothermus marinus (RmCel12A), was overproduced in Escherichiacoli, purified and characterized. LC-CelA exhibited its highest activity across a broad pH range (pH 5–9) and at 90 °C, indicating that LC-CelA is a highly thermostable cellulase, like RmCel12A. The crystal structure of LC-CelA was determined at 1.85 Å resolution and is nearly identical to that of RmCel12A determined in a form without the FL. Both proteins contain two disulfide bonds. LC-CelA has a 16-residue FL (residues 20–35), most of which is not visible in the electron density map, probably due to structural disorder. However, Glu34 and Pro35 form hydrogen bonds with the central region of the protein. ΔFL-LC-CelA (residues 36–261) and E34A-LC-CelA with a single Glu34 → Ala mutation were therefore constructed and characterized. ΔFL-LC-CelA and E34A-LC-CelA had lower melting temperatures (Tm) than LC-CelA by 14.7 and 12.0 °C respectively. The Tm of LC-CelA was also decreased by 28.0 °C in the presence of dithiothreitol. These results suggest that Glu34-mediated hydrogen bonds and the two disulfide bonds contribute to the stabilization of LC-CelA.
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Affiliation(s)
- Hiroyuki Okano
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masashi Ozaki
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiko Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Joong-Jae Kim
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Clement Angkawidjaja
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan ; International College, Osaka University, 1-30 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Koga
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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232
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Miño G, Barriga R, Gutierrez G. Hydrogen Bonds and Heat Diffusion in α-Helices: A Computational Study. J Phys Chem B 2014; 118:10025-34. [DOI: 10.1021/jp503420e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- German Miño
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
- Centro
Interdisciplinario de Neurociencias de Valparaíso (CINV), Universidad de Valparaíso, Valparaíso, Chile
- Facultad
de Ciencias Biologicas, Centro de Bioinformatica y Biologia Integrativa, Universidad Andres Bello, Av.Republica 239, Santiago, Chile
| | - Raul Barriga
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Gonzalo Gutierrez
- Group
of NanoMaterials, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
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