1
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Vardar-Yel N, Tütüncü HE, Sürmeli Y. Lipases for targeted industrial applications, focusing on the development of biotechnologically significant aspects: A comprehensive review of recent trends in protein engineering. Int J Biol Macromol 2024; 273:132853. [PMID: 38838897 DOI: 10.1016/j.ijbiomac.2024.132853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
Lipases are remarkable biocatalysts, adept at catalyzing the breakdown of diverse compounds into glycerol, fatty acids, and mono- and di-glycerides via hydrolysis. Beyond this, they facilitate esterification, transesterification, alcoholysis, acidolysis, and more, making them versatile in industrial applications. In industrial processes, lipases that exhibit high stability are favored as they can withstand harsh conditions. However, most native lipases are unable to endure adverse conditions, making them unsuitable for industrial use. Protein engineering proves to be a potent technology in the development of lipases that can function effectively under challenging conditions and fulfill criteria for various industrial processes. This review concentrated on new trends in protein engineering to enhance the diversity of lipase genes and employed in silico methods for predicting and comprehensively analyzing target mutations in lipases. Additionally, key molecular factors associated with industrial characteristics of lipases, including thermostability, solvent tolerance, catalytic activity, and substrate preference have been elucidated. The present review delved into how industrial traits can be enhanced through directed evolution (epPCR, gene shuffling), rational design (FRESCO, ASR), combined engineering strategies (i.e. CAST, ISM, and FRISM) as protein engineering methodologies in contexts of biodiesel production, food processing, and applications of detergent, pharmaceutics, and plastic degradation.
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Affiliation(s)
- Nurcan Vardar-Yel
- Department of Medical Laboratory Techniques, Altınbaş University, 34145 İstanbul, Turkey
| | - Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey.
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2
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Sánchez-Morán H, Kaar JL, Schwartz DK. Supra-biological performance of immobilized enzymes enabled by chaperone-like specific non-covalent interactions. Nat Commun 2024; 15:2299. [PMID: 38485940 PMCID: PMC10940687 DOI: 10.1038/s41467-024-46719-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
Designing complex synthetic materials for enzyme immobilization could unlock the utility of biocatalysis in extreme environments. Inspired by biology, we investigate the use of random copolymer brushes as dynamic immobilization supports that enable supra-biological catalytic performance of immobilized enzymes. This is demonstrated by immobilizing Bacillus subtilis Lipase A on brushes doped with aromatic moieties, which can interact with the lipase through multiple non-covalent interactions. Incorporation of aromatic groups leads to a 50 °C increase in the optimal temperature of lipase, as well as a 50-fold enhancement in enzyme activity. Single-molecule FRET studies reveal that these supports act as biomimetic chaperones by promoting enzyme refolding and stabilizing the enzyme's folded and catalytically active state. This effect is diminished when aromatic residues are mutated out, suggesting the importance of π-stacking and π-cation interactions for stabilization. Our results underscore how unexplored enzyme-support interactions may enable uncharted opportunities for using enzymes in industrial biotransformations.
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Affiliation(s)
- Héctor Sánchez-Morán
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA.
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Campus Box 596, Boulder, CO, 80309, USA.
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3
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Rengachari S, Schilbach S, Cramer P. Mediator structure and function in transcription initiation. Biol Chem 2023; 404:829-837. [PMID: 37078249 DOI: 10.1515/hsz-2023-0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/06/2023] [Indexed: 04/21/2023]
Abstract
Recent advances in cryo-electron microscopy have led to multiple structures of Mediator in complex with the RNA polymerase II (Pol II) transcription initiation machinery. As a result we now hold in hands near-complete structures of both yeast and human Mediator complexes and have a better understanding of their interactions with the Pol II pre-initiation complex (PIC). Herein, we provide a summary of recent achievements and discuss their implications for future studies of Mediator and its role in gene regulation.
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Affiliation(s)
- Srinivasan Rengachari
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Sandra Schilbach
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, D-37077 Göttingen, Germany
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4
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Yamaguchi T, Taborosi A, Sakai C, Akao K, Mori S, Kohzuma T. Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin. J Inorg Biochem 2023; 246:112292. [PMID: 37354604 DOI: 10.1016/j.jinorgbio.2023.112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.
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Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano, Nagano 380-8553, Japan
| | - Chihiro Sakai
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Kohei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan.
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5
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Elsawy MA, Wychowaniec JK, Castillo Díaz LA, Smith AM, Miller AF, Saiani A. Controlling Doxorubicin Release from a Peptide Hydrogel through Fine-Tuning of Drug-Peptide Fiber Interactions. Biomacromolecules 2022; 23:2624-2634. [PMID: 35543610 PMCID: PMC9198986 DOI: 10.1021/acs.biomac.2c00356] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Hydrogels are versatile
materials that have emerged in the last
few decades as promising candidates for a range of applications in
the biomedical field, from tissue engineering and regenerative medicine
to controlled drug delivery. In the drug delivery field, in particular,
they have been the subject of significant interest for the spatially
and temporally controlled delivery of anticancer drugs and therapeutics.
Self-assembling peptide-based hydrogels, in particular, have recently
come to the fore as potential candidate vehicles for the delivery
of a range of drugs. In order to explore how drug–peptide interactions
influence doxorubicin (Dox) release, five β-sheet-forming self-assembling
peptides with different physicochemical properties were used for the
purpose of this study, namely: FEFKFEFK (F8), FKFEFKFK (FK), FEFEFKFE
(FE), FEFKFEFKK (F8K), and KFEFKFEFKK (KF8K) (F: phenylalanine; E:
glutamic acid; K: lysine). First, Dox-loaded hydrogels were characterized
to ensure that the incorporation of the drug did not significantly
affect the hydrogel properties. Subsequently, Dox diffusion out of
the hydrogels was investigated using UV absorbance. The amount of
drug retained in F8/FE composite hydrogels was found to be directly
proportional to the amount of charge carried by the peptide fibers.
When cation−π interactions were used, the position and
number of end-lysine were found to play a key role in the retention
of Dox. In this case, the amount of Dox retained in F8/KF8K composite
hydrogels was linked to the amount of end-lysine introduced, and an
end-lysine/Dox interaction stoichiometry of 3/1 was obtained. For
pure FE and KF8K hydrogels, the maximum amount of Dox retained was
also found to be related to the overall concentration of the hydrogels
and, therefore, to the overall fiber surface area available for interaction
with the drug. For 14 mM hydrogel, ∼170–200 μM
Dox could be retained after 24 h. This set of peptides also showed
a broad range of susceptibilities to enzymatic degradation opening
the prospect of being able to control also the rate of degradation
of these hydrogels. Finally, the Dox released from the hydrogel was
shown to be active and affect 3T3 mouse fibroblasts viability in vitro.
Our study clearly shows the potential of this peptide design as a
platform for the formulation of injectable or sprayable hydrogels
for controlled drug delivery.
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Affiliation(s)
- Mohamed A Elsawy
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.,Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K
| | - Jacek K Wychowaniec
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.,Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K
| | - Luis A Castillo Díaz
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.,Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K
| | - Andrew M Smith
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.,Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K
| | - Aline F Miller
- Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K.,Department of Chemical Engineering and Analytical Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Alberto Saiani
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, U.K.,Manchester Institute of Biotechnology, Oxford Road, Manchester M13 9PL, U.K
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6
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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7
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Talens-Perales D, Jiménez-Ortega E, Sánchez-Torres P, Sanz-Aparicio J, Polaina J. Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity. Comput Struct Biotechnol J 2021; 19:2676-2686. [PMID: 34093984 PMCID: PMC8148631 DOI: 10.1016/j.csbj.2021.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 01/31/2023] Open
Abstract
Endoxylanases active under extreme conditions of
temperature and alkalinity can replace the use of highly pollutant chemicals in
the pulp and paper industry. Searching for enzymes with these properties, we
carried out a comprehensive bioinformatics study of the GH10 family. The
phylogenetic analysis allowed the construction of a radial cladogram in which
protein sequences putatively ascribed as thermophilic and alkaliphilic appeared
grouped in a well-defined region of the cladogram, designated TAK Cluster. One
among five TAK sequences selected for experimental analysis (Xyn11) showed
extraordinary xylanolytic activity under simultaneous conditions of high
temperature (90 °C) and alkalinity (pH 10.5). Addition of a carbohydrate binding
domain (CBM2) at the C-terminus of the protein sequence further improved the
activity of the enzyme at high pH. Xyn11 structure, which has been solved at
1.8 Å resolution by X-ray crystallography, reveals an unusually high number of
hydrophobic, ionic and hydrogen bond atomic interactions that could account for
the enzyme’s extremophilic nature.
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Affiliation(s)
- David Talens-Perales
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Elena Jiménez-Ortega
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Paloma Sánchez-Torres
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Julia Sanz-Aparicio
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Polaina
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
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8
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Bovone G, Dudaryeva OY, Marco-Dufort B, Tibbitt MW. Engineering Hydrogel Adhesion for Biomedical Applications via Chemical Design of the Junction. ACS Biomater Sci Eng 2021; 7:4048-4076. [PMID: 33792286 DOI: 10.1021/acsbiomaterials.0c01677] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrogel adhesion inherently relies on engineering the contact surface at soft and hydrated interfaces. Upon contact, adhesion normally occurs through the formation of chemical or physical interactions between the disparate surfaces. The ability to form these adhesion junctions is challenging for hydrogels as the interfaces are wet and deformable and often contain low densities of functional groups. In this Review, we link the design of the binding chemistries or adhesion junctions, whether covalent, dynamic covalent, supramolecular, or physical, to the emergent adhesive properties of soft and hydrated interfaces. Wet adhesion is useful for bonding to or between tissues and implants for a range of biomedical applications. We highlight several recent and emerging adhesive hydrogels for use in biomedicine in the context of efficient junction design. The main focus is on engineering hydrogel adhesion through molecular design of the junctions to tailor the adhesion strength, reversibility, stability, and response to environmental stimuli.
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Affiliation(s)
- Giovanni Bovone
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Oksana Y Dudaryeva
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Bruno Marco-Dufort
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
| | - Mark W Tibbitt
- Macromolecular Engineering Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland
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9
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Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
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Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
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10
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Mitra D, Das Mohapatra PK. Discovery of Novel Cyclic Salt Bridge in Thermophilic Bacterial Protease and Study of its Sequence and Structure. Appl Biochem Biotechnol 2021; 193:1688-1700. [PMID: 33683551 DOI: 10.1007/s12010-021-03547-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022]
Abstract
The plausible explanation behind the stability of thermophilic protein is still yet to be defined more clearly. Here, an in silico study has been undertaken by investigating the sequence and structure of protease from thermophilic (tPro) bacteria and mesophilic (mPro) bacteria. Results showed that charged and uncharged polar residues have higher abundance in tPro. In extreme environment, the tPro is stabilized by high number of isolated and network salt bridges. A novel cyclic salt bridge is also found in a structure of tPro. High number of metal ion-binding site also helps in protein stabilization of thermophilic protease. Aromatic-aromatic interactions also play a crucial role in tPro stabilization. Formation of long network aromatic-aromatic interactions also first time reported here. Finally, the present study provides a major insight with a newly identified cyclic salt bridge in the stability of the enzyme, which may be helpful for protein engineering. It is also used in industrial applications for human welfare.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB, India
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11
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Liu H, Fu H, Shao X, Cai W, Chipot C. Accurate Description of Cation-π Interactions in Proteins with a Nonpolarizable Force Field at No Additional Cost. J Chem Theory Comput 2020; 16:6397-6407. [PMID: 32852943 DOI: 10.1021/acs.jctc.0c00637] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cation-π interactions play a significant role in a host of processes eminently relevant to biology. However, polarization effects arising from the interaction of cations with aromatic moieties have long been recognized to be inadequately described by pairwise additive force fields. In the present work, we address this longstanding shortcoming through the nonbonded FIX (NBFIX) feature of the CHARMM36 force field, modifying pair-specific Lennard-Jones (LJ) parameters, while circumventing the limitations of the Lorentz-Berthelot combination rules. The potentials of mean force (PMFs) characterizing prototypical cation-π interactions in aqueous solutions are first determined using a hybrid quantum mechanical/molecular mechanics (QM/MM) strategy in conjunction with an importance-sampling algorithm. The LJ parameters describing the cation-π pairs are then optimized to match the QM/MM PMFs. The standard binding free energies of nine cation-π complexes, i.e., toluene, para-cresol, and 3-methyl-indole interacting with either ammonium, guanidinium, or tetramethylammonium, determined with this new set of parameters agree well with the experimental measurements. Additional simulations were carried out on three different classes of biological objects featuring cation-π interactions, including five individual proteins, three protein-ligand complexes, and two protein-protein complexes. Our results indicate that the description of cation-π interactions is overall improved using NBFIX corrections, compared with the standard pairwise additive force field. Moreover, an accurate binding free energy calculation for a protein-ligand complex containing cation-π interactions (2BOK) shows that using the new parameters, the experimental binding affinity can be reproduced quantitatively. Put together, the present work suggests that the NBFIX parameters optimized here can be broadly utilized in the simulation of proteins in an aqueous solution to enhance the representation of cation-π interactions, at no additional computational cost.
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Affiliation(s)
- Han Liu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Haohao Fu
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xueguang Shao
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China.,State Key Laboratory of Medicinal Chemical Biology, Tianjin 300071, China
| | - Wensheng Cai
- Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Christophe Chipot
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, UMR n°7019, Université de Lorraine, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
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12
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Grahame DSA, Dupuis JH, Bryksa BC, Tanaka T, Yada RY. Comparative bioinformatic and structural analyses of pepsin and renin. Enzyme Microb Technol 2020; 141:109632. [PMID: 33051007 DOI: 10.1016/j.enzmictec.2020.109632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/25/2020] [Accepted: 07/08/2020] [Indexed: 11/16/2022]
Abstract
Pepsin, the archetypal pepsin-like aspartic protease, is irreversibly denatured when exposed to neutral pH conditions whereas renin, a structural homologue of pepsin, is fully stable and optimally active in the same conditions despite sharing highly similar enzyme architecture. To gain insight into the structural determinants of differential aspartic protease pH stability, the present study used comparative bioinformatic and structural analyses. In pepsin, an abundance of polar and aspartic acid residues were identified, a common trait with other acid-stable enzymes. Conversely, renin was shown to have increased levels of basic amino acids. In both pepsin and renin, the solvent exposure of these charged groups was high. Having similar overall acidic residue content, the solvent-exposed basic residues may allow for extensive salt bridge formation in renin, whereas in pepsin, these residues are protonated and serve to form stabilizing hydrogen bonds at low pH. Relative differences in structure and sequence in the turn and joint regions of the β-barrel and ψ-loop in both the N- and C-terminal lobes were identified as regions of interest in defining divergent pH stability. Compared to the structural rigidity of renin, pepsin has more instability associated with the N-terminus, specifically the B/C connector. By contrast, renin exhibits greater C-terminal instability in turn and connector regions. Overall, flexibility differences in connector regions, and amino acid composition, particularly in turn and joint regions of the β-barrel and ψ-loops, likely play defining roles in determining pH stability for renin and pepsin.
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Affiliation(s)
- Douglas S A Grahame
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - John H Dupuis
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Brian C Bryksa
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Takuji Tanaka
- Department of Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, S7N 5A8 Canada
| | - Rickey Y Yada
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON, N1G 2W1, Canada; Food, Nutrition, and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, BC, V6T 1Z4 Canada.
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13
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Stiers KM, Hansen RP, Daghlas BA, Mason KN, Zhu JS, Jakeman DL, Beamer LJ. A missense variant remote from the active site impairs stability of human phosphoglucomutase 1. J Inherit Metab Dis 2020; 43:861-870. [PMID: 32057119 DOI: 10.1002/jimd.12222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
Missense variants of human phosphoglucomutase 1 (PGM1) cause the inherited metabolic disease known as PGM1 deficiency. This condition is categorised as both a glycogen storage disease and a congenital disorder of glycosylation. Approximately 20 missense variants of PGM1 are linked to PGM1 deficiency, and biochemical studies have suggested that they fall into two general categories: those affecting the active site and catalytic efficiency, and those that appear to impair protein folding and/or stability. In this study, we characterise a novel variant of Arg422, a residue distal from the active site of PGM1 and the site of a previously identified disease-related variant (Arg422Trp). In prior studies, the R422W variant was found to produce insoluble protein in a recombinant expression system, precluding further in vitro characterisation. Here we investigate an alternative variant of this residue, Arg422Gln, which is amenable to experimental characterisation presumably due to its more conservative physicochemical substitution. Biochemical, crystallographic, and computational studies of R422Q establish that this variant causes only minor changes in catalytic efficiency and 3D structure, but is nonetheless dramatically reduced in stability. Unexpectedly, binding of a substrate analog is found to further destabilise the protein, in contrast to its stabilising effect on wild-type PGM1 and several other missense variants. This work establishes Arg422 as a lynchpin residue for the stability of PGM1 and supports the impairment of protein stability as a pathomechanism for variants that cause PGM1 deficiency. SYNOPSIS: Biochemical and structural studies of a missense variant far from the active site of human PGM1 identify a residue with a key role in enzyme stability.
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Affiliation(s)
- Kyle M Stiers
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Reed P Hansen
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Bana A Daghlas
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Kelly N Mason
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
| | - Jian-She Zhu
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David L Jakeman
- College of Pharmacy, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lesa J Beamer
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
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14
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Lin FY, MacKerell AD. Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. J Comput Chem 2020; 41:439-448. [PMID: 31518010 PMCID: PMC7322827 DOI: 10.1002/jcc.26067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/15/2019] [Accepted: 08/25/2019] [Indexed: 12/22/2022]
Abstract
Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Fang-Yu Lin
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
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15
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Hait S, Mallik S, Basu S, Kundu S. Finding the generalized molecular principles of protein thermal stability. Proteins 2019; 88:788-808. [PMID: 31872464 DOI: 10.1002/prot.25866] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/14/2019] [Indexed: 11/09/2022]
Abstract
Are there any generalized molecular principles of thermal adaptation? Here, integrating the concepts of structural bioinformatics, sequence analysis, and classical knot theory, we develop a robust computational framework that seeks for mechanisms of thermal adaptation by comparing orthologous mesophilic-thermophilic and mesophilic-hyperthermophilic proteins of remarkable structural and topological similarities, and still leads us to context-independent results. A comprehensive analysis of 4741 high-resolution, non-redundant X-ray crystallographic structures collected from 11 hyperthermophilic, 32 thermophilic and 53 mesophilic prokaryotes unravels at least five "nearly universal" signatures of thermal adaptation, irrespective of the enormous sequence, structure, and functional diversity of the proteins compared. A careful investigation further extracts a set of amino acid changes that can potentially enhance protein thermal stability, and remarkably, these mutations are overrepresented in protein crystallization experiments, in disorder-to-order transitions and in engineered thermostable variants of existing mesophilic proteins. These results could be helpful to find a precise, global picture of thermal adaptation.
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Affiliation(s)
- Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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16
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Joshi S, Sharma P, Siddiqui R, Kaushal K, Sharma S, Verma G, Saini A. A review on peptide functionalized graphene derivatives as nanotools for biosensing. Mikrochim Acta 2019; 187:27. [PMID: 31811393 DOI: 10.1007/s00604-019-3989-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022]
Abstract
Peptides exhibit unique binding behavior with graphene and its derivatives by forming bonds on its edges and planes. This makes them useful for sensing and imaging applications. This review with (155 refs.) summarizes the advances made in the last decade in the field of peptide-GO bioconjugation, and the use of these conjugates in analytical sciences and imaging. The introduction emphasizes the need for understanding the biotic-abiotic interactions in order to construct controllable peptide-functionalized graphitic material-based nanotools. The next section covers covalent and non-covalent interactions between peptide and oxidized graphene derivatives along with a discussion of the adsorption events during interfacing. We then describe applications of peptide-graphene conjugates in bioassays, with subsections on (a) detection of cancer cells, (b) monitoring protease activity, (c) determination of environmental pollutants and (d) determination of pathogenic microorganisms. The concluding section describes the current status of peptide functionalized graphitic bioconjugates and addresses future perspectives. Graphical abstractSchematic representation depicting biosensing applications of peptide functionalized graphene oxide.
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Affiliation(s)
- Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Pratibha Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Ruby Siddiqui
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Kanica Kaushal
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India
| | - Shweta Sharma
- Institute of Forensic Science & Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Gaurav Verma
- Dr. S.S. Bhatnagar University Institute of Chemical Engineering & Technology (Dr.SSBUICET), Panjab University, Sector 14, Chandigarh, 160014, India
- Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, 160014, India.
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17
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Orabi EA, Davis RL, Lamoureux G. Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. J Comput Chem 2019; 41:472-481. [DOI: 10.1002/jcc.26084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Esam A. Orabi
- Department of ChemistryFaculty of Science, Assiut University Assiut 71516 Egypt
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Rebecca L. Davis
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Center for Computational and Integrative Biology (CCIB)Rutgers University Camden New Jersey 08102
- Centre for Research in Molecular Modeling (CERMM), Concordia University Montréal Québec H4B 1R6 Canada
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18
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Veno J, Rahman RNZRA, Masomian M, Ali MSM, Kamarudin NHA. Insight into Improved Thermostability of Cold-Adapted Staphylococcal Lipase by Glycine to Cysteine Mutation. Molecules 2019; 24:molecules24173169. [PMID: 31480403 PMCID: PMC6749283 DOI: 10.3390/molecules24173169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/17/2019] [Accepted: 07/23/2019] [Indexed: 11/16/2022] Open
Abstract
Thermostability remains one of the most desirable traits in many lipases. Numerous studies have revealed promising strategies to improve thermostability and random mutagenesis often leads to unexpected yet interesting findings in engineering stability. Previously, the thermostability of C-terminal truncated cold-adapted lipase from Staphylococcus epidermidis AT2 (rT-M386) was markedly enhanced by directed evolution. The newly evolved mutant, G210C, demonstrated an optimal temperature shift from 25 to 45 °C and stability up to 50 °C. Interestingly, a cysteine residue was randomly introduced on the loop connecting the two lids and accounted for the only cysteine found in the lipase. We further investigated the structural and mechanistic insights that could possibly cause the significant temperature shift. Both rT-M386 and G210C were modeled and simulated at 25 °C and 50 °C. The results clearly portrayed the effect of cysteine substitution primarily on the lid stability. Comparative molecular dynamics simulation analysis revealed that G210C exhibited greater stability than the wild-type at high temperature simulation. The compactness of the G210C lipase structure increased at 50 °C and resulted in enhanced rigidity hence stability. This observation is supported by the improved and stronger non-covalent interactions formed in the protein structure. Our findings suggest that the introduction of a single cysteine residue at the lid region of cold-adapted lipase may result in unexpected increased in thermostability, thus this approach could serve as one of the thermostabilization strategies in engineering lipase stability.
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Affiliation(s)
- Jiivittha Veno
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Malihe Masomian
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Centre of Vaccine Research, School of Science and Technology, Sunway University, Bandar Sunway, Selangor 47500, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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19
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Rojas-Rengifo DF, Ulloa-Guerrero CP, Joppich M, Haas R, Del Pilar Delgado M, Jaramillo C, Jiménez-Soto LF. Tryptophan usage by Helicobacter pylori differs among strains. Sci Rep 2019; 9:873. [PMID: 30696868 PMCID: PMC6351589 DOI: 10.1038/s41598-018-37263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/19/2018] [Indexed: 11/14/2022] Open
Abstract
Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.
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Affiliation(s)
- Diana F Rojas-Rengifo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Cindy P Ulloa-Guerrero
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Markus Joppich
- Lehr- und Forschungseinheit Bioinformatik. Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstr. 17, D-80333, Munich, Germany
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Maria Del Pilar Delgado
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Carlos Jaramillo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Luisa F Jiménez-Soto
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany. .,Ludwig-Maximillians University, Munich, Germany.
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20
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Najor M, Leverson BD, Goossens JL, Kothawala S, Olsen KW, Mota de Freitas D. Folding of G α Subunits: Implications for Disease States. ACS OMEGA 2018; 3:12320-12329. [PMID: 30411001 PMCID: PMC6210069 DOI: 10.1021/acsomega.8b01174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
G-proteins play a central role in signal transduction by fluctuating between "on" and "off" phases that are determined by a conformational change. cAMP is a secondary messenger whose formation is inhibited or stimulated by activated Giα1 or Gsα subunit. We used tryptophan fluorescence, UV/vis spectrophotometry, and circular dichroism to probe distinct structural features within active and inactive conformations from wild-type and tryptophan mutants of Giα1 and Gsα. For all proteins studied, we found that the active conformations were more stable than the inactive conformations, and upon refolding from higher temperatures, activated wild-type subunits recovered significantly more native structure. We also observed that the wild-type subunits partially regained the ability to bind nucleotide. The increased compactness observed upon activation was consistent with the calculated decrease in solvent accessible surface area for wild-type Giα1. We found that as the temperature increased, Gα subunits, which are known to be rich in α-helices, converted to proteins with increased content of β-sheets and random coil. For active conformations from wild-type and tryptophan mutants of Giα1, melting temperatures indicated that denaturation starts around hydrophobic tryptophan microenvironments and then radiates toward tyrosine residues at the surface, followed by alteration of the secondary structure. For Gsα, however, disruption of secondary structure preceded unfolding around tyrosine residues. In the active conformations, a π-cation interaction between essential arginine and tryptophan residues, which was characterized by a fluorescence-measured red shift and modeled by molecular dynamics, was also shown to be a contributor to the stability of Gα subunits. The folding properties of Gα subunits reported here are discussed in the context of diseases associated to G-proteins.
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21
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Experimental and molecular docking study on graphene/Fe3O4 composites as a sorbent for magnetic solid-phase extraction of seven imidazole antifungals in environmental water samples prior to LC-MS/MS for enantiomeric analysis. Microchem J 2018. [DOI: 10.1016/j.microc.2018.04.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Kesinger E, Liu J, Jensen A, Chia CP, Demers A, Moriyama H. Influenza D virus M2 protein exhibits ion channel activity in Xenopus laevis oocytes. PLoS One 2018; 13:e0199227. [PMID: 29927982 PMCID: PMC6013169 DOI: 10.1371/journal.pone.0199227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/04/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND A new type of influenza virus, known as type D, has recently been identified in cattle and pigs. Influenza D virus infection in cattle is typically asymptomatic; however, its infection in swine can result in clinical disease. Swine can also be infected with all other types of influenza viruses, namely A, B, and C. Consequently, swine can serve as a "mixing vessel" for highly pathogenic influenza viruses, including those with zoonotic potential. Currently, the only antiviral drug available targets influenza M2 protein ion channel is not completely effective. Thus, it is necessary to develop an M2 ion channel blocker capable of suppressing the induction of resistance to the genetic shift. To provide a basis for developing novel ion channel-blocking compounds, we investigated the properties of influenza D virus M2 protein (DM2) as a drug target. RESULTS To test the ion channel activity of DM2, the DNA corresponding to DM2 with cMyc-tag conjugated to its carboxyl end was cloned into the shuttle vector pNCB1. The mRNA of the DM2-cMyc gene was synthesized and injected into Xenopus oocytes. The translation products of DM2-cMyc mRNA were confirmed by immunofluorescence and mass spectrometry analyses. The DM2-cMyc mRNA-injected oocytes were subjected to the two-electrode voltage-clamp (TEVC) method, and the induced inward current was observed. The midpoint (Vmid) values in Boltzmann modeling for oocytes injected with DM2-cMyc RNA or a buffer were -152 and -200 mV, respectively. Assuming the same expression level in the Xenopus oocytes, DM2 without tag and influenza C virus M2 protein (CM2) were subjected to the TEVC method. DM2 exhibited ion channel activity under the condition that CM2 ion channel activity was reproduced. The gating voltages represented by Vmid for CM2 and DM2 were -141 and -146 mV, respectively. The reversal potentials observed in ND96 for CM2 and DM2 were -21 and -22 mV, respectively. Compared with intact DM2, DM2 variants with mutation in the YxxxK motif, namely Y72A and K76A DM2, showed lower Vmid values while showing no change in reversal potential. CONCLUSION The M2 protein from newly isolated influenza D virus showed ion channel activity similar to that of CM2. The gating voltage was shown to be affected by the YxxxK motif and by the hydrophobicity and bulkiness of the carboxyl end of the molecule.
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Affiliation(s)
- Evan Kesinger
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Jianing Liu
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Aaron Jensen
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Catherine P. Chia
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Andrew Demers
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- * E-mail:
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23
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Orabi EA, Lamoureux G. Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution. J Phys Chem B 2018; 122:2251-2260. [PMID: 29397727 DOI: 10.1021/acs.jpcb.7b11983] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH3+ and RN(CH3)3+) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA+) and tetraethylammonium (TEA+). Polarizable molecular models are calibrated for NH4+, TMA+, and TEA+ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH4+ > TMA+ > TEA+, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA+ (the largest ion), the most stable solvent-separated complexes involve TMA+ (the intermediate-size ion).
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling (CERMM), Concordia University , 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
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24
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Goldenzweig A, Fleishman SJ. Principles of Protein Stability and Their Application in Computational Design. Annu Rev Biochem 2018; 87:105-129. [PMID: 29401000 DOI: 10.1146/annurev-biochem-062917-012102] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteins are increasingly used in basic and applied biomedical research. Many proteins, however, are only marginally stable and can be expressed in limited amounts, thus hampering research and applications. Research has revealed the thermodynamic, cellular, and evolutionary principles and mechanisms that underlie marginal stability. With this growing understanding, computational stability design methods have advanced over the past two decades starting from methods that selectively addressed only some aspects of marginal stability. Current methods are more general and, by combining phylogenetic analysis with atomistic design, have shown drastic improvements in solubility, thermal stability, and aggregation resistance while maintaining the protein's primary molecular activity. Stability design is opening the way to rational engineering of improved enzymes, therapeutics, and vaccines and to the application of protein design methodology to large proteins and molecular activities that have proven challenging in the past.
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Affiliation(s)
- Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel;
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25
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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Kadej A, Kuczer M, Czarniewska E, Urbański A, Rosiński G, Kowalik-Jankowska T. High stability and biological activity of the copper(II) complexes of alloferon 1 analogues containing tryptophan. J Inorg Biochem 2016; 163:147-161. [PMID: 27453534 DOI: 10.1016/j.jinorgbio.2016.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 06/21/2016] [Accepted: 07/07/2016] [Indexed: 11/28/2022]
Abstract
Copper(II) complex formation processes between the alloferon 1 (Allo1) (HGVSGHGQHGVHG) analogues where the tryptophan residue is introducing in the place His residue H1W, H6W, H9W and H12W have been studied by potentiometric, UV-visible, CD and EPR spectroscopic, and MS methods. For all analogues of alloferon 1 complex speciation have been obtained for a 1:1 metal-to-ligand molar ratio and 2:1 of H1W because of precipitation at higher (2:1, 3:1 and 4:1) ratios. At physiological pH7.4 and a 1:1 metal-to-ligand molar ratio the tryptophan analogues of alloferon 1 form the CuH-1L and/or CuH-2L complexes with the 4N binding mode. The introduction of tryptophan in place of histidine residues changes the distribution diagram of the complexes formed with the change of pH and their stability constants compared to the respective substituted alanine analogues of alloferon 1. The CuH-1L, CuH-2L and CuH-3L complexes of the tryptophan analogues are more stable from 1 to 5 log units in comparison to those of the alanine analogues. This stabilization of the complexes may result from cation(Cu(II))-π and indole/imidazole ring interactions. The induction of apoptosis in vivo, in Tenebrio molitor cells by the ligands and their copper(II) complexes at pH7.4 was studied. The biological results show that copper(II) ions in vivo did not cause any apparent apoptotic features. The most active were the H12W peptide and Cu(II)-H12W complex formed at pH7.4.
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Affiliation(s)
- Agnieszka Kadej
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Mariola Kuczer
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Elżbieta Czarniewska
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Arkadiusz Urbański
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland; Department of Systematic Zoology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Grzegorz Rosiński
- Department of Animal Physiology and Development, Institute of Experimental Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
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Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry 2016; 55:6056-6069. [PMID: 27753291 DOI: 10.1021/acs.biochem.6b00624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.
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Affiliation(s)
- Karan Kapoor
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
| | - Michael R Duff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Amit Upadhyay
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States
| | - Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Arnold M Saxton
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Elizabeth E Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
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28
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Petaccia M, Giansanti L, Leonelli F, Bella AL, Gradella Villalva D, Mancini G. Synthesis, characterization and inclusion into liposomes of a new cationic pyrenyl amphiphile. Chem Phys Lipids 2016; 200:83-93. [DOI: 10.1016/j.chemphyslip.2016.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/26/2016] [Accepted: 08/08/2016] [Indexed: 01/08/2023]
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Tripathi A, Gupta K, Khare S, Jain PC, Patel S, Kumar P, Pulianmackal AJ, Aghera N, Varadarajan R. Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data. Mol Biol Evol 2016; 33:2960-2975. [PMID: 27563054 PMCID: PMC5062330 DOI: 10.1093/molbev/msw182] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Understanding how mutations affect protein activity and organismal fitness is a major challenge. We used saturation mutagenesis combined with deep sequencing to determine mutational sensitivity scores for 1,664 single-site mutants of the 101 residue Escherichia coli cytotoxin, CcdB at seven different expression levels. Active-site residues could be distinguished from buried ones, based on their differential tolerance to aliphatic and charged amino acid substitutions. At nonactive-site positions, the average mutational tolerance correlated better with depth from the protein surface than with accessibility. Remarkably, similar results were observed for two other small proteins, PDZ domain (PSD95pdz3) and IgG-binding domain of protein G (GB1). Mutational sensitivity data obtained with CcdB were used to derive a procedure for predicting functional effects of mutations. Results compared favorably with those of two widely used computational predictors. In vitro characterization of 80 single, nonactive-site mutants of CcdB showed that activity in vivo correlates moderately with thermal stability and solubility. The inability to refold reversibly, as well as a decreased folding rate in vitro, is associated with decreased activity in vivo. Upon probing the effect of modulating expression of various proteases and chaperones on mutant phenotypes, most deleterious mutants showed an increased in vivo activity and solubility only upon over-expression of either Trigger factor or SecB ATP-independent chaperones. Collectively, these data suggest that folding kinetics rather than protein stability is the primary determinant of activity in vivo. This study enhances our understanding of how mutations affect phenotype, as well as the ability to predict fitness effects of point mutations.
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Affiliation(s)
- Arti Tripathi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Pankaj C Jain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Siddharth Patel
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Prasanth Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore, India
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30
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Wiloch MZ, Wawrzyniak UE, Ufnalska I, Piotrowski G, Bonna A, Wróblewski W. Redox Activity of Copper(II) Complexes with NSFRY Pentapeptide and Its Analogues. PLoS One 2016; 11:e0160256. [PMID: 27517864 PMCID: PMC4982629 DOI: 10.1371/journal.pone.0160256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022] Open
Abstract
The influence of cation-π interactions on the electrochemical properties of copper(II) complexes with synthesized pentapeptide C-terminal fragment of Atrial Natriuretic Factor (ANF) hormone was studied in this work. Molecular modeling performed for Cu(II)-NSFRY-NH2 complex indicated that the cation-π interactions between Tyr and Cu(II), and also between Phe-Arg led to specific conformation defined as peptide box, in which the metal cation is isolated from the solvent by peptide ligand. Voltammetry experiments enabled to compare the redox properties and stability of copper(II) complexes with NSFRY-NH2 and its analogues (namely: NSFRA-NH2, NSFRF-NH2, NSAAY-NH2, NSAAA-NH2, AAAAA-NH2) as well as to evaluate the contribution of individual amino acid residues to these properties. The obtained results led to the conclusion, that cation-π interactions play a crucial role in the effective stabilization of copper(II) complexes with the fragments of ANF peptide hormone and therefore could control the redox processes in other metalloproteins.
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Affiliation(s)
- Magdalena Zofia Wiloch
- Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00–664, Warsaw, Poland
| | - Urszula Elżbieta Wawrzyniak
- Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00–664, Warsaw, Poland
- * E-mail: ;
| | - Iwona Ufnalska
- Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00–664, Warsaw, Poland
| | - Grzegorz Piotrowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80–308, Gdańsk, Poland
| | - Arkadiusz Bonna
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego, 5a, 02–106, Warsaw, Poland
- * E-mail: ;
| | - Wojciech Wróblewski
- Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00–664, Warsaw, Poland
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Craven TW, Cho MK, Traaseth NJ, Bonneau R, Kirshenbaum K. A Miniature Protein Stabilized by a Cation-π Interaction Network. J Am Chem Soc 2016; 138:1543-50. [PMID: 26812069 PMCID: PMC4867217 DOI: 10.1021/jacs.5b10285] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The design of folded miniature proteins is predicated on establishing noncovalent interactions that direct the self-assembly of discrete thermostable tertiary structures. In this work, we describe how a network of cation-π interactions present in proteins containing "WSXWS motifs" can be emulated to stabilize the core of a miniature protein. This 19-residue protein sequence recapitulates a set of interdigitated arginine and tryptophan residues that stabilize a distinctive β-strand:loop:PPII-helix topology. Validation of the compact fold determined by NMR was carried out by mutagenesis of the cation-π network and by comparison to the corresponding disulfide-bridged structure. These results support the involvement of a coordinated set of cation-π interactions that stabilize the tertiary structure.
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Affiliation(s)
- Timothy W. Craven
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
| | - Min-Kyu Cho
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Nathaniel J. Traaseth
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Pl., New York, NY
- Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, NY
- Simons Center for Data Analysis, New York, NY
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY
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Gao S, Shi G, Fang H. Impact of cation-π interactions on the cell voltage of carbon nanotube-based Li batteries. NANOSCALE 2016; 8:1451-1455. [PMID: 26676257 DOI: 10.1039/c5nr06456b] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Carbon nanotube (CNT)-based Li batteries have attracted wide attention because of their high capacity, high cyclability and high energy density and are believed to be one of the most promising electrochemical energy storage systems. In CNT-based Li batteries, the main interaction between the Li(+) ions and the CNT is the cation-π interaction. However, up to now, it is still not clear how this interaction affects the storage characteristics of CNT-based Li batteries. Here, using density functional theory (DFT) calculations, we report a highly favorable impact of cation-π interactions on the cell voltage of CNT-based Li batteries. Considering both Li(+)-π interaction and Li-π interaction, we show that cell voltage enhances with the increase of the CNT diameter. In addition, when the Li(+) ion adsorbs on the external wall, the cell voltage is larger than that when it adsorbs on the internal wall. This suggests that CNTs with a large diameter and a low array density are more advantageous to enhance storage performance of CNT-based Li batteries. Compared with Li(+) ions on the (4,4) CNT internal wall, the cell voltage of Li(+) on the (10,10) CNT external wall is 0.55 V higher, which indicates an improvement of about 38%. These results will be helpful for the design of more efficient CNT-based Li batteries.
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Affiliation(s)
- Shaohua Gao
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China.
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800 China.
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33
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Sarmah N, Bhattacharyya PK. Behaviour of cation–pi interaction in presence of external electric field. RSC Adv 2016. [DOI: 10.1039/c6ra21334k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
External electric field effects cation–π interaction.
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Affiliation(s)
- Nabajit Sarmah
- Department of Chemistry
- Arya Vidyapeeth College
- Guwahati-781016
- India
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34
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Chan CH, Tsai CJ, Chiang YW. Side-Chain Packing Interactions Stabilize an Intermediate of BAX Protein against Chemical and Thermal Denaturation. J Phys Chem B 2014; 119:54-64. [DOI: 10.1021/jp5091334] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chun-Hui Chan
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chia-Jung Tsai
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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Dockter C, Gruszka D, Braumann I, Druka A, Druka I, Franckowiak J, Gough SP, Janeczko A, Kurowska M, Lundqvist J, Lundqvist U, Marzec M, Matyszczak I, Müller AH, Oklestkova J, Schulz B, Zakhrabekova S, Hansson M. Induced variations in brassinosteroid genes define barley height and sturdiness, and expand the green revolution genetic toolkit. PLANT PHYSIOLOGY 2014; 166:1912-27. [PMID: 25332507 PMCID: PMC4256852 DOI: 10.1104/pp.114.250738] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 10/16/2014] [Indexed: 05/18/2023]
Abstract
Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE, CONSTITUTIVE PHOTOMORPHOGENIC DWARF, and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROID-INSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroid-related genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars.
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Affiliation(s)
- Christoph Dockter
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Damian Gruszka
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Ilka Braumann
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Arnis Druka
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Ilze Druka
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Jerome Franckowiak
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Simon P Gough
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Anna Janeczko
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Marzena Kurowska
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Joakim Lundqvist
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Udda Lundqvist
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Marek Marzec
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Izabela Matyszczak
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - André H Müller
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Jana Oklestkova
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Burkhard Schulz
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Shakhira Zakhrabekova
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
| | - Mats Hansson
- Carlsberg Laboratory, DK-1799 Copenhagen V, Denmark (C.D., I.B., S.P.G., J.L., I.M., A.H.M., S.Z., M.H.);Department of Genetics, Faculty of Biology and Environment Protection, University of Silesia, PL-40-032 Katowice, Poland (D.G., M.K., M.M.);James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom (A.D., I.D.);Department of Agriculture, Fishery, and Forestry, Agri-Science Queensland, Hermitage Research Facility, Warwick, Queensland 4370, Australia (J.F.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Krakow, Poland (A.J.);Nordic Genetic Resource Center, SE-230 53 Alnarp, Sweden (U.L.);Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, and Institute of Experimental Botany, Academy of Sciences of the Czech Republic, CZ-783 71 Olomouc, Czech Republic (J.O.); and Department of Plant Science and Landscape Architecture,University of Maryland, College Park, Maryland 20742 (B.S.)
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Eldridge K, Wu R, Martens JK, McMahon TB. Gas-Phase Solvation of Protonated Amino Acids by Methanol. J Phys Chem A 2014; 118:11629-40. [DOI: 10.1021/jp5086729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kris Eldridge
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Jonathan K. Martens
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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37
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Structure-based inhibition of protein-protein interactions. Eur J Med Chem 2014; 94:480-8. [PMID: 25253637 DOI: 10.1016/j.ejmech.2014.09.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 09/03/2014] [Accepted: 09/12/2014] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) are emerging as attractive targets for drug design because of their central role in directing normal and aberrant cellular functions. These interactions were once considered "undruggable" because their large and dynamic interfaces make small molecule inhibitor design challenging. However, landmark advances in computational analysis, fragment screening and molecular design have enabled development of a host of promising strategies to address the fundamental molecular recognition challenge. An attractive approach for targeting PPIs involves mimicry of protein domains that are critical for complex formation. This approach recognizes that protein subdomains or protein secondary structures are often present at interfaces and serve as organized scaffolds for the presentation of side chain groups that engage the partner protein(s). Design of protein domain mimetics is in principle rather straightforward but is enabled by a host of computational strategies that provide predictions of important residues that should be mimicked. Herein we describe a workflow proceeding from interaction network analysis, to modeling a complex structure, to identifying a high-affinity sub-structure, to developing interaction inhibitors. We apply the design procedure to peptidomimetic inhibitors of Ras-mediated signaling.
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38
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Fang X, Yuan X, Song YB, Wang JD, Lin MJ. Cooperative lone pair–π and coordination interactions in naphthalene diimide coordination networks. CrystEngComm 2014. [DOI: 10.1039/c4ce01233j] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Wu YJ, Zheng QC, Zhang JL, Chu WT, Cui YL, Wang Y, Zhang HX. Fosfomycin induced structural change in fosfomycin resistance kinases FomA: molecular dynamics and molecular docking studies. J Mol Model 2014; 20:2236. [PMID: 24770549 DOI: 10.1007/s00894-014-2236-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/10/2014] [Indexed: 10/25/2022]
Abstract
Fosfomycin resistance kinases FomA, one of the key enzymes responsible for bacterial resistances to fosfomycin, has gained much attention recently due to the raising public concern for multi-drug resistant bacteria. Using molecular docking followed by molecular dynamics simulations, our group illustrated the process of fosfomycin induced conformational change of FomA. The detailed roles of the catalytic residues (Lys18, His58 and Thr210) during the formation of the enzyme-substrate complex were shown in our research. The organization functions of Gly53, Gly54, Ile61 and Leu75 were also highlighted. Furthermore, the cation-π interaction between Arg62 and Trp207 was observed and speculated to play an auxiliary role in the conformation change process of the enzyme. This detailed molecular level illustration of the formation of FomA·ATP·Mg·Fosfomycin complex could provide insight for both anti-biotic discovery and improvement of fosfomycin in the future.
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Affiliation(s)
- Yun-Jian Wu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, Jilin, P R China
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40
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del Pozo-Yauner L, Wall JS, González Andrade M, Sánchez-López R, Rodríguez-Ambriz SL, Pérez Carreón JI, Ochoa-Leyva A, Fernández-Velasco DA. The N-terminal strand modulates immunoglobulin light chain fibrillogenesis. Biochem Biophys Res Commun 2013; 443:495-9. [PMID: 24321098 DOI: 10.1016/j.bbrc.2013.11.123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/27/2013] [Indexed: 12/20/2022]
Abstract
It has been suggested that the N-terminal strand of the light chain variable domain (V(L)) protects the molecule from aggregation by hindering spurious intermolecular contacts. We evaluated the impact of mutations in the N-terminal strand on the thermodynamic stability and kinetic of fibrillogenesis of the V(L) protein 6aJL2. Mutations in this strand destabilized the protein in a position-dependent manner, accelerating the fibrillogenesis by shortening the lag time; an effect that correlated with the extent of destabilization. In contrast, the effect on the kinetics of fibril elongation, as assessed in seeding experiments was of different nature, as it was not directly dependant on the degree of destabilization. This finding suggests different factors drive the nucleation-dependent and elongation phases of light chain fibrillogenesis. Finally, taking advantage of the dependence of the Trp fluorescence upon environment, four single Trp substitutions were made in the N-terminal strand, and changes in solvent exposure during aggregation were evaluated by acrylamide-quenching. The results suggest that the N-terminal strand is buried in the fibrillar state of 6aJL2 protein. This finding suggest a possible explanation for the modulating effect exerted by the mutations in this strand on the aggregation behavior of 6aJL2 protein.
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Affiliation(s)
- Luis del Pozo-Yauner
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico.
| | - Jonathan S Wall
- Departments of Radiology and Medicine, The University of Tennessee Medical Center, 1924 Alcoa Highway, Knoxville, TN, USA
| | - Martín González Andrade
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico
| | - Rosana Sánchez-López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa Cuernavaca, Morelos C.P. 62210, Mexico
| | - Sandra L Rodríguez-Ambriz
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle CEPROBI No. 8, Col. San Isidro, Yautepec, Morelos C.P. 62731, Mexico
| | - Julio I Pérez Carreón
- Instituto Nacional de Medicina Genómica, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, México, D.F. C.P. 14610, Mexico
| | - Adrián Ochoa-Leyva
- Unidad de Genómica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica (INMEGEN), Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan México, D.F. C.P. 14610, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Interior, Ciudad Universitaria, Av. Universidad 3000, México, D.F. C.P. 04510, Mexico
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González-Andrade M, Becerril-Luján B, Sánchez-López R, Ceceña-Álvarez H, Pérez-Carreón JI, Ortiz E, Fernández-Velasco DA, del Pozo-Yauner L. Mutational and genetic determinants of λ6 light chain amyloidogenesis. FEBS J 2013; 280:6173-83. [DOI: 10.1111/febs.12538] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Martín González-Andrade
- Consorcio Bioquímica de Enfermedades Crónicas; Instituto Nacional de Medicina Genómica (INMEGEN); México
| | | | - Rosana Sánchez-López
- Instituto de Biotecnología; Universidad Nacional Autónoma de México; Cuernavaca México
| | - Héctor Ceceña-Álvarez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas; Departamento de Bioquímica; Facultad de Medicina; Universidad Nacional Autónoma de México; México
| | - Julio I. Pérez-Carreón
- Consorcio Bioquímica de Enfermedades Crónicas; Instituto Nacional de Medicina Genómica (INMEGEN); México
| | - Ernesto Ortiz
- Instituto de Biotecnología; Universidad Nacional Autónoma de México; Cuernavaca México
| | - D. Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas; Departamento de Bioquímica; Facultad de Medicina; Universidad Nacional Autónoma de México; México
| | - Luis del Pozo-Yauner
- Consorcio Bioquímica de Enfermedades Crónicas; Instituto Nacional de Medicina Genómica (INMEGEN); México
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42
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Strong lone pair⋯π interactions between amine and tri-s-triazine derivatives: A theoretical investigation. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 731] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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44
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Bhardwaj A, Mahanta P, Ramakumar S, Ghosh A, Leelavathi S, Reddy VS. Emerging role of N- and C-terminal interactions in stabilizing (β/α)8 fold with special emphasis on Family 10 xylanases. Comput Struct Biotechnol J 2012; 2:e201209014. [PMID: 24688655 PMCID: PMC3962208 DOI: 10.5936/csbj.201209014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/24/2012] [Accepted: 10/24/2012] [Indexed: 11/22/2022] Open
Abstract
Xylanases belong to an important class of industrial enzymes. Various xylanases have been purified and characterized from a plethora of organisms including bacteria, marine algae, plants, protozoans, insects, snails and crustaceans. Depending on the source, the enzymatic activity of xylanases varies considerably under various physico-chemical conditions such as temperature, pH, high salt and in the presence of proteases. Family 10 or glycosyl hydrolase 10 (GH10) xylanases are one of the well characterized and thoroughly studied classes of industrial enzymes. The TIM-barrel fold structure which is ubiquitous in nature is one of the characteristics of family 10 xylanases. Family 10 xylanases have been used as a “model system” due to their TIM-barrel fold to dissect and understand protein stability under various conditions. A better understanding of structure-stability-function relationships of family 10 xylanases allows one to apply these governing molecular rules to engineer other TIM-barrel fold proteins to improve their stability and retain function(s) under adverse conditions. In this review, we discuss the implications of N-and C-terminal interactions, observed in family 10 xylanases on protein stability under extreme conditions. The role of metal binding and aromatic clusters in protein stability is also discussed. Studying and understanding family 10 xylanase structure and function, can contribute to our protein engineering knowledge.
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Affiliation(s)
- Amit Bhardwaj
- Molecular Pathology Lab, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149, Trieste, Italy
| | - Pranjal Mahanta
- Department of Physics, Indian Institute of Science, Bangalore, India
| | | | - Amit Ghosh
- National Institute of Cholera and Enteric diseases, Kolkata, India
| | - Sadhu Leelavathi
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
| | - Vanga Siva Reddy
- Plant Transformation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi - 110067, India
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45
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Chakravarty S, Sheng ZZ, Iverson B, Moore B. “η6”-Type anion-π in biomolecular recognition. FEBS Lett 2012; 586:4180-5. [DOI: 10.1016/j.febslet.2012.10.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 09/24/2012] [Accepted: 10/01/2012] [Indexed: 01/10/2023]
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46
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Duan M, Song B, Shi G, Li H, Ji G, Hu J, Chen X, Fang H. Cation⊗3π: Cooperative Interaction of a Cation and Three Benzenes with an Anomalous Order in Binding Energy. J Am Chem Soc 2012; 134:12104-9. [DOI: 10.1021/ja302918t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Manyi Duan
- School of Physics Science and
Technology, Sichuan University, Chengdu
610064, P.R. China
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
| | - Bo Song
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
| | - Guosheng Shi
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
| | - Haikuo Li
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
| | - Guangfu Ji
- School of Physics Science and
Technology, Sichuan University, Chengdu
610064, P.R. China
- National
Key Laboratory of Shock
Wave and Detonation Physics, Institute of Fluid Physics, China Academy of Engineering Physics, Mianyang 621900,
P.R. China
| | - Jun Hu
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
| | - Xiangrong Chen
- School of Physics Science and
Technology, Sichuan University, Chengdu
610064, P.R. China
| | - Haiping Fang
- Division
of Interfacial Water
and Laboratory of Physical Biology, Shanghai Institute of Applied
Physics, Chinese Academy of Sciences, Shanghai
201800, P.R. China
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Pandey R, Mukhopadhyay S, Ramasesha S, Das PK, Zyss J. Influence of anion on the quadratic nonlinearity and depolarization ratios of scattered second harmonic light from cation- π complexes. J Chem Phys 2012; 136:194504. [DOI: 10.1063/1.4716020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Li Q, Li R, Liu X, Cheng J, Li W. Ab initiostudy of synergetic effects of two strong interactions of cation–π interaction and lithium bond in M+ ··· phenyl lithium ··· N (M = Li, Na, K; N = H2O and NH3) complex. Mol Phys 2012. [DOI: 10.1080/00268976.2012.655793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Yang T, An JJ, Wang X, Wu DY, Chen W, Fossey JS. A theoretical exploration of unexpected amine⋯π interactions. Phys Chem Chem Phys 2012; 14:10747-53. [DOI: 10.1039/c2cp00025c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Dołęga A, Marynowski W, Baranowska K, Śmiechowski M, Stangret J. Intramolecular Interactions in Crystals of Tris(2,6-diisopropylphenoxy)silanethiol and Its Sodium Salts. Inorg Chem 2011; 51:836-43. [DOI: 10.1021/ic2013073] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Dołęga
- Department
of Inorganic Chemistry and ‡Department of Physical Chemistry, Gdansk University of Technology, Chemical Faculty,
ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Wojciech Marynowski
- Department
of Inorganic Chemistry and ‡Department of Physical Chemistry, Gdansk University of Technology, Chemical Faculty,
ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Katarzyna Baranowska
- Department
of Inorganic Chemistry and ‡Department of Physical Chemistry, Gdansk University of Technology, Chemical Faculty,
ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department
of Inorganic Chemistry and ‡Department of Physical Chemistry, Gdansk University of Technology, Chemical Faculty,
ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Janusz Stangret
- Department
of Inorganic Chemistry and ‡Department of Physical Chemistry, Gdansk University of Technology, Chemical Faculty,
ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
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