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Herrero‐Alfonso P, Pejenaute A, Millet O, Ortega‐Quintanilla G. Electrostatics introduce a trade-off between mesophilic stability and adaptation in halophilic proteins. Protein Sci 2024; 33:e5003. [PMID: 38747380 PMCID: PMC11094771 DOI: 10.1002/pro.5003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024]
Abstract
Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease protein stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that halophilic amino acids decrease the stability of halophilic proteins under mesophilic conditions, but in exchange improve salt-induced stabilization and solubility. We also find that, in contrast to traditional assumptions, contributions arising from hydrophobic effect and preferential ion exclusion are more relevant for haloadaptation than electrostatics. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize proteins for hypersaline environments.
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Affiliation(s)
- Pablo Herrero‐Alfonso
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
| | - Alba Pejenaute
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
- Tekniker, Basque Research and Technology Alliance (BRTA)EibarSpain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
| | - Gabriel Ortega‐Quintanilla
- Precision Medicine and Metabolism Laboratory, Center for Cooperative Research in Biosciences CIC bioGUNEBizkaia Science and Technology ParkDerioSpain
- Ikerbasque, Basque Foundation for ScienceBilbaoSpain
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2
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Kittler S, Ebner J, Besleaga M, Larsbrink J, Darnhofer B, Birner-Gruenberger R, Schobesberger S, Akhgar CK, Schwaighofer A, Lendl B, Spadiut O. Recombinant Protein L: Production, Purification and Characterization of a Universal Binding Ligand. J Biotechnol 2022; 359:108-115. [DOI: 10.1016/j.jbiotec.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 11/26/2022]
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3
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Qiu Y, Shan W, Zhang H. Force Field Benchmark of Amino Acids. 3. Hydration with Scaled Lennard-Jones Interactions. J Chem Inf Model 2021; 61:3571-3582. [PMID: 34185520 DOI: 10.1021/acs.jcim.1c00339] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Classical protein force fields were reported with too weak protein-water interactions relative to protein-protein interactions, leading to more compact structures and artificial protein aggregation. Here we investigated the impacts of scaled Lennard-Jones (LJ) interactions on the hydration of amino acids and the simulation of folded and intrinsically disordered proteins (IDPs). The obtained optimal scaling parameters reproduce accurately hydration free energies of neutral amino acid side chain analogues and do not affect the compactness and structural stability of folded proteins significantly. The scaling leads to less compact IDPs and varies from case to case. Strengthening the interactions between protein and water oxygen or hydrogen atoms by increasing the interacting LJ well depth (ε) appears more effective than weakening protein-protein interactions by reducing the interacting dispersion coefficients (C6). We demonstrate that weakening water-water interactions is a solution as well to obtaining more favorable protein-water interactions in an indirect way, although modern force fields like Amber ff19SB and a99SB-disp tend to use water models with strong water-water interactions. This is likely a compromise between strong protein-protein interactions and strong water-water interactions. Independent optimization of protein force fields and water models is therefore needed to make both interactions more close to reality, leading to good accuracy without bias or scaling.
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Affiliation(s)
- Yejie Qiu
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Wenjie Shan
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
| | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, 100083 Beijing, China
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4
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Abstract
In the past 30 years, highly specific drugs, known as antibodies, have conquered the biopharmaceutical market. In addition to monoclonal antibodies (mAbs), antibody fragments are successfully applied. However, recombinant production faces challenges. Process analytical tools for monitoring and controlling production processes are scarce and time-intensive. In the downstream process (DSP), affinity ligands are established as the primary and most important step, while the application of other methods is challenging. The use of these affinity ligands as monitoring tools would enable a platform technology to monitor process steps in the USP and DSP. In this review, we highlight the current applications of affinity ligands (proteins A, G, and L) and discuss further applications as process analytical tools.
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5
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Li BW, Zhang Y, Wang YC, Xue Y, Nie XY. Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes. ACS Synth Biol 2020; 9:2267-2273. [PMID: 32810400 DOI: 10.1021/acssynbio.0c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A streamlined approach toward the rapid fabrication of streptavidin-biotin-based protein microarrays was investigated. First, using our engineered versatile plasmid (pBADcM-tBirA) and an optimal coexpression strategy for biotin ligase and biotin acceptor peptide (BAP) chimeric recombinant protein, an autogeneration system for biotinylated probes was developed. This system permitted an advantageous biotinylation of BAP chimeric recombinant proteins, providing a strategy for the high-throughput synthesis of biotinylated probes. Then, to bypass the conventional rate-limiting steps, we employed an on-chip purification process to immobilize the biotinylated probes with high-throughput recombinant lysates. The integration of the autogeneration of probes and on-chip purification not only contributed to the effective and reliable fabrication of the protein microarray, but also enabled simplification of the process and an automated throughput format. This labor- and cost-effective approach may facilitate the use of protein microarrays for diagnosis, pharmacology, proteomics, and other laboratory initiatives.
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Affiliation(s)
- Bo-Wen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yi Zhang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yin-Chun Wang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yang Xue
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Xin-Yi Nie
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
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6
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Ortega G, Kurnik M, Gautam BK, Plaxco KW. Attachment of Proteins to a Hydroxyl-Terminated Surface Eliminates the Stabilizing Effects of Polyols. J Am Chem Soc 2020; 142:15349-15354. [PMID: 32786756 DOI: 10.1021/jacs.0c05719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The physics of proteins interacting with surfaces can differ significantly from those seen when the same proteins are free in bulk solution. As an example, we describe here the extent to which site-specific attachment to a chemically well-defined macroscopic surface alters the ability of several stabilizing and destabilizing cosolutes to modulate protein folding thermodynamics. We determined this via guanidinium denaturations performed in the presence of varying concentrations of cosolutes when proteins were either site-specifically attached to self-assembled monolayers on gold or free in bulk solution. Doing this we found that the extent to which guanidinium (a destabilizing Hofmeister cation), sulfate (a stabilizing Hofmeister anion), and urea (a neutral denaturant) alter the folding free energy remains indistinguishable whether proteins are surface-attached or free in bulk solution. In sharp contrast, however, neutral osmolytes sucrose and glycerol, which significantly stabilize proteins in bulk solution, do not measurably affect their stability when they are attached to a hydroxyl-terminated surface. In contrast, we recovered bulk solution-like stabilization when the attachment surface was instead carboxyl-terminated. It thus appears that chemistry-specific surface interactions can dramatically alter the way in which biomolecules interact with other components of the system.
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Affiliation(s)
- Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Martin Kurnik
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Bishal K Gautam
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California-Santa Barbara, Santa Barbara, California 93106, United States.,Center for Bioengineering, University of California-Santa Barbara, Santa Barbara, California 93106, United States
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7
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Arsiccio A, McCarty J, Pisano R, Shea JE. Heightened Cold-Denaturation of Proteins at the Ice–Water Interface. J Am Chem Soc 2020; 142:5722-5730. [DOI: 10.1021/jacs.9b13454] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Andrea Arsiccio
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - James McCarty
- Department of Chemistry, Western Washington University, Bellingham, Washington 98225, United States
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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8
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Dahal N, Nowitzke J, Eis A, Popa I. Binding-Induced Stabilization Measured on the Same Molecular Protein Substrate Using Single-Molecule Magnetic Tweezers and Heterocovalent Attachments. J Phys Chem B 2020; 124:3283-3290. [DOI: 10.1021/acs.jpcb.0c00167] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Narayan Dahal
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Joel Nowitzke
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Annie Eis
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
| | - Ionel Popa
- Department of Physics, University of Wisconsin-Milwaukee, 3135 North Maryland Avenue, Milwaukee, Wisconsin 53211, United States
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9
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Parui S, Jana B. Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. J Phys Chem B 2019; 123:8889-8900. [DOI: 10.1021/acs.jpcb.9b06859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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10
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11
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Ortega G, Kurnik M, Dauphin‐Ducharme P, Li H, Arroyo‐Currás N, Caceres A, Plaxco KW. Surface Attachment Enhances the Thermodynamic Stability of Protein L. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gabriel Ortega
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Protein Stability and Inherited Disease LaboratoryCIC bioGUNE Bizkaia Science and Technology Park, building 800 48160 Derio Spain
| | - Martin Kurnik
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
| | - Philippe Dauphin‐Ducharme
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
| | - Hui Li
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Engineering Research Center of Nano-Geomaterials of Ministry of EducationFaculty of Materials Science and ChemistryUniversity of Geosciences Wuhan 430074 China
| | - Netzahualcóyotl Arroyo‐Currás
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Department of Pharmacology and Molecular SciencesJohns Hopkins School of Medicine Baltimore MD 93106 USA
| | - Amanda Caceres
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
| | - Kevin W. Plaxco
- Department of Chemistry and BiochemistryUniversity of California Santa Barbara Santa Barbara CA 93106 USA
- Center for BioengineeringUniversity of California Santa Barbara Santa Barbara CA 93106 USA
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12
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Ortega G, Kurnik M, Dauphin-Ducharme P, Li H, Arroyo-Currás N, Caceres A, Plaxco KW. Surface Attachment Enhances the Thermodynamic Stability of Protein L. Angew Chem Int Ed Engl 2019; 58:1714-1718. [PMID: 30549169 DOI: 10.1002/anie.201812231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Despite the importance of protein-surface interactions in both biology and biotechnology, our understanding of their origins is limited due to a paucity of experimental studies of the thermodynamics behind such interactions. In response, we have characterized the extent to which interaction with a chemically well-defined macroscopic surface alters the stability of protein L. To do so, we site-specifically attached a redox-reporter-modified protein variant to a hydroxy-terminated monolayer on a gold surface and then used electrochemistry to monitor its guanidine denaturation and determine its folding free energy. Comparison with the free energy seen in solution indicates that interaction with this surface stabilizes the protein by 6 kJ mol-1 , a value that is in good agreement with theoretical estimates of the entropic consequences of surface-induced excluded volume effects, thus suggesting that chemically specific interactions with this surface (e.g., electrostatic interactions) are limited in magnitude.
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Affiliation(s)
- Gabriel Ortega
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Protein Stability and Inherited Disease Laboratory, CIC bioGUNE, Bizkaia Science and Technology Park, building 800, 48160, Derio, Spain
| | - Martin Kurnik
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Philippe Dauphin-Ducharme
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Hui Li
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, University of Geosciences, Wuhan, 430074, China
| | - Netzahualcóyotl Arroyo-Currás
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 93106, USA
| | - Amanda Caceres
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Kevin W Plaxco
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Center for Bioengineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
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13
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Paloni M, Cavallotti C. Molecular Modeling of the Interaction of Protein L with Antibodies. ACS OMEGA 2017; 2:6464-6472. [PMID: 31457247 PMCID: PMC6645367 DOI: 10.1021/acsomega.7b01123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/27/2017] [Indexed: 06/10/2023]
Abstract
Protein L (PpL) is a bacterial protein which is used in the affinity chromatography stage of the production of monoclonal antibodies because of its ability to form high affinity complexes with the light chains of immunoglobulins. In the present work, the binding interfaces between one domain of PpL and antigen-binding fragments (Fab) have been investigated adopting molecular dynamics with the aim of determining the binding contribution of the residues located at the Fab-PpL interface. Because it is known that PpL binds antibodies through two distinct binding sites with different affinities, simulations were performed for both sites to determine interaction free energies to assess the relative binding contribution of the two sites. Mutational studies were then performed only on the dominant binding site. The binding free energy was evaluated with the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and umbrella sampling/weighted histogram analysis methods. Key residues for the formation of the dominant binding site complex were identified by means of alanine scanning performed both for the Fab and PpL domains. Residues of the light chain of the antibody that contribute most to binding were found to be located between SER7 and VAL13. Four residues from PpL are important for the stability of the complex: PHE839, LYS840, GLU849, and TYR853. Three residues of PpL that do not contribute to the interaction were mutated to histidine (HIS), which changes its protonation state as a function of pH, to find whether this could allow us to control the binding interaction energy. This can be useful in the elution stage of the affinity chromatography purification of antibodies if PpL is used as a ligand. These residues are GLN835, THR836, and ALA837. Molecular dynamics simulations with both protonated and unprotonated HIS were performed to mimic how changing pH may reflect on protein-ligand interaction energies. The MMPBSA approach was used to evaluate the variation of the affinity of the mutated systems with reference to the wild type. Our results show that these mutations could help in disrupting the complex under acidic conditions without impairing the affinity of PpL for the light chains at higher pHs.
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14
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Affiliation(s)
- Nika Kruljec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
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15
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He W, Ye X, Yao X, Wu X, Lin Q, Huang G, Hua Y, Hui Y. Characterization of the binding of shikonin to human immunoglobulin using scanning electron microscope, molecular modeling and multi-spectroscopic methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:514-522. [PMID: 26073597 DOI: 10.1016/j.saa.2015.04.085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/01/2015] [Accepted: 04/21/2015] [Indexed: 06/04/2023]
Abstract
Shikonin, one of the active components isolated from the root of Arnebia euchroma (Royle) Johnst, have anti-tumor, anti-bacterial and anti-inflammatory activities and has been used clinically in phlebitis and vascular purpura. In the present work, the interaction of human immunoglobulin (HIg) with shikonin has been investigated by using scanning electron microscope (SEM), Fourier transform infrared (FT-IR) spectroscopy, fluorescence polarization, synchronous and 3D fluorescence spectroscopy in combination with molecular modeling techniques under physiological conditions with drug concentrations of 3.33-36.67 μM. The results of SEM exhibited visually the special effect on aggregation behavior of the complex formed between HIg and shikonin. The fluorescence polarization values indicated that shikonin molecules were found in a motionally unrestricted environment introduced by HIg. Molecular docking showed the shikonin moiety bound to the hydrophobic cavity of HIg, and there are four hydrogen-bonding interactions between shikonin and the residues of protein. The synchronous and 3D fluorescence spectra confirmed that shikonin could quench the intrinsic fluorescence of HIg and has an effect on the microenvironment around HIg in aqueous solution. The changes in the secondary structure of HIg were estimated by qualitative and quantitative FT-IR spectroscopic analysis. The binding constants and thermodynamic parameters for shikonin-HIg systems were obtained under different temperatures (300 K, 310 K and 320 K). The above results revealed the binding mechanism of shikonin and HIg at the ultrastructure and molecular level.
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Affiliation(s)
- Wenying He
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China.
| | - Xinyu Ye
- College of Chemical and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Xiaojun Yao
- College of Chemical and Chemical Engineering, Lanzhou University, Lanzhou 730000, PR China
| | - Xiuli Wu
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China
| | - Qiang Lin
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China
| | - Guolei Huang
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China
| | - Yingjie Hua
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China
| | - Yang Hui
- College of Chemical and Chemical Engineering, Hainan Normal University, Haikou 571158, PR China
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16
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Piana S, Donchev AG, Robustelli P, Shaw DE. Water dispersion interactions strongly influence simulated structural properties of disordered protein states. J Phys Chem B 2015; 119:5113-23. [PMID: 25764013 DOI: 10.1021/jp508971m] [Citation(s) in RCA: 567] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many proteins can be partially or completely disordered under physiological conditions. Structural characterization of these disordered states using experimental methods can be challenging, since they are composed of a structurally heterogeneous ensemble of conformations rather than a single dominant conformation. Molecular dynamics (MD) simulations should in principle provide an ideal tool for elucidating the composition and behavior of disordered states at an atomic level of detail. Unfortunately, MD simulations using current physics-based models tend to produce disordered-state ensembles that are structurally too compact relative to experiments. We find that the water models typically used in MD simulations significantly underestimate London dispersion interactions, and speculate that this may be a possible reason for these erroneous results. To test this hypothesis, we create a new water model, TIP4P-D, that approximately corrects for these deficiencies in modeling water dispersion interactions while maintaining compatibility with existing physics-based models. We show that simulations of solvated proteins using this new water model typically result in disordered states that are substantially more expanded and in better agreement with experiment. These results represent a significant step toward extending the range of applicability of MD simulations to include the study of (partially or fully) disordered protein states.
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Affiliation(s)
- Stefano Piana
- †D. E. Shaw Research, New York, New York 10036, United States
| | | | - Paul Robustelli
- †D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- †D. E. Shaw Research, New York, New York 10036, United States.,‡Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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17
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Yang YH, Jiang YL, Zhang J, Wang L, Bai XH, Zhang SJ, Ren YM, Li N, Zhang YH, Zhang Z, Gong Q, Mei Y, Xue T, Zhang JR, Chen Y, Zhou CZ. Structural insights into SraP-mediated Staphylococcus aureus adhesion to host cells. PLoS Pathog 2014; 10:e1004169. [PMID: 24901708 PMCID: PMC4047093 DOI: 10.1371/journal.ppat.1004169] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/22/2014] [Indexed: 11/18/2022] Open
Abstract
Staphylococcus aureus, a Gram-positive bacterium causes a number of devastating human diseases, such as infective endocarditis, osteomyelitis, septic arthritis and sepsis. S. aureus SraP, a surface-exposed serine-rich repeat glycoprotein (SRRP), is required for the pathogenesis of human infective endocarditis via its ligand-binding region (BR) adhering to human platelets. It remains unclear how SraP interacts with human host. Here we report the 2.05 Å crystal structure of the BR of SraP, revealing an extended rod-like architecture of four discrete modules. The N-terminal legume lectin-like module specifically binds to N-acetylneuraminic acid. The second module adopts a β-grasp fold similar to Ig-binding proteins, whereas the last two tandem repetitive modules resemble eukaryotic cadherins but differ in calcium coordination pattern. Under the conditions tested, small-angle X-ray scattering and molecular dynamic simulation indicated that the three C-terminal modules function as a relatively rigid stem to extend the N-terminal lectin module outwards. Structure-guided mutagenesis analyses, in addition to a recently identified trisaccharide ligand of SraP, enabled us to elucidate that SraP binding to sialylated receptors promotes S. aureus adhesion to and invasion into host epithelial cells. Our findings have thus provided novel structural and functional insights into the SraP-mediated host-pathogen interaction of S. aureus.
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Affiliation(s)
- Yi-Hu Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Juan Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Lei Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Xiao-Hui Bai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Shi-Jie Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yan-Min Ren
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Na Li
- Shanghai Institute of Biochemistry and Cell Biology, Shanghai, China
| | - Yong-Hui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Yide Mei
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Ting Xue
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, People's Republic of China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
- * E-mail: (YC); (CZZ)
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, People's Republic of China
- * E-mail: (YC); (CZZ)
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18
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Roy S, Bagchi B. Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting. J Phys Chem B 2014; 118:5691-7. [DOI: 10.1021/jp5037348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Susmita Roy
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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19
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20
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Murphy EC, Frick IM. Gram-positive anaerobic cocci--commensals and opportunistic pathogens. FEMS Microbiol Rev 2012; 37:520-53. [PMID: 23030831 DOI: 10.1111/1574-6976.12005] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 07/30/2012] [Accepted: 09/24/2012] [Indexed: 12/30/2022] Open
Abstract
Among the Gram-positive anaerobic bacteria associated with clinical infections, the Gram-positive anaerobic cocci (GPAC) are the most prominent and account for approximately 25-30% of all isolated anaerobic bacteria from clinical specimens. Still, routine culture and identification of these slowly growing anaerobes to the species level has been limited in the diagnostic laboratory, mainly due to the requirement of prolonged incubation times and time-consuming phenotypic identification. In addition, GPAC are mostly isolated from polymicrobial infections with known pathogens and therefore their relevance has often been overlooked. However, through improvements in diagnostic and in particular molecular techniques, the isolation and identification of individual genera and species of GPAC associated with specific infections have been enhanced. Furthermore, the taxonomy of GPAC has undergone considerable changes over the years, mainly due to the development of molecular identification methods. Existing species have been renamed and novel species have been added, resulting in changes of the nomenclature. As the abundance and significance of GPAC in clinical infections grow, knowledge of virulence factors and antibiotic resistance patterns of different species becomes more important. The present review describes recent advances of GPAC and what is known of the biology and pathogenic effects of Anaerococcus, Finegoldia, Parvimonas, Peptoniphilus and Peptostreptococcus, the most important GPAC genera isolated from human infections.
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Affiliation(s)
- Elizabeth Carmel Murphy
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden.
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21
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Xia Z, Das P, Shakhnovich EI, Zhou R. Collapse of unfolded proteins in a mixture of denaturants. J Am Chem Soc 2012; 134:18266-74. [PMID: 23057830 DOI: 10.1021/ja3031505] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Both urea and guanidinium chloride (GdmCl) are frequently used as protein denaturants. Given that proteins generally adopt extended or unfolded conformations in either aqueous urea or GdmCl, one might expect that the unfolded protein chains will remain or become further extended due to the addition of another denaturant. However, a collapse of denatured proteins is revealed using atomistic molecular dynamics simulations when a mixture of denaturants is used. Both hen egg-white lysozyme and protein L are found to undergo collapse in the denaturant mixture. The collapse of the protein conformational ensembles is accompanied by a decreased solubility and increased non-native self-interactions of hydrophobic residues in the urea/GdmCl mixture. The increase of non-native interactions rather than the native contacts indicates that the proteins experience a simple collapse transition from the fully denatured states. During the protein collapse, the relatively stronger denaturant GdmCl displays a higher tendency to be absorbed onto the protein surface due to their stronger electrostatic interactions with proteins. At the same time, urea molecules also accumulate near the protein surface, resulting in an enhanced "local crowding" for the protein near its first solvation shell. This rearrangement of denaturants near the protein surface and crowded local environment induce the protein collapse, mainly by burying their hydrophobic residues. These findings from molecular simulations are then further explained by a simple analytical model based on statistical mechanics.
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Affiliation(s)
- Zhen Xia
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA
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22
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Wales DJ, Carr JM. Quasi-Continuous Interpolation Scheme for Pathways between Distant Configurations. J Chem Theory Comput 2012; 8:5020-34. [PMID: 26593194 DOI: 10.1021/ct3004832] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A quasi-continuous interpolation (QCI) scheme is introduced for characterizing physically realistic initial pathways from which to initiate transition state searches and construct kinetic transition networks. Applications are presented for peptides, proteins, and a morphological transformation in an atomic cluster. The first step in each case involves end point alignment, and we describe the use of a shortest augmenting path algorithm for optimizing permutational isomers. The QCI procedure then employs an interpolating potential, which preserves the covalent bonding framework for the biomolecules and includes repulsive terms between unconstrained atoms. This potential is used to identify an interpolating path by minimizing contributions from a connected set of images, including terms corresponding to minima in the interatomic distances between them. This procedure detects unphysical geometries in the line segments between images. The most difficult cases, where linear interpolation would involve chain crossings, are treated by growing the structure an atom at a time using the interpolating potential. To test the QCI procedure, we carry through a series of benchmark calculations where the initial interpolation is coupled to explicit transition state searches to produce complete pathways between specified local minima.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Joanne M Carr
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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23
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Wales DJ, Head-Gordon T. Evolution of the potential energy landscape with static pulling force for two model proteins. J Phys Chem B 2012; 116:8394-411. [PMID: 22432920 DOI: 10.1021/jp211806z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The energy landscape is analyzed for off-lattice bead models of protein L and protein G as a function of a static pulling force. Two different pairs of attachment points (pulling directions) are compared in each case, namely, residues 1/56 and 10/32. For the terminal residue pulling direction 1/56, the distinct global minimum structures are all extended, aside from the compact geometry that correlates with zero force. The helical turns finally disappear at the highest pulling forces considered. For the 10/32 pulling direction, the changes are more complicated, with a variety of competing arrangements for beads outside the region where the force is directly applied. These alternatives produce frustrated energy landscapes, with low-lying minima separated by high barriers. The calculated folding pathways in the absence of force are in good agreement with previous work. The N-terminal hairpin folds first for protein L and the C-terminal hairpin for protein G, which exhibits an intermediate. However, for a relatively low static force, where the global minimum retains its structure, the folding mechanisms change, sometimes dramatically, depending on the protein and the attachment points. The scaling relations predicted by catastrophe theory are found to hold in the limit of short path lengths.
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Affiliation(s)
- David J Wales
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK.
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24
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Qvist J, Ortega G, Tadeo X, Millet O, Halle B. Hydration Dynamics of a Halophilic Protein in Folded and Unfolded States. J Phys Chem B 2012; 116:3436-44. [DOI: 10.1021/jp3000569] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan Qvist
- Department of Biophysical Chemistry,
Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
| | | | - Xavier Tadeo
- Structural Biology Unit, CIC bioGUNE,
Derio, Spain
| | - Oscar Millet
- Structural Biology Unit, CIC bioGUNE,
Derio, Spain
| | - Bertil Halle
- Department of Biophysical Chemistry,
Center for Molecular Protein Science, Lund University, SE-22100 Lund, Sweden
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25
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Abstract
Among thousands of homo-oligomeric protein structures, there is a small but growing subset of ‘domain-swapped’ proteins. The term ‘domain swapping,’ originally coined by D. Eisenberg, describes a scenario in which two or more polypeptide chains exchange identical units for oligomerization. This type of assembly could play a role in disease-related aggregation and amyloid formation or as a specific mechanism for regulating function. This chapter introduces terms and features concerning domain swapping, summarizes ideas about its putative mechanisms, reports on domain-swapped structures collected from the literature, and describes a few notable examples in detail.
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26
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Abstract
Proteins capable of non-immune binding of immunoglobulins G (IgG) of various mammalian species, i.e. without the involvement of the antigen-binding sites of the immunoglobulins, are widespread in bacteria. These proteins are located on the surface of bacterial cells and help them to evade the host's immune response due to protection against the action of complement and to decrease in phagocytosis. This review summarizes data on the structure of immunoglobulin-binding proteins (IBP) and their complexes with IgG. Common and distinctive structural features of IBPs of gram-positive bacteria (staphylococci, streptococci, peptostreptococci) are discussed. Conditions for IBP expression by bacteria and their functional heterogeneity are considered. Data on IBPs of gram-negative bacteria are presented.
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Affiliation(s)
- E V Sidorin
- Pacific Institute of Bioorganic Chemistry, Far-Eastern Division of the Russian Academy of Sciences, Vladivostok, Russia.
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27
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Crampton N, Alzahrani K, Beddard GS, Connell SD, Brockwell DJ. Mechanically unfolding protein L using a laser-feedback-controlled cantilever. Biophys J 2011; 100:1800-9. [PMID: 21463594 DOI: 10.1016/j.bpj.2011.02.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 01/20/2011] [Accepted: 02/14/2011] [Indexed: 10/18/2022] Open
Abstract
Force spectroscopy using the atomic force microscope (AFM) can yield important information on the strength and lifetimes of the folded states of single proteins and their complexes when they are loaded with force. For example, by mechanically unfolding concatenated proteins at different velocities, a dynamic force spectrum can be built up that allows reconstruction of the energy landscape that the protein traverses during unfolding. To characterize fully the unfolding landscape, however, it is necessary both to explore the entire force spectrum and to characterize each species populated during unfolding. In the conventional AFM apparatus, force is applied to the protein construct through a compliant cantilever. This limits the dynamic range of the force spectrum that can be probed, and the cantilever recoil after unfolding may mask the presence of metastable intermediates. Here, we describe to our knowledge a new technique-constant-deflection AFM-in which the compliance of the AFM cantilever is removed. Using this technique, we show that protein L exhibits a more complex unfolding energy landscape than previously detected using the conventional technique. This technique is also able to detect the presence of a refolding intermediate whose formation is otherwise prevented by cantilever recoil.
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Affiliation(s)
- Neal Crampton
- School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom.
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28
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Schlesinger AP, Wang Y, Tadeo X, Millet O, Pielak GJ. Macromolecular crowding fails to fold a globular protein in cells. J Am Chem Soc 2011; 133:8082-5. [PMID: 21534566 DOI: 10.1021/ja201206t] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins perform their functions in cells where macromolecular solutes reach concentrations of >300 g/L and occupy >30% of the volume. The volume excluded by these macromolecules stabilizes globular proteins because the native state occupies less space than the denatured state. Theory predicts that crowding can increase the ratio of folded to unfolded protein by a factor of 100, amounting to 3 kcal/mol of stabilization at room temperature. We tested the idea that volume exclusion dominates the crowding effect in cells using a variant of protein L, a 7 kDa globular protein with seven lysine residues replaced by glutamic acids; 84% of the variant molecules populate the denatured state in dilute buffer at room temperature, compared with 0.1% for the wild-type protein. We then used in-cell NMR spectroscopy to show that the cytoplasm of Escherichia coli does not overcome even this modest (∼1 kcal/mol) free-energy deficit. The data are consistent with the idea that nonspecific interactions between cytoplasmic components can overcome the excluded-volume effect. Evidence for these interactions is provided by the observations that adding simple salts folds the variant in dilute solution but increasing the salt concentration inside E. coli does not fold the protein. Our data are consistent with the results of other studies of protein stability in cells and suggest that stabilizing excluded-volume effects, which must be present under crowded conditions, can be ameliorated by nonspecific interactions between cytoplasmic components.
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Affiliation(s)
- Alexander P Schlesinger
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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29
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Lammert H, Schug A, Onuchic JN. Robustness and generalization of structure-based models for protein folding and function. Proteins 2010; 77:881-91. [PMID: 19626713 DOI: 10.1002/prot.22511] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Functional dynamics of native proteins share the energy landscape that guides folding into the native state. Folding simulations of structure-based protein models, using an minimally frustrated energy landscape dominated by native interactions, can describe the geometrical aspects of the folding mechanism. Technical limitations imposed by the fixed shape of conventional contact potentials are a key obstacle toward advanced applications of structure-based models like allostery or ligand binding, which require multiple stable conformations. Generalizations of existing models, commonly using Lennard-Jones-like potentials, lead to inevitable clashes between their repulsive branches. To resolve these challenges, a new contact potential is developed that combines an attractive part based on Gaussians with a separate repulsive term allowing flexibility for adjustments of the potential shape. With this new model multiple minima for studies of functional transitions can be introduced easily and consistently. A sensitivity analysis for five small proteins confirms the robust behavior of structure-based models with our adaptable potential and explores their capacity for quantitative adjustment of the folding thermodynamics. We demonstrate its ability to incorporate alternative contact distances in simulations of structural transitions for the well-studied ROP dimer. Individual contact pairs can switch between distinct states to match the competing syn and anti structures. The flexibility of the new potential facilitates advanced uses of structure-based models. Depending on the application, features can be chosen from physical considerations or to match experiments. Generalized models can be built from multiple structures to study structural transitions or effects of disorder.
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Affiliation(s)
- Heiko Lammert
- Center for Theoretical Biological Physics and Department of Physics, University of California, San Diego, La Jolla, California 92093, USA
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30
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Tadeo X, López-Méndez B, Trigueros T, Laín A, Castaño D, Millet O. Structural basis for the aminoacid composition of proteins from halophilic archea. PLoS Biol 2009; 7:e1000257. [PMID: 20016684 PMCID: PMC2780699 DOI: 10.1371/journal.pbio.1000257] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 11/05/2009] [Indexed: 11/24/2022] Open
Abstract
In order to survive in highly saline environments, proteins from halophilic archea have evolved with biased amino acid compositions that have the capacity to reduce contacts with the solvent. Proteins from halophilic organisms, which live in extreme saline conditions, have evolved to remain folded at very high ionic strengths. The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids, a low frequency of lysine, and a high occurrence of amino acids with a low hydrophobic character. Using extensive mutational studies on the protein surfaces, we show that it is possible to decrease the salt dependence of a typical halophilic protein to the level of a mesophilic form and engineer a protein from a mesophilic organism into an obligate halophilic form. NMR studies demonstrate complete preservation of the three-dimensional structure of extreme mutants and confirm that salt dependency is conferred exclusively by surface residues. In spite of the statistically established fact that most halophilic proteins are strongly acidic, analysis of a very large number of mutants showed that the effect of salt on protein stability is largely independent of the total protein charge. Conversely, we quantitatively demonstrate that halophilicity is directly related to a decrease in the accessible surface area. Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments. The halophilic archea are a group of microorganisms that grow best in highly salted lakes (with KCl concentrations between 2 and 6 molar). To avoid osmotic shock, halophilic archea have the same ionic strength inside their cells as outside. All their macromolecules, including the proteins, have therefore adapted to remain folded and functional under such ionic strength conditions. As a result, the amino acid composition of proteins adapted to a hypersaline environment is very characteristic: they have an abundance of negatively charged residues combined with a low frequency of lysines. In this study, we have investigated the relationship between this biased amino-acid composition and protein stability. Three model proteins – one from a strict halophile, its homolog from a mesophile and a totally unrelated protein from a mesophile - have been largely redesigned by site-directed mutagenesis, and the resulting mutants have been characterized structurally and thermodynamically. Our results show that amino acids with short side-chains (like aspartic and glutamic acid) are preferred to the longer lysine because they succeed in reducing the interaction surface between the protein and the solvent, which is beneficial in an environment where water is in limited availability because it also has to hydrate the salt ions.
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Affiliation(s)
- Xavier Tadeo
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- Institute of Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | | | | | - Ana Laín
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
| | | | - Oscar Millet
- Structural Biology Unit, CIC bioGUNE, Derio, Spain
- * E-mail:
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31
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Tadeo X, López-Méndez B, Castaño D, Trigueros T, Millet O. Protein stabilization and the Hofmeister effect: the role of hydrophobic solvation. Biophys J 2009; 97:2595-603. [PMID: 19883603 PMCID: PMC2770621 DOI: 10.1016/j.bpj.2009.08.029] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 08/18/2009] [Accepted: 08/21/2009] [Indexed: 11/21/2022] Open
Abstract
Using the IGg binding domain of protein L from Streptoccocal magnus (ProtL) as a case study, we investigated how the anions of the Hofmeister series affect protein stability. To that end, a suite of lysine-to-glutamine modifications were obtained and structurally and thermodynamically characterized. The changes in stability introduced with the mutation are related to the solvent-accessible area of the side chain, specifically to the solvation of the nonpolar moiety of the residue. The thermostability for the set of ProtL mutants was determined in the presence of varying concentrations (0-1 M) of six sodium salts from the Hofmeister series: sulfate, phosphate, fluoride, nitrate, perchlorate, and thiocyanate. For kosmotropic anions (sulfate, phosphate, and fluoride), the stability changes induced by the cosolute (encoded in m(3)=deltaDeltaG(0)/deltaC(3)) are proportional to the surface changes introduced with the mutation. In contrast, the m(3) values measured for chaotropic anions are much more independent of such surface modifications. Our results are consistent with a model in which the increase in the solution surface tension induced by the anion stabilizes the folded conformation of the protein. This contribution complements the nonspecific and weak interactions between the ions and the protein backbone that shift the equilibrium toward the unfolded state.
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Affiliation(s)
| | | | | | | | - Oscar Millet
- Structural Biology Unit, Centro de Investigación Cooperativa bioGUNE, Derio, Spain
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32
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MacKenzie DA, Tailford LE, Hemmings AM, Juge N. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. J Biol Chem 2009; 284:32444-53. [PMID: 19758995 DOI: 10.1074/jbc.m109.040907] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lactobacillus reuteri mucus-binding protein (MUB) is a cell-surface protein that is involved in bacterial interaction with mucus and colonization of the digestive tract. The 353-kDa mature protein is representative of a broadly important class of adhesins that have remained relatively poorly characterized due to their large size and highly modular nature. MUB contains two different types of repeats (Mub1 and Mub2) present in six and eight copies, respectively, and shown to be responsible for the adherence to intestinal mucus. Here we report the 1.8-A resolution crystal structure of a type 2 Mub repeat (184 amino acids) comprising two structurally related domains resembling the functional repeat found in a family of immunoglobulin (Ig)-binding proteins. The N-terminal domain bears striking structural similarity to the repeat unit of Protein L (PpL) from Peptostreptococcus magnus, suggesting binding in a non-immune Fab-dependent manner. A distorted PpL-like fold is also seen in the C-terminal domain. As with PpL, Mub repeats were able to interact in vitro with a large repertoire of mammalian Igs, including secretory IgA. This hitherto undetected activity is consistent with the current model that antibody responses against commensal flora are of broad specificity and low affinity.
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Affiliation(s)
- Donald A MacKenzie
- Institute of Food Research, Colney Lane, Norwich NR4 7UA, United Kingdom
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33
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Åkerström B, Björck L. Bacterial Surface Protein L Binds and Inactivates Neutrophil Proteins S100A8/A9. THE JOURNAL OF IMMUNOLOGY 2009; 183:4583-92. [DOI: 10.4049/jimmunol.0901487] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Sadler DP, Petrik E, Taniguchi Y, Pullen JR, Kawakami M, Radford SE, Brockwell DJ. Identification of a mechanical rheostat in the hydrophobic core of protein L. J Mol Biol 2009; 393:237-48. [PMID: 19683005 PMCID: PMC2796179 DOI: 10.1016/j.jmb.2009.08.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/23/2009] [Accepted: 08/07/2009] [Indexed: 11/22/2022]
Abstract
The ability of proteins and their complexes to withstand or respond to mechanical stimuli is vital for cells to maintain their structural organisation, to relay external signals and to facilitate unfolding and remodelling. Force spectroscopy using the atomic force microscope allows the behaviour of single protein molecules under an applied extension to be investigated and their mechanical strength to be quantified. protein L, a simple model protein, displays moderate mechanical strength and is thought to unfold by the shearing of two mechanical sub-domains. Here, we investigate the importance of side-chain packing for the mechanical strength of protein L by measuring the mechanical strength of a series of protein L variants containing single conservative hydrophobic volume deletion mutants. Of the five thermodynamically destabilised variants characterised, only one residue (I60V) close to the interface between two mechanical sub-domains was found to differ in mechanical properties to wild type (ΔFI60V–WT = − 36 pN at 447 nm s− 1, ΔxuI60V–WT = 0.2 nm). Φ-value analysis of the unfolding data revealed a highly native transition state. To test whether the number of hydrophobic contacts across the mechanical interface does affect the mechanical strength of protein L, we measured the mechanical properties of two further variants. protein L L10F, which increases core packing but does not enhance interfacial contacts, increased mechanical strength by 13 ± 11 pN at 447 nm s− 1. By contrast, protein L I60F, which increases both core and cross-interface contacts, increased mechanical strength by 72 ± 13 pN at 447 nm s− 1. These data suggest a method by which nature can evolve a varied mechanical response from a limited number of topologies and demonstrate a generic but facile method by which the mechanical strength of proteins can be rationally modified.
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Affiliation(s)
- David P Sadler
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
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35
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Zhao L, Wang J, Dou X, Cao Z. Studying the unfolding process of protein G and protein L under physical property space. BMC Bioinformatics 2009; 10 Suppl 1:S44. [PMID: 19208146 PMCID: PMC2648779 DOI: 10.1186/1471-2105-10-s1-s44] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The studies on protein folding/unfolding indicate that the native state topology is an important determinant of protein folding mechanism. The folding/unfolding behaviors of proteins which have similar topologies have been studied under Cartesian space and the results indicate that some proteins share the similar folding/unfolding characters. RESULTS We construct physical property space with twelve different physical properties. By studying the unfolding process of the protein G and protein L under the property space, we find that the two proteins have the similar unfolding pathways that can be divided into three types and the one which with the umbrella-shape represents the preferred pathway. Moreover, the unfolding simulation time of the two proteins is different and protein L unfolding faster than protein G. Additionally, the distributing area of unfolded state ensemble of protein L is larger than that of protein G. CONCLUSION Under the physical property space, the protein G and protein L have the similar folding/unfolding behaviors, which agree with the previous results obtained from the studies under Cartesian coordinate space. At the same time, some different unfolding properties can be detected easily, which can not be analyzed under Cartesian coordinate space.
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Affiliation(s)
- Liling Zhao
- Key Lab of Biophysics in universities of Shandong (Dezhou University), Dezhou 253023, PR China.
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36
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Morra G, Colombo G. Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. Proteins 2008; 72:660-72. [PMID: 18247351 DOI: 10.1002/prot.21963] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Most proteins must fold to a well-defined structure with a minimal stability to perform their function. Here we use a simple, molecular dynamics-based, energy decomposition approach to map the principal energetic interactions in a set of proteins representative of different folds. This work involves the all-atom simulation and analysis of the native structures and mutants of five different proteins representative of an all-alpha (yACPB, Protein A), all-beta (SH3), and a mixed alpha/beta fold (Proteins G and L). Given a certain structure, a native sequence and a set of mutants, we show that our model discriminates the ability of a mutation to yield a more or less stable protein, in agreement with experimental data, catching the principal energetic determinants of protein stabilization. Our approach identifies the interaction determinants responsible to define a fold and shows that mutations can either modulate the strength of pair-wise coupling between residues important for folding, or modify the profile of the principal interactions. Furthermore, we address the question of how to evaluate the fitness of a sequence to a given structure by comparing the information contained in the energy map, which recapitulates the chemistry of the sequence, to that contained in the contact map, which recapitulates the fold topology. The results show that the better fit between the energetic properties of the sequence and the fold topology corresponds to a higher stabilization of the protein. We discuss the relevance of these observations to the analysis of protein designability and to the rational evolution of new sequences.
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Affiliation(s)
- Giulia Morra
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131, Milano, Italy
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37
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Evolutional selection of a combinatorial phage library displaying randomly-rearranged various single domains of immunoglobulin (Ig)-binding proteins (IBPs) with four kinds of Ig molecules. BMC Microbiol 2008; 8:137. [PMID: 18700046 PMCID: PMC2532689 DOI: 10.1186/1471-2180-8-137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 08/13/2008] [Indexed: 11/19/2022] Open
Abstract
Background Protein A, protein G and protein L are three well-defined immunoglobulin (Ig)-binding proteins (IBPs), which show affinity for specific sites on Ig of mammalian hosts. Although the precise functions of these molecules are not fully understood, it is thought that they play an important role in pathogenicity of bacteria. The single domains of protein A, protein G and protein L were all demonstrated to have function to bind to Ig. Whether combinations of Ig-binding domains of various IBPs could exhibit useful novel binding is interesting. Results We used a combinatorial phage library which displayed randomly-rearranged various-peptide-linked molecules of D and A domains of protein A, designated PA(D) and PA(A) respectively, B2 domain of protein G (PG) and B3 domain of protein L (PL) for affinity selection with human IgG (hIgG), human IgM (hIgM), human IgA (hIgA) and recombinant hIgG1-Fc as bait respectively. Two kinds of novel combinatorial molecules with characteristic structure of PA(A)-PG and PA(A)-PL were obtained in hIgG (hIgG1-Fc) and hIgM (hIgA) post-selection populations respectively. In addition, the linking peptides among all PA(A)-PG and PA(A)-PL structures was strongly selected, and showed interestingly divergent and convergent distribution. The phage binding assays and competitive inhibition experiments demonstrated that PA(A)-PG and PA(A)-PL combinations possess comparable binding advantages with hIgG/hIgG1-Fc and hIgM/hIgA respectively. Conclusion In this work, a combinatorial phage library displaying Ig-binding domains of protein A, protein G, or protein L joined by various random linking peptides was used to conducted evolutional selection in vitro with four kinds of Ig molecules. Two kinds of novel combinations of Ig-binding domains, PA(A)-PG and PA(A)-PL, were obtained, and demonstrate the novel Ig binding properties.
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38
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Fawzi NL, Yap EH, Okabe Y, Kohlstedt KL, Brown SP, Head-Gordon T. Contrasting disease and nondisease protein aggregation by molecular simulation. Acc Chem Res 2008; 41:1037-47. [PMID: 18646868 DOI: 10.1021/ar800062k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[Figurre: see text]. Protein aggregation can be defined as the sacrifice of stabilizing intrachain contacts of the functional state that are replaced with interchain contacts to form non-functional states. The resulting aggregate morphologies range from amorphous structures without long-range order typical of nondisease proteins involved in inclusion bodies to highly structured fibril assemblies typical of amyloid disease proteins. In this Account, we describe the development and application of computational models for the investigation of nondisease and disease protein aggregation as illustrated for the proteins L and G and the Alzheimer's Abeta systems. In each case, we validate the models against relevant experimental observables and then expand on the experimental window to better elucidate the link between molecular properties and aggregation outcomes. Our studies show that each class of protein exhibits distinct aggregation mechanisms that are dependent on protein sequence, protein concentration, and solution conditions. Nondisease proteins can have native structural elements in the denatured state ensemble or rapidly form early folding intermediates, which offers avenues of protection against aggregation even at relatively high concentrations. The possibility that early folding intermediates may be evolutionarily selected for their protective role against unwanted aggregation could be a useful strategy for reengineering sequences to slow aggregation and increase folding yield in industrial protein production. The observed oligomeric aggregates that we see for nondisease proteins L and G may represent the nuclei for larger aggregates, not just for large amorphous inclusion bodies, but potentially as the seeds of ordered fibrillar aggregates, since most nondisease proteins can form amyloid fibrils under conditions that destabilize the native state. By contrast, amyloidogenic protein sequences such as Abeta 1-40,42 and the familial Alzheimer's disease (FAD) mutants favor aggregation into ordered fibrils once the free-energy barrier for forming a critical nucleus is crossed. However, the structural characteristics and oligomer size of the soluble nucleation species have yet to be determined experimentally for any disease peptide sequence, and the molecular mechanism of polymerization that eventually delineates a mature fibril is unknown. This is in part due to the limited experimental access to very low peptide concentrations that are required to characterize these early aggregation events, providing an opportunity for theoretical studies to bridge the gap between the monomer and fibril end points and to develop testable hypotheses. Our model shows that Abeta 1-40 requires as few as 6-10 monomer chains (depending on sequence) to begin manifesting the cross-beta order that is a signature of formation of amyloid filaments or fibrils assessed in dye-binding kinetic assays. The richness of the oligomeric structures and viable filament and fibril polymorphs that we observe may offer structural clues to disease virulence variations that are seen for the WT and hereditary mutants.
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Affiliation(s)
- Nicolas Lux Fawzi
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
| | - Eng-Hui Yap
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
| | - Yuka Okabe
- Department of Bioengineering, University of California, Berkeley, California 94720
| | - Kevin L. Kohlstedt
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208
| | - Scott P. Brown
- Abbott Laboratories, 1401 Sheridan Road, North Chicago, Illinois 60064-400
| | - Teresa Head-Gordon
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
- Department of Bioengineering, University of California, Berkeley, California 94720
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Yap EH, Fawzi NL, Head-Gordon T. A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding. Proteins 2008; 70:626-38. [PMID: 17879350 PMCID: PMC3474853 DOI: 10.1002/prot.21515] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We develop a sequence based alpha-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize alpha-helices and beta-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein-protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain.
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Affiliation(s)
- Eng-Hui Yap
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
| | - Nicolas Lux Fawzi
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
| | - Teresa Head-Gordon
- UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, California 94720
- Department of Bioengineering, University of California, Berkeley, California 94720
- Correspondence to: UCSF/UCB Joint Graduate Group in Bioengineering, Berkeley, CA 94720 and Department of Bioengineering, University of California, Berkeley, CA 94720.
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40
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Zouali M. Exploitation of host signaling pathways by B cell superantigens--potential strategies for developing targeted therapies in systemic autoimmunity. Ann N Y Acad Sci 2007; 1095:342-54. [PMID: 17404047 DOI: 10.1196/annals.1397.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Some infectious agents produce molecules capable of interacting specifically with the immunoglobulin heavy- or light-chain variable regions, independently of the conventional-binding site. They are referred to as B cell superantigens (SAgs) and include protein A of Staphylococcus aureus (S. aureus), gp120 of HIV-1, and protein L of Peptostreptococcus magnus (P. magnus). In contrast to conventional antigens, B cell superantigens interact with conserved framework regions of immunoglobulins and can target a large proportion of B cells. In experimental models, they have been demonstrated to deplete B cell subsets responsible for innate functions, namely B-1a and marginal zone (MZ) B cells. As a result, the interactions of these superantigens with host cells impair the humoral immune response. In addition to providing clues toward understanding host-pathogen interactions and microbial pathogenesis, B cell superantigens represent potential therapeutic agents that could be used to specifically modulate expansion of B cell subsets in diseased subjects. In systemic autoimmune diseases, for example, there is activation and expansion of B cells that secrete pathogenic autoantibodies. Their depletion results in clinical improvement in both experimental animals and patients. Currently, attempts are being made to specifically deplete pathogenic autoantibody-producing B cells. Since B-1a and MZ B cells have been found to be expanded in autoimmune disorders, B cell superantigens, used alone or in combination with other biological agents, may have beneficial effects in autoimmune disease management.
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Affiliation(s)
- Moncef Zouali
- Inserm U606, Centre Viggo Petersen, Hôpital Lariboisière, 2, rue Ambroise Paré, F-75475 Paris Cedex 10, France.
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Xie H, Vucetic S, Iakoucheva LM, Oldfield CJ, Dunker AK, Obradovic Z, Uversky VN. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. J Proteome Res 2007; 6:1917-32. [PMID: 17391016 PMCID: PMC2588348 DOI: 10.1021/pr060394e] [Citation(s) in RCA: 298] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. As many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bionformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200 000 proteins from the Swiss-Prot database, each annotated with at least one of the 875 functional keywords, was described in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V.N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Using this tool, we have found that out of the 710 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (see above). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic, S.; Xie, H.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions. J. Proteome Res. 2007, 5, 1899-1916). Protein structure and functionality can be modulated by various post-translational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes approximately 80 Swiss-Prot functional keywords that are related to ligands, post-translational modifications, and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins.
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Affiliation(s)
- Hongbo Xie
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Slobodan Vucetic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Lilia M. Iakoucheva
- Laboratory of Statistical Genetics, The Rockefeller University, New York, NY 10021
| | - Christopher J. Oldfield
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
| | - Zoran Obradovic
- Center for Information Science and Technology, Temple University, Philadelphia, PA 19122
| | - Vladimir N. Uversky
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University, School of Medicine, Indianapolis, IN 46202
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Correspondence should be addressed to: Vladimir N. Uversky, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, MS#4021, Indianapolis, IN 46202, USA; Phone: 317-278-9194; Fax: 317-274-4686; E-mail:
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42
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Yang X, Wang M, Fitzgerald MC. Direct analysis of backbone-backbone hydrogen bond formation in protein folding transition states. J Mol Biol 2006; 363:506-19. [PMID: 16963082 DOI: 10.1016/j.jmb.2006.07.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2006] [Revised: 07/24/2006] [Accepted: 07/25/2006] [Indexed: 11/29/2022]
Abstract
Here we investigate the role of backbone-backbone hydrogen bonding interactions in stabilizing the protein folding transition states of two model protein systems, the B1 domain of protein L (ProtL) and the P22 Arc repressor. A backbone modified analogue of ProtL containing an amide-to-ester bond substitution between residues 105 and 106 was prepared by total chemical synthesis, and the thermodynamic and kinetic parameters associated with its folding reaction were evaluated. Ultimately, these parameters were used in a Phi-value analysis to determine if the native backbone-backbone hydrogen bonding interaction perturbed in this analogue (i.e. a hydrogen bond in the first beta-turn of ProtL's beta-beta-alpha-beta-beta fold) was formed in the transition state of ProtL's folding reaction. Also determined were the kinetic parameters associated with the folding reactions of two Arc repressor analogues, each containing an amide-to-ester bond substitution in the backbone of their polypeptide chains. These parameters were used together with previously established thermodynamic parameters for the folding of these analogues in Phi-value analyses to determine if the native backbone-backbone hydrogen bonding interactions perturbed in these analogues (i.e. a hydrogen bond at the end of the intersubunit beta-sheet interface and hydrogen bonds at the beginning of the second alpha-helix in Arc repressor's beta-alpha-alpha structure) were formed in the transition state of Arc repressor's folding reaction. Our results reveal that backbone-backbone hydrogen bonding interactions are formed in the beta-turn and alpha-helical transition state structures of ProtL and Arc repressor, respectively; and they were not formed in the intersubunit beta-sheet interface of Arc repressor, a region of Arc repressor's polypeptide chain previously shown to have other non-native-like conformations in Arc's protein folding transition state.
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Affiliation(s)
- Xiaoye Yang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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43
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Yang X, Fitzgerald MC. Total chemical synthesis of the B1 domain of protein L from Peptostreptococcus magnus. Bioorg Chem 2006; 34:131-41. [PMID: 16690101 DOI: 10.1016/j.bioorg.2006.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2006] [Accepted: 02/13/2006] [Indexed: 10/24/2022]
Abstract
Reported here is a native chemical ligation strategy for the total chemical synthesis of the B1 domain of protein L. A synthetic construct of this 76 amino acid protein domain was prepared by the chemoselective ligation of two unprotected polypeptide fragments, one containing an N-terminal cysteine residue and one containing a C-terminal thioester moiety. The polypeptide fragments utilized in the ligation reaction were readily prepared by stepwise solid phase peptide synthesis (SPPS) methods for Boc-chemistry. The milligram quantities of protein required for conventional biophysical studies were readily accessible using the synthetic protocol described here. The folding properties of the synthetic protein L construct were also determined and found to be very similar to those of a similar wild-type protein L constructs prepared by recombinant-DNA methods. This work facilitates future unnatural amino acid mutagenesis experiments on this model protein system to further dissect the molecular basis of its folding and stability.
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Affiliation(s)
- Xiaoye Yang
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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44
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Tunnicliffe RB, Waby JL, Williams RJ, Williamson MP. An Experimental Investigation of Conformational Fluctuations in Proteins G and L. Structure 2005; 13:1677-84. [PMID: 16271891 DOI: 10.1016/j.str.2005.08.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 07/28/2005] [Accepted: 08/02/2005] [Indexed: 11/21/2022]
Abstract
The B1 domains of streptococcal proteins G and L are structurally similar, but they have different sequences and they fold differently. We have measured their NMR spectra at variable temperature using a range of concentrations of denaturant. Many residues have curved amide proton temperature dependence, indicating that they significantly populate alternative, locally unfolded conformations. The results, therefore, provide a view of the locations of low-lying, locally unfolded conformations. They indicate approximately 4-6 local minima for each protein, all within ca. 2.5 kcal/mol of the native state, implying a locally rough energy landscape. Comparison with folding data for these proteins shows that folding involves most molecules traversing a similar path, once a transition state containing a beta hairpin has been formed, thereby defining a well-populated pathway down the folding funnel. The hairpin that directs the folding pathway differs for the two proteins and remains the most stable part of the folded protein.
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Affiliation(s)
- Richard B Tunnicliffe
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
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45
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Goodyear CS, Silverman GJ. B cell superantigens: a microbe's answer to innate-like B cells and natural antibodies. ACTA ACUST UNITED AC 2005; 26:463-84. [PMID: 15633015 DOI: 10.1007/s00281-004-0190-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Marginal zone B cells and B-1 cells have been termed innate-like B cells as they express limited repertoires that play special roles in immune defenses against common infections. These B cells are the sources of natural antibodies and are capable of highly accelerated clonal responses that help counter blood-borne infections. We have characterized a class of microbial product with highly adapted binding interactions with host immunoglobulins/B cell receptors (BCRs), which enable the targeting of large supra-clonal sets of B cells for activation-associated apoptotic death. In recent studies, we have shown that all B cells with V region-targeted BCRs are susceptible. However, compared to follicular B cells, in vivo exposure preferentially causes innate-like B cells to undergo induced death with subsequent long-lasting supra-clonal depletion and immune tolerance. Based on these properties, it is likely that B cell superantigens influence the pathogenesis of some common infections, but also may provide novel therapeutic opportunities to treat B cell neoplastic and autoimmune diseases.
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Affiliation(s)
- Carl S Goodyear
- Rheumatic Disease Core Center, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0663, USA.
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46
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Brockwell DJ, Beddard GS, Paci E, West DK, Olmsted PD, Smith DA, Radford SE. Mechanically unfolding the small, topologically simple protein L. Biophys J 2005; 89:506-19. [PMID: 15863479 PMCID: PMC1366550 DOI: 10.1529/biophysj.105.061465] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
beta-sheet proteins are generally more able to resist mechanical deformation than alpha-helical proteins. Experiments measuring the mechanical resistance of beta-sheet proteins extended by their termini led to the hypothesis that parallel, directly hydrogen-bonded terminal beta-strands provide the greatest mechanical strength. Here we test this hypothesis by measuring the mechanical properties of protein L, a domain with a topology predicted to be mechanically strong, but with no known mechanical function. A pentamer of this small, topologically simple protein is resistant to mechanical deformation over a wide range of extension rates. Molecular dynamics simulations show the energy landscape for protein L is highly restricted for mechanical unfolding and that this protein unfolds by the shearing apart of two structural units in a mechanism similar to that proposed for ubiquitin, which belongs to the same structural class as protein L, but unfolds at a significantly higher force. These data suggest that the mechanism of mechanical unfolding is conserved in proteins within the same fold family and demonstrate that although the topology and presence of a hydrogen-bonded clamp are of central importance in determining mechanical strength, hydrophobic interactions also play an important role in modulating the mechanical resistance of these similar proteins.
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Affiliation(s)
- David J Brockwell
- School of Biochemistry and Microbiology, Institute of Molecular Biophysics, Centre for Chemical Dynamics, University of Leeds, Leeds, United Kingdom.
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47
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Du HN, Zhang TY, Chang YG, Lin DH, Hu HY. Effects of segment substitution on the structure and stability of immunoglobulin G binding domain of streptococcal protein G. Biopolymers 2005; 79:9-17. [PMID: 15838890 DOI: 10.1002/bip.20283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Structural formation of segments plays pivotal roles in protein folding and stability, but how the segment influences the structural ensemble remains elusive. We engineered two hybrid proteins by replacing the central helical segment of immunoglobulin G binding domain of streptococcal protein G with an alpha-helix or beta(2)-strand element of a structural homologue, the immunoglobulin G binding domain of streptococcal protein L. The results show that substitution by the alpha-helical sequence retains a folded structure predominantly with a three-stranded beta-sheet but slightly destabilizes the compact ensemble, while substitution by the beta(2)-strand sequence completely destroys the structural formation. The finding implies that the local segment may influence the tertiary structure and overall stability, and the tertiary interactions may modulate structural formation of the segment, which might be considered when studying protein folding, prediction, design, and engineering.
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Affiliation(s)
- Hai-Ning Du
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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48
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Abstract
Understanding the sequence determinants of protein structure, stability and folding is critical for understanding how natural proteins have evolved and how proteins can be engineered to perform novel functions. The complexity of the protein folding problem requires the ability to search large volumes of sequence space for proteins with specific structural or functional characteristics. Here we describe our efforts to identify novel proteins using a phage-display selection strategy from a 'mini-exon' shuffling library generated from the yeast genome and from completely random sequence libraries, and compare the results to recent successes in generating novel proteins using in silico protein design.
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Affiliation(s)
- Alexander L Watters
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
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49
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Abstract
Superantigens (SAGs) cause a massive T-cell proliferation by simultaneously binding to major histocompatibility complex (MHC) class II on antigen-presenting cells and T-cell receptors (TCRs) on T cells. These T-cell mitogens can cause disease in host, such as food poisoning or toxic shock. The best characterized groups of SAGs are the bacterial SAGs secreted by Staphylococcus aureus and Streptococcus pyogenes. Despite a common overall three-dimensional fold of these SAGs, they have been shown to bind to MHC class II in different ways. Recently, it has also been shown that SAGs have individual preferences in their binding to the TCRs. They can interact with various regions of the variable beta-chain of TCRs and at least one SAG seems to bind to the alpha-chain of TCRs. In this review, different subclasses of SAGs are classified based upon their binding mode to MHC class II, and models of trimolecular complexes of MHC-SAG-TCR molecules are described in order to reveal and understand the complexity of SAG-mediated T-cell activation.
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50
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Smith D, D'Argy R, Nilsson M, Yrlid U, de Jersey J, Björck L, Wick MJ. Whole-body autoradiography reveals that the Peptostreptococcus magnus immunoglobulin-binding domains of protein L preferentially target B lymphocytes in the spleen and lymph nodes in vivo. Cell Microbiol 2004; 6:609-23. [PMID: 15186398 DOI: 10.1111/j.1462-5822.2004.00386.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein L is an immunoglobulin (Ig)-binding protein produced by the Gram-positive bacterium Peptostreptococcus magnus that interacts with the variable region of Ig kappa light chains. The Ig light chain-binding capacity of protein L gives it the potential to interact with cells expressing surface Ig such as B cells. The present study was performed to address the in vivo trafficking of protein L at both the organ and the cellular level. Using the powerful technique of whole-body autoradiography in a murine model system, we demonstrate specific targeting of protein L to secondary lymphoid tissues in whole-animal analysis. The observed targeting depends on the capacity to interact with murine Ig, as tissue targeting was not apparent in mice given protein H, an Ig-binding protein produced by Streptococcus pyogenes with affinity for human but not murine Ig. Tissue targeting data were combined with flow cytometry analysis, which demonstrated the capacity of protein L to target and activate B lymphocytes in vivo. B cells targeted by protein L had increased surface expression of CD86 and MHC-II, and protein L was present in vacuolar compartments of B cells. Protein L did not bind T cells or natural killer cells but had some capacity to target dendritic cells and macrophages. The data show that protein L preferentially targets secondary lymphoid organs, and activates and is internalized by B cells in vivo. Furthermore, the observed tissue and cell targeting properties require an affinity for murine Ig. These data support the potential use of this Ig-binding protein as a targeting approach to deliver agents to defined cell populations in vivo.
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Affiliation(s)
- David Smith
- Section for Immunology, Department of Cell and Molecular Biology, Lund University, Lund, Sweden
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