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Visibelli A, Finetti R, Niccolai N, Spiga O, Santucci A. Molecular Origins of the Mendelian Rare Diseases Reviewed by Orpha.net: A Structural Bioinformatics Investigation. Int J Mol Sci 2024; 25:6953. [PMID: 39000061 PMCID: PMC11241713 DOI: 10.3390/ijms25136953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024] Open
Abstract
The study of rare diseases is important not only for the individuals affected but also for the advancement of medical knowledge and a deeper understanding of human biology and genetics. The wide repertoire of structural information now available from reliable and accurate prediction methods provides the opportunity to investigate the molecular origins of most of the rare diseases reviewed in the Orpha.net database. Thus, it has been possible to analyze the topology of the pathogenic missense variants found in the 2515 proteins involved in Mendelian rare diseases (MRDs), which form the database for our structural bioinformatics study. The amino acid substitutions responsible for MRDs showed different mutation site distributions at different three-dimensional protein depths. We then highlighted the depth-dependent effects of pathogenic variants for the 20,061 pathogenic variants that are present in our database. The results of this structural bioinformatics investigation are relevant, as they provide additional clues to mitigate the damage caused by MRD.
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Affiliation(s)
- Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
| | - Rebecca Finetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Le Ricerche del BarLume Free Association, Ville di Corsano, 53014 Monteroni d’Arbia, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Industry 4.0 Competence Center ARTES 4.0, Viale Rinaldo Piaggio, 56025 Pontedera, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; (A.V.); (R.F.); (O.S.); (A.S.)
- Industry 4.0 Competence Center ARTES 4.0, Viale Rinaldo Piaggio, 56025 Pontedera, Italy
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2
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Rerick MT, Chen J, Weber SG. Electroosmotic Perfusion, External Microdialysis: Simulation and Experiment. ACS Chem Neurosci 2023. [PMID: 37379416 PMCID: PMC10360060 DOI: 10.1021/acschemneuro.3c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023] Open
Abstract
Information about the rates of hydrolysis of neuropeptides by extracellular peptidases can lead to a quantitative understanding of how the steady-state and transient concentrations of neuropeptides are controlled. We have created a small microfluidic device that electroosmotically infuses peptides into, through, and out of the tissue to a microdialysis probe outside the head. The device is created by two-photon polymerization (Nanoscribe). Inferring quantitative estimates of a rate process from the change in concentration of a substrate that has passed through tissue is challenging for two reasons. One is that diffusion is significant, so there is a distribution of peptide substrate residence times in the tissue. This affects the product yield. The other is that there are multiple paths taken by the substrate as it passes through tissue, so there is a distribution of residence times and thus reaction times. Simulation of the process is essential. The simulations presented here imply that a range of first order rate constants of more than 3 orders of magnitude is measurable and that 5-10 min is required to reach a steady state value of product concentration following initiation of substrate infusion. Experiments using a peptidase-resistant d-amino acid pentapeptide, yaGfl, agree with simulations.
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Affiliation(s)
- Michael T Rerick
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jun Chen
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stephen G Weber
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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3
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Heparin-Induced Changes of Vascular Endothelial Growth Factor (VEGF 165) Structure. Biomolecules 2023; 13:biom13010098. [PMID: 36671483 PMCID: PMC9856036 DOI: 10.3390/biom13010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Vascular endothelial growth factor-A (VEGF-A), a secreted homodimeric glycoprotein, is a critical regulator of angiogenesis in normal and pathological states. The binding of heparin (HE) to VEGF165 (the major form of VEGF-A) modulates the angiogenesis-related cascade, but the mechanism of the observed changes at the structural level is still insufficiently explored. In the present study, we examined the effect of HE on the structural and physicochemical properties of recombinant human VEGF165 (rhVEGF165). The HE binding results in an increase of hydrophobic surface exposure in rhVEGF165 without changes in its secondary structure. Differential scanning calorimetry measurements for intact and HE-bound rhVEGF165 reveals the absence of any pronounced thermally induced transitions in the protein in the temperature range from 20 to 100 °C. The apolar area increase during the heparin binding explains the pronounced HE-induced oligomerization/aggregation of rhVEGF165, as studied by chemical glutaraldehyde cross-linking and dynamic light scattering. Molecular modeling and docking techniques were used to model the full structure of dimeric VEGF165 and to reveal putative molecular mechanisms underlying the function of the VEGF165/HE system. In general, the results obtained can be a basis for explaining the modulating effect of HE on the biological activity of VEGF-A.
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4
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Weeder BR, Wood MA, Li E, Nellore A, Thompson RF. pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. Bioinformatics 2021; 37:3723-3733. [PMID: 34478497 DOI: 10.1093/bioinformatics/btab628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/21/2021] [Accepted: 08/31/2021] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Proteasomal cleavage is a key component in protein turnover, as well as antigen processing and presentation. Although tools for proteasomal cleavage prediction are available, they vary widely in their performance, options, and availability. RESULTS Herein we present pepsickle, an open-source tool for proteasomal cleavage prediction with better in vivo prediction performance (AUC) and computational speed than current models available in the field and with the ability to predict sites based on both constitutive and immunoproteasome profiles. Post-hoc filtering of predicted patient neoepitopes using pepsickle significantly enriches for immune-responsive epitopes and may improve current epitope prediction and vaccine development pipelines. AVAILABILITY pepsickle is open source and available at https://github.com/pdxgx/pepsickle. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Benjamin R Weeder
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | | | - Ellysia Li
- Pacific University, Forest Grove, OR, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA.,Department of Surgery, Oregon Health & Science University, Portland, Oregon, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, Oregon, USA.,Department of Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA.,Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA.,Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, Oregon, USA
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5
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Structural Analysis of the Menangle Virus P Protein Reveals a Soft Boundary between Ordered and Disordered Regions. Viruses 2021; 13:v13091737. [PMID: 34578318 PMCID: PMC8472933 DOI: 10.3390/v13091737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022] Open
Abstract
The paramyxoviral phosphoprotein (P protein) is the non-catalytic subunit of the viral RNA polymerase, and coordinates many of the molecular interactions required for RNA synthesis. All paramyxoviral P proteins oligomerize via a centrally located coiled-coil that is connected to a downstream binding domain by a dynamic linker. The C-terminal region of the P protein coordinates interactions between the catalytic subunit of the polymerase, and the viral nucleocapsid housing the genomic RNA. The inherent flexibility of the linker is believed to facilitate polymerase translocation. Here we report biophysical and structural characterization of the C-terminal region of the P protein from Menangle virus (MenV), a bat-borne paramyxovirus with zoonotic potential. The MenV P protein is tetrameric but can dissociate into dimers at sub-micromolar protein concentrations. The linker is globally disordered and can be modeled effectively as a worm-like chain. However, NMR analysis suggests very weak local preferences for alpha-helical and extended beta conformation exist within the linker. At the interface between the disordered linker and the structured C-terminal binding domain, a gradual disorder-to-order transition occurs, with X-ray crystallographic analysis revealing a dynamic interfacial structure that wraps the surface of the binding domain.
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6
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Teng KW, Tsai ST, Hattori T, Fedele C, Koide A, Yang C, Hou X, Zhang Y, Neel BG, O'Bryan JP, Koide S. Selective and noncovalent targeting of RAS mutants for inhibition and degradation. Nat Commun 2021; 12:2656. [PMID: 33976200 PMCID: PMC8113534 DOI: 10.1038/s41467-021-22969-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Activating mutants of RAS are commonly found in human cancers, but to date selective targeting of RAS in the clinic has been limited to KRAS(G12C) through covalent inhibitors. Here, we report a monobody, termed 12VC1, that recognizes the active state of both KRAS(G12V) and KRAS(G12C) up to 400-times more tightly than wild-type KRAS. The crystal structures reveal that 12VC1 recognizes the mutations through a shallow pocket, and 12VC1 competes against RAS-effector interaction. When expressed intracellularly, 12VC1 potently inhibits ERK activation and the proliferation of RAS-driven cancer cell lines in vitro and in mouse xenograft models. 12VC1 fused to VHL selectively degrades the KRAS mutants and provides more extended suppression of mutant RAS activity than inhibition by 12VC1 alone. These results demonstrate the feasibility of selective targeting and degradation of KRAS mutants in the active state with noncovalent reagents and provide a starting point for designing noncovalent therapeutics against oncogenic RAS mutants.
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Affiliation(s)
- Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Steven T Tsai
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Takamitsu Hattori
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Carmine Fedele
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Chao Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Xuben Hou
- Department of Chemistry, New York University, New York, NY, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, USA
| | - Benjamin G Neel
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA.
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7
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The Highly Conservative Cysteine of Oncomodulin as a Feasible Redox Sensor. Biomolecules 2021; 11:biom11010066. [PMID: 33419032 PMCID: PMC7825312 DOI: 10.3390/biom11010066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/01/2021] [Accepted: 01/03/2021] [Indexed: 11/17/2022] Open
Abstract
Oncomodulin (Ocm), or parvalbumin β, is an 11-12 kDa Ca2+-binding protein found inside and outside of vertebrate cells, which regulates numerous processes via poorly understood mechanisms. Ocm consists of two active Ca2+-specific domains of the EF-hand type ("helix-loop-helix" motif), covered by an EF-hand domain with inactive EF-hand loop, which contains a highly conservative cysteine with unknown function. In this study, we have explored peculiarities of the microenvironment of the conservative Cys18 of recombinant rat Ocm (rWT Ocm), redox properties of this residue, and structural/functional sensitivity of rWT Ocm to the homologous C18S substitution. We have found that pKa
of the Cys18 thiol lays beyond the physiological pH range. The measurement of redox dependence of rWT Ocm thiol-disulfide equilibrium (glutathione redox pair) showed that redox potential of Cys18 for the metal-free and Ca2+-loaded protein is of -168 mV and -176 mV, respectively. Therefore, the conservative thiol of rWT Ocm is prone to disulfide dimerization under physiological redox conditions. The C18S substitution drastically reduces α-helices content of the metal-free and Mg2+-bound Ocm, increases solvent accessibility of its hydrophobic residues, eliminates the cooperative thermal transition in the apo-protein, suppresses Ca2+/Mg2+ affinity of the EF site, and accelerates Ca2+ dissociation from Ocm. The distinct structural and functional consequences of the minor structural modification of Cys18 indicate its possible redox sensory function. Since some other EF-hand proteins also contain a conservative redox-sensitive cysteine located in an inactive EF-hand loop, it is reasonable to suggest that in the course of evolution, some of the EF-hands attained redox sensitivity at the expense of the loss of their Ca2+ affinity.
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8
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N-methylacetamide is a solvent better than water for amino acid side chains: A rationalization grounded in the solvent-excluded volume effect. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Permyakov SE, Yundina EN, Kazakov AS, Permyakova ME, Uversky VN, Permyakov EA. Mouse S100G protein exhibits properties characteristic of a calcium sensor. Cell Calcium 2020; 87:102185. [PMID: 32114281 DOI: 10.1016/j.ceca.2020.102185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 01/09/2023]
Abstract
Bovine S100 G (calbindin D9k, small Ca2+-binding protein of the EF-hand superfamily) is considered as a calcium buffer protein; i.e., the binding of Ca2+ practically does not change its general conformation. A set of experimental approaches has been used to study structural properties of apo- and Ca2+-loaded forms of mouse S100 G (81.4% identity in amino acid sequence with bovine S100 G). This analysis revealed that, in contrast to bovine S100 G, the removal of calcium ions increases α-helices content of mouse S100 G protein and enhances its accessibility to digestion by α-chymotrypsin. Furthermore, mouse apo-S100 G is characterized by a decreased surface hydrophobicity and reduced tendency for oligomerization. Such behavior is typical of calcium sensor proteins. Apo-state of mouse S100 G still has rather compact structure, which can be cooperatively unfolded by temperature and GdnHCl. Computational analysis of amino acid sequences of S100 G proteins shows that these proteins could be in a disordered state upon a removal of the bound calcium ions. The experimental data show that, although mouse apo-S100 G is flexible compared to the Ca2+-loaded state, the apo-form is not completely disordered and preserves some cooperatively meting structure. The origin of the unexpectedly high stability of mouse S100 G can be rationalized by an exceptionally strong association of its N- and C-terminal parts containing the EF-hands I and II, respectively.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Elena N Yundina
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Permyakov SE, Denesyuk AI, Denessiouk KA, Permyakova ME, Kazakov AS, Ismailov RG, Rastrygina VA, Sokolov AS, Permyakov EA. Monomeric state of S100P protein: Experimental and molecular dynamics study. Cell Calcium 2019; 80:152-159. [PMID: 31103949 DOI: 10.1016/j.ceca.2019.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/13/2019] [Accepted: 04/27/2019] [Indexed: 02/05/2023]
Abstract
S100 proteins constitute a large subfamily of the EF-hand superfamily of calcium binding proteins. They possess one classical EF-hand Ca2+-binding domain and an atypical EF-hand domain. Most of the S100 proteins form stable symmetric homodimers. An analysis of literature data on S100 proteins showed that their physiological concentrations could be much lower than dissociation constants of their dimeric forms. It means that just monomeric forms of these proteins are important for their functioning. In the present work, thermal denaturation of apo-S100P protein monitored by intrinsic tyrosine fluorescence has been studied at various protein concentrations within the region from 0.04-10 μM. A transition from the dimeric to monomeric form results in a decrease in protein thermal stability shifting the mid-transition temperature from 85 to 75 °C. Monomeric S100P immobilized on the surface of a sensor chip of a surface plasmon resonance instrument forms calcium dependent 1 to 1 complexes with human interleukin-11 (equilibrium dissociation constant 1.2 nM). In contrast, immobilized interleukin-11 binds two molecules of dimeric S100P with dissociation constants of 32 nM and 288 nM. Since effective dissociation constant of dimeric S100P protein is very low (0.5 μM as evaluated from our data) the sensitivity of the existing physical methods does not allow carrying out a detailed study of S100P monomer properties. For this reason, we have used molecular dynamics methods to evaluate structural changes in S100P upon its transition from the dimeric to monomeric state. 80-ns molecular dynamics simulations of kinetics of formation of S100P, S100B and S100A11 monomers from the corresponding dimers have been carried out. It was found that during the transition from the homo-dimer to monomer form, the three S100 monomer structures undergo the following changes: (1) the helices in the four-helix bundles within each monomer rotate in order to shield the exposed non-polar residues; (2) almost all lost contacts at the dimer interface are substituted with equivalent and newly formed interactions inside each monomer, and new stabilizing interactions are formed; and (3) all monomers recreate functional hydrophobic cores. The results of the present study show that both dimeric and monomeric forms of S100 proteins can be functional.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia.
| | - Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland
| | - Konstantin A Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku 20520, Finland; Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku 20520, Finland
| | - Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia
| | - Alixey S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia
| | - Ramis G Ismailov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia
| | - Victoria A Rastrygina
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia
| | - Andrei S Sokolov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Pushchino, Moscow region 142290, Russia.
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Permyakova ME, Permyakov SE, Kazakov AS, Denesyuk AI, Denessiouk K, Uversky VN, Permyakov EA. Analyzing the structural and functional roles of residues from the 'black' and 'gray' clusters of human S100P protein. Cell Calcium 2019; 80:46-55. [PMID: 30953998 DOI: 10.1016/j.ceca.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
Two highly conserved structural motifs observed in members of the EF-hand family of calcium binding proteins. The motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif represents a cluster of three amino acids called cluster I ('black' cluster) and cluster II ('grey' cluster). Cluster I is more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II is noticeably less conserved and includes a mix of aromatic, hydrophobic, and polar amino acids of different sizes. In the human calcium binding S100 P protein, these 'black' and 'gray' clusters include residues F15, F71, and F74 and L33, L58, and K30, respectively. To evaluate the effects of these clusters on structure and functionality of human S100 P, we have performed Ala scanning. The resulting mutants were studied by a multiparametric approach that included circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probes. Spectrofluorimetric Ca2+-titration of wild type S100 P showed that S100 P dimer has 1-2 strong calcium binding sites (K1 = 4 × 106 M-1) and two cooperative low affinity (K2 = 4 × 104 M-1) binding sites. Similarly, the S100 P mutants possess two types of calcium binding sites. This analysis revealed that the alanine substitutions in the clusters I and II caused comparable changes in the S100 P functional properties. However, analysis of heat- or GuHCl-induced unfolding of these proteins showed that the alanine substitutions in the cluster I caused notably more pronounced decrease in the protein stability compared to the changes caused by alanine substitutions in the cluster II. Opposite to literature data, the F15 A substitution did not cause the S100 P dimer dissociation, indicating that F15 is not crucial for dimer stability. Overall, similar to parvalbumins, the S100 P cluster I is more important for protein conformational stability than the cluster II.
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Affiliation(s)
- Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia.
| | - Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia.
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
| | - Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland; Pharmaceutical Sciences Laboratory, Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow region, 142290, Russia
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Ravi Sharma, Thakur RC. Molecular Interactions of Pyridoxine Hydrochloride in Aqueous Mixed Solutions of D-Glucose, D-Fructose, and D-Lactose at Different Temperatures. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2019. [DOI: 10.1134/s0036024418130241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Vologzhannikova AA, Khorn PA, Kazakov AS, Permyakov EA, Uversky VN, Permyakov SE. Effects of his-tags on physical properties of parvalbumins. Cell Calcium 2019; 77:1-7. [DOI: 10.1016/j.ceca.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022]
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15
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Permyakov SE, Vologzhannikova AA, Khorn PA, Shevelyova MP, Kazakov AS, Emelyanenko VI, Denesyuk AI, Denessiouk K, Uversky VN, Permyakov EA. Comprehensive analysis of the roles of 'black' and 'gray' clusters in structure and function of rat β-parvalbumin. Cell Calcium 2018; 75:64-78. [PMID: 30176502 DOI: 10.1016/j.ceca.2018.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/26/2018] [Indexed: 01/05/2023]
Abstract
Recently we found two highly conserved structural motifs in the proteins of the EF-hand calcium binding protein family. These motifs provide a supporting scaffold for the Ca2+ binding loops and contribute to the hydrophobic core of the EF-hand domain. Each structural motif forms a cluster of three amino acids called cluster I ('black' cluster) and cluster II ('grey' cluster). Cluster I is much more conserved and mostly incorporates aromatic amino acids. In contrast, cluster II includes a mix of aromatic, hydrophobic, and polar amino acids. The 'black' and 'gray' clusters in rat β-parvalbumin consist of F48, A100, F103 and G61, L64, M87, respectively. In the present work, we sequentially substituted these amino acids residues by Ala, except Ala100, which was substituted by Val. Physical properties of the mutants were studied by circular dichroism, scanning calorimetry, dynamic light scattering, chemical crosslinking, and fluorescent probe methods. The Ca2+ and Mg2+ binding affinities of these mutants were evaluated by intrinsic fluorescence and equilibrium dialysis methods. In spite of a rather complicated pattern of contributions of separate amino acid residues of the 'black' and 'gray' clusters into maintenance of rat β-parvalbumin structural and functional status, the alanine substitutions in the cluster I cause noticeably more pronounced changes in various structural parameters of proteins, such as hydrodynamic radius of apo-form, thermal stability of Ca2+/Mg2+-loaded forms, and total energy of Ca2+ binding in comparison with the changes caused by amino acid substitutions in the cluster II. These findings were further supported by the outputs of computational analysis of the effects of these mutations on the intrinsic disorder predisposition of rat β-parvalbumin, which also indicated that local intrinsic disorder propensities and the overall levels of predicted disorder were strongly affected by mutations in the cluster I, whereas mutations in cluster II had less pronounced effects. These results demonstrate that amino acids of the cluster I provide more essential contribution to the maintenance of structuraland functional properties of the protein in comparison with the residues of the cluster II.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alisa A Vologzhannikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Polina A Khorn
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Marina P Shevelyova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Victor I Emelyanenko
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexander I Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland
| | - Konstantin Denessiouk
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Åbo Akademi University, Turku, 20520, Finland; Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, Turku, 20520, Finland
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Biomedical Engineering, Pushchino State Institute of Natural Sciences, Pushchino, Moscow Region, 142290, Russia
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In search for globally disordered apo-parvalbumins: Case of parvalbumin β-1 from coho salmon. Cell Calcium 2017; 67:53-64. [DOI: 10.1016/j.ceca.2017.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/08/2017] [Accepted: 08/31/2017] [Indexed: 11/22/2022]
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17
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Probing the cooperativity of Thermoplasma acidophilum proteasome core particle gating by NMR spectroscopy. Proc Natl Acad Sci U S A 2017; 114:E9846-E9854. [PMID: 29087330 DOI: 10.1073/pnas.1712297114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The 20S proteasome core particle (20S CP) plays an integral role in cellular homeostasis by degrading proteins no longer required for function. The process is, in part, controlled via gating residues localized to the ends of the heptameric barrel-like CP structure that occlude substrate entry pores, preventing unregulated degradation of substrates that might otherwise enter the proteasome. Previously, we showed that the N-terminal residues of the α-subunits of the CP from the archaeon Thermoplasma acidophilum are arranged such that, on average, two of the seven termini are localized inside the lumen of the proteasome, thereby plugging the entry pore and functioning as a gate. However, the mechanism of gating remains unclear. Using solution NMR and a labeling procedure in which a series of mixed proteasome rings are prepared such that the percentage of gate-containing subunits is varied, we address the energetics of gating and establish whether gating is a cooperative process involving the concerted action of residues from more than a single protomer. Our results establish that the intrinsic probability of a gate entering the lumen favors the in state by close to 20-fold, that entry of each gate is noncooperative, with the number of gates that can be accommodated inside the lumen a function of the substrate entry pore size and the bulkiness of the gating residues. Insight into the origin of the high affinity for the in state is obtained from spin-relaxation experiments. More generally, our approach provides an avenue for dissecting interactions of individual protomers in homo-oligomeric complexes.
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18
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Spencer RK, Hochbaum AI. X-ray Crystallographic Structure and Solution Behavior of an Antiparallel Coiled-Coil Hexamer Formed by de Novo Peptides. Biochemistry 2016; 55:3214-23. [DOI: 10.1021/acs.biochem.6b00201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
| | - Allon I. Hochbaum
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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Witmer JR, Wetherell BJ, Wagner BA, Du J, Cullen JJ, Buettner GR. Direct spectrophotometric measurement of supra-physiological levels of ascorbate in plasma. Redox Biol 2016; 8:298-304. [PMID: 26928133 PMCID: PMC4776628 DOI: 10.1016/j.redox.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 12/03/2022] Open
Abstract
Background Supra-physiological concentrations of ascorbate, vitamin C, in blood, greater than 1 mM, achieved through intravenous administration (IV), are being tested in clinical trials to treat human disease, e.g. cancer. These trials need information on the high levels of ascorbate achieved in blood upon IV administration of pharmacological ascorbate so appropriate clinical decisions can be made. Methods Here we demonstrate that in the complex matrix of human blood plasma supra-physiological levels of ascorbate can be quantified by direct UV spectroscopy with use of a microvolume UV–vis spectrophotometer. Results Direct quantitation of ascorbate in plasma in the range of 2.9 mM, lower limit of detection, up to at least 35 mM can be achieved without any sample processing, other than centrifugation. Conclusions This approach is rapid, economical, and can be used to quantify supraphysiological blood levels of ascorbate associated with the use of IV administration of pharmacological ascorbate to treat disease. A microvolume UV/Vis spectrometer can be used to determine supra-physiological levels of vitamin C in blood plasma directly. The effective molar extinction coefficient for the ascorbate monoanion in blood plasma is ε265=13,000 M−1 cm−1. With appropriate sample handling, oxidation of AscH− to DHA in the plasma is not a concern.
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Affiliation(s)
- Jordan R Witmer
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
| | - Bailey J Wetherell
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
| | - Brett A Wagner
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
| | - Juan Du
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
| | - Joseph J Cullen
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
| | - Garry R Buettner
- Department of Radiation Oncology, Free Radical and Radiation Biology Program, B180 Medical Laboratories, The University of Iowa, Iowa City, IA 52242-1181, United States.
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20
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Ambroggio EE, Caruso B, Villarreal MA, Raussens V, Fidelio GD. Reversing the peptide sequence impacts on molecular surface behaviour. Colloids Surf B Biointerfaces 2015; 139:25-32. [PMID: 26700230 DOI: 10.1016/j.colsurfb.2015.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/20/2015] [Accepted: 12/02/2015] [Indexed: 01/01/2023]
Abstract
The protein's primary structure has all the information for specific protein/peptide folding and, in many cases, can define specific amphiphilic regions along molecules that are important for interaction with membranes. In order to shed light on how peptide sequence is important for the surface properties of amphiphilic peptides, we designed three pairs of peptides with the following characteristics: (1) all molecules have the same hydrophobic residues; (2) the couples differ from each other in their hydrophilic amino acids: positively, negatively and non-charged; (3) each pair has the same residues (same global molecular hydrophobicity) but the primary structure is reversed in comparison to its partner (retro-isomer), giving a molecule with a hydrophilic N or C-terminus and a hydrophobic C or N-terminus. Using the Langmuir monolayer approach, we observed that sequence reversal has a central role in the lateral stability of peptide monolayers, in the ability of the molecules to partition into the air-water interface and in the rheological properties of peptide films, whereas the peptide's secondary structure, determined by ATR-FTIR, was the same for all peptides. Reversing the sequence also gives a differential way of peptide/lipid interaction when peptides are in the presence of POPC lipid bilayers. Our results show how sequence inversion confers a distinctive peptide surface behaviour and lipid interaction for molecules with a similar structure.
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Affiliation(s)
- Ernesto E Ambroggio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina.
| | - Benjamín Caruso
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
| | - Marcos A Villarreal
- Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC), CONICET, Departamento de Matemática y Física, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, Córdoba, Argentina
| | - Vincent Raussens
- Centre for Structural Biology and Bioinformatics, Laboratory for Structure and Function of Biological Membranes, Universit é Libre de Bruxelles, CP 206/02, Blvd. du Triomphe, B-1050 Brussels, Belgium
| | - Gerardo D Fidelio
- CIQUIBIC, CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
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21
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Ergometric studies of proteins: New insights into protein functionality in food systems. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.06.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Lomonosova AV, Ovchinnikova EV, Kazakov AS, Denesyuk AI, Sofin AD, Mikhailov RV, Ulitin AB, Mirzabekov TA, Permyakov EA, Permyakov SE. Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold. PLoS One 2015; 10:e0134906. [PMID: 26247602 PMCID: PMC4527664 DOI: 10.1371/journal.pone.0134906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023] Open
Abstract
Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.
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Affiliation(s)
- Anna V. Lomonosova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Elena V. Ovchinnikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexei S. Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Department of Biosciences, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander D. Sofin
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Roman V. Mikhailov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Andrei B. Ulitin
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Tajib A. Mirzabekov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Biomirex Inc., 304 Pleasant Street, Watertown, Massachusetts, 02472, United States of America
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- * E-mail:
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23
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Lafarga T, O’Connor P, Hayes M. In silico methods to identify meat-derived prolyl endopeptidase inhibitors. Food Chem 2015; 175:337-43. [DOI: 10.1016/j.foodchem.2014.11.150] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 11/05/2014] [Accepted: 11/27/2014] [Indexed: 12/13/2022]
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24
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Breydo L, Sales AE, Ferreira L, Fedotoff O, Shevelyova MP, Permyakov SE, Kroeck KG, Permyakov EA, Zaslavsky BY, Uversky VN. Effects of osmolytes on protein-solvent interactions in crowded environment: Analyzing the effect of TMAO on proteins in crowded solutions. Arch Biochem Biophys 2015; 570:66-74. [PMID: 25712220 DOI: 10.1016/j.abb.2015.02.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 11/20/2022]
Abstract
We analyzed the effect of a natural osmolyte, trimethylamine N-oxide (TMAO), on structural properties and conformational stabilities of several proteins under macromolecular crowding conditions by a set of biophysical techniques. We also used the solvent interaction analysis method to look at the peculiarities of the TMAO-protein interactions under crowded conditions. To this end, we analyzed the partitioning of these proteins in TMAO-free and TMAO-containing aqueous two-phase systems (ATPSs). These ATPSs had the same polymer composition of 6.0 wt.% PEG-8000 and 12.0 wt.% dextran-75, and same ionic composition of 0.01 M K/NaPB, pH 7.4. These analyses revealed that there is no direct interaction of TMAO with proteins, suggesting that the TMAO effects on the protein structure in crowded solutions occur via the effects of this osmolyte on solvent properties of aqueous media. The effects of TMAO on protein structure in the presence of polymers were rather complex and protein-specific. Curiously, our study revealed that in highly concentrated polymer solutions, TMAO does not always act to promote further protein folding.
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Affiliation(s)
- Leonid Breydo
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Amanda E Sales
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Department of Morphology and Animal Physiology, Federal Rural University of Pernambuco, 52171-900 Recife, PE, Brazil
| | - Luisa Ferreira
- Analiza, Inc., 3516 Superior Ave., Suite 4407B, Cleveland, USA
| | - Olga Fedotoff
- Analiza, Inc., 3516 Superior Ave., Suite 4407B, Cleveland, USA
| | - Marina P Shevelyova
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Sergei E Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Eugene A Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
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Fang Z, Zhang J, Liu B, Du G, Chen J. Insight into the substrate specificity of keratinase KerSMD from Stenotrophomonas maltophilia by site-directed mutagenesis studies in the S1 pocket. RSC Adv 2015. [DOI: 10.1039/c5ra12598g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mutagenesis at position 215 could shift the catalytic ability of keratinase KerSMD to hydrolyze synthetic peptides and macromolecular substrates. We improved keratinolytic activity of five mutants and obtained two thermophilic keratinases.
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Affiliation(s)
- Zhen Fang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Juan Zhang
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Baihong Liu
- Key Laboratory of Industrial Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology
- Jiangnan University
- Wuxi 214122
- China
- School of Biotechnology
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Mao J, Do NN, Scholz F, Reggie L, Mehler M, Lakatos A, Ong YS, Ullrich SJ, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C. Structural basis of the green-blue color switching in proteorhodopsin as determined by NMR spectroscopy. J Am Chem Soc 2014; 136:17578-90. [PMID: 25415762 DOI: 10.1021/ja5097946] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteorhodopsins (PRs) found in marine microbes are the most abundant retinal-based photoreceptors on this planet. PR variants show high levels of environmental adaptation, as their colors are tuned to the optimal wavelength of available light. The two major green and blue subfamilies can be interconverted through a L/Q point mutation at position 105. Here we reveal the structural basis behind this intriguing color-tuning effect. High-field solid-state NMR spectroscopy was used to visualize structural changes within green PR directly within the lipid bilayer upon introduction of the green-blue L105Q mutation. The observed effects are localized within the binding pocket and close to retinal carbons C14 and C15. Subsequently, magic-angle spinning (MAS) NMR spectroscopy with sensitivity enhancement by dynamic nuclear polarization (DNP) was applied to determine precisely the retinal structure around C14-C15. Upon mutation, a significantly stretched C14-C15 bond, deshielding of C15, and a slight alteration of the retinal chain's out-of-plane twist was observed. The L105Q blue switch therefore acts locally on the retinal itself and induces a conjugation defect between the isomerization region and the imine linkage. Consequently, the S0-S1 energy gap increases, resulting in the observed blue shift. The distortion of the chromophore structure also offers an explanation for the elongated primary reaction detected by pump-probe spectroscopy, while chemical shift perturbations within the protein can be linked to the elongation of late-photocycle intermediates studied by flash photolysis. Besides resolving a long-standing problem, this study also demonstrates that the combination of data obtained from high-field and DNP-enhanced MAS NMR spectroscopy together with time-resolved optical spectroscopy enables powerful synergies for in-depth functional studies of membrane proteins.
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Affiliation(s)
- Jiafei Mao
- Institute of Biophysical Chemistry and Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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Dias CL, Chan HS. Pressure-Dependent Properties of Elementary Hydrophobic Interactions: Ramifications for Activation Properties of Protein Folding. J Phys Chem B 2014; 118:7488-7509. [DOI: 10.1021/jp501935f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Cristiano L. Dias
- Department
of Physics, New Jersey Institute of Technology, University Heights, Tiernan Hall, Room 463, Newark, New Jersey 07102, United States
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
| | - Hue Sun Chan
- Departments
of Biochemistry, Molecular Genetics, and Physics, University of Toronto, 1 King’s College Circle, Toronto, Ontario Canada M5S 1A8
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28
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Medvedev NN, Voloshin VP, Kim AV, Anikeenko AV, Geiger A. Culation of partial molar volume and its components for molecular dynamics models of dilute solutions. J STRUCT CHEM+ 2014. [DOI: 10.1134/s0022476613080088] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Engineering Hydrogenases for H2 Production: Bolts and Goals. MICROBIAL BIOENERGY: HYDROGEN PRODUCTION 2014. [DOI: 10.1007/978-94-017-8554-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Nemashkalova EL, Kazakov AS, Khasanova LM, Permyakov EA, Permyakov SE. Structural characterization of more potent alternatives to HAMLET, a tumoricidal complex of α-lactalbumin and oleic acid. Biochemistry 2013; 52:6286-99. [PMID: 23947814 DOI: 10.1021/bi400643s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HAMLET is a complex of human α-lactalbumin (hLA) with oleic acid (OA) that kills various tumor cells and strains of Streptococcus pneumoniae. More potent protein-OA complexes were previously reported for bovine α-lactalbumin (bLA) and β-lactoglobulin (bLG), and pike parvalbumin (pPA), and here we explore their structural features. The concentration dependencies of the tryptophan fluorescence of hLA, bLA, and bLG complexes with OA reveal their disintegration at protein concentrations below the micromolar level. Chemical cross-linking experiments provide evidence that association with OA shifts the distribution of oligomeric forms of hLA, bLA, bLG, and pPA toward higher-order oligomers. This effect is confirmed for bLA and bLG using the dynamic light scattering method, while pPA is shown to associate with OA vesicles. Like hLA binding, OA binding increases the affinity of bLG for small unilamellar dipalmitoylphosphatidylcholine vesicles, while pPA efficiently binds to the vesicles irrespective of OA binding. The association of OA with bLG and pPA increases their α-helix and cross-β-sheet content and resistance to enzymatic proteolysis, which is indicative of OA-induced protein structuring. The lack of excess heat sorption during melting of bLG and pPA in complex with OA and the presence of a cooperative thermal transition at the level of their secondary structure suggest that the OA-bound forms of bLG and pPA lack a fixed tertiary structure but exhibit a continuous thermal transition. Overall, despite marked differences, the HAMLET-like complexes that were studied exhibit a common feature: a tendency toward protein oligomerization. Because OA-induced oligomerization has been reported for other proteins, this phenomenon is inherent to many proteins.
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Affiliation(s)
- Ekaterina L Nemashkalova
- Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region 142290, Russia
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Permyakov SE, Vologzhannikova AA, Emelyanenko VI, Knyazeva EL, Kazakov AS, Lapteva YS, Permyakova ME, Zhadan AP, Permyakov EA. The impact of alpha-N-acetylation on structural and functional status of parvalbumin. Cell Calcium 2012; 52:366-76. [DOI: 10.1016/j.ceca.2012.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 05/30/2012] [Accepted: 06/01/2012] [Indexed: 01/09/2023]
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Cloning, expression, purification, and biochemical characterisation of the FIC motif containing protein of Mycobacterium tuberculosis. Protein Expr Purif 2012; 86:58-67. [PMID: 22982230 DOI: 10.1016/j.pep.2012.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 01/01/2023]
Abstract
The role of FIC (Filamentation induced by cAMP)(2) domain containing proteins in the regulation of many vital pathways, mostly through the transfer of NMPs from NTPs to specific target proteins (NMPylation), in microorganisms, higher eukaryotes, and plants is emerging. The identity and function of FIC domain containing protein of the human pathogen, Mycobacterium tuberculosis, remains unknown. In this regard, M. tuberculosis fic gene (Mtfic) was cloned, overexpressed, and purified to homogeneity for its biochemical characterisation. It has the characteristic FIC motif, HPFREGNGRSTR (HPFxxGNGRxxR), spanning 144th to 155th residue. Neither the His-tagged nor the GST-tagged MtFic protein, overexpressed in Escherichia coli, nor expression of Mtfic in Mycobacterium smegmatis, yielded the protein in the soluble fraction. However, the maltose binding protein (MBP) tagged MtFic (MBP-MtFic) could be obtained partly in the soluble fraction. The cloned, overexpressed, and purified recombinant MBP-MtFic showed conversion of ATP, GTP, CTP, and UTP into AMP, GMP, CMP, and UMP, respectively. Sequence alignment with several FIC motif containing proteins, complemented with homology modeling on the FIC motif containing protein, VbhT of Bartonella schoenbuchensis as the template, showed conservation and interaction of residues constituting the FIC domain. Site-specific mutagenesis of the His144, or Glu148, or Asn150 of the FIC motif, or of Arg87 residue that constitutes the FIC domain, or complete deletion of the FIC motif, abolished the NTP to NMP conversion activity. The design of NMP formation assay using the recombinant, soluble MtFic would enable identification of its target substrate for NMPylation.
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Arumugam M, Ajitkumar P. Histidine 117 in the His-Gly-Ser-Asp motif is Required for the Biochemical Activities of Nucleoside Diphosphate Kinase of Mycobacterium smegmatis. Open Biochem J 2012; 6:71-7. [PMID: 22888372 PMCID: PMC3414718 DOI: 10.2174/1874091x01206010071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 04/16/2012] [Accepted: 04/19/2012] [Indexed: 11/28/2022] Open
Abstract
Nucleoside diphosphate kinase (NDK), which is widely conserved in both prokaryotes and eukaryotes, maintains a balanced pool of nucleotide triphosphates and their deoxy derivatives. NDKs from bacterial and other systems contain the conserved HGSD motif, where the His residue is required for the biochemical activities, namely the NTPase (AT-Pase and GTPase), NTP synthesising, and autophosphorylation activities of the enzyme. Amino acid sequence homology comparison of the NDK of Mycobacterium smegmatis (MsmNDK) with the NDKs of other bacterial genera showed the presence of H117GSD motif. While the recombinant wild type MsmNDK showed the NTPase, NTP synthesising, and autophosphorylation activities, the H117Q mutation abolished the biochemical activities of the recombinant MsmNDK-H117Q mutant protein in vitro. These observations demonstrate that the H117 residue in the HGSD motif is required for the biochemical activities of MsmNDK.
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Affiliation(s)
- Muthu Arumugam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
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34
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Hutt M, Kulschewski T, Pleiss J. Molecular modelling of the mass density of single proteins. J Biomol Struct Dyn 2012; 30:318-27. [DOI: 10.1080/07391102.2012.680031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Hedwig GR, Høiland H. Partial Molar Isentropic Compressions of Some Tetra- and Pentapeptides in Aqueous Solution: Implications for Group Additivity Schemes for Unfolded Proteins. J SOLUTION CHEM 2012. [DOI: 10.1007/s10953-012-9818-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Abstract
Ultrasensitive differential scanning calorimetry (DSC) is an indispensable thermophysical technique enabling to get direct information on enthalpies accompanying heating/cooling of dilute biopolymer solutions. The thermal dependence of protein heat capacity extracted from DSC data is a valuable source of information on intrinsic disorder level of a protein. Application details and limitations of DSC technique in exploration of protein intrinsic disorder are described.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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37
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Shimizu S. The effect of urea on hydrophobic hydration: Preferential interaction and the enthalpy of transfer. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.10.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Voloshin VP, Medvedev NN, Andrews MN, Burri RR, Winter R, Geiger A. Volumetric Properties of Hydrated Peptides: Voronoi–Delaunay Analysis of Molecular Simulation Runs. J Phys Chem B 2011; 115:14217-28. [DOI: 10.1021/jp2050788] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir P. Voloshin
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
| | - Nikolai N. Medvedev
- Institute of Chemical Kinetics and Combustion, SB RAS, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - R. Reddy Burri
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Roland Winter
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
| | - Alfons Geiger
- Physikalische Chemie, Technische Universität Dortmund, 44221 Dortmund, Germany
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39
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The Partial Molar Volumes and Heat Capacities of the Arginyl Side-chain of Proteins in Aqueous Solution over the Temperature Range 288.15 to 328.15 K. J SOLUTION CHEM 2010. [DOI: 10.1007/s10953-010-9605-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Farber P, Darmawan H, Sprules T, Mittermaier A. Analyzing protein folding cooperativity by differential scanning calorimetry and NMR spectroscopy. J Am Chem Soc 2010; 132:6214-22. [PMID: 20377225 DOI: 10.1021/ja100815a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Some marginally stable proteins undergo microsecond time scale folding reactions that involve significant populations of partly ordered forms, making it difficult to discern individual steps in their folding pathways. It has been suggested that many of these proteins fold non-cooperatively, with no significant barriers to separate the energy landscape into distinct thermodynamic states. Here we present an approach for studying the cooperativity of rapid protein folding with a combination of differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR) relaxation dispersion experiments, and an analysis of the temperature dependence of amide (1)H and (15)N chemical shifts. We applied this method to the PBX homeodomain (PBX-HD), which folds on the microsecond time scale and produces a broad DSC thermogram with an elevated and steeply sloping native-state heat capacity baseline, making it a candidate for barrierless folding. However, by globally fitting the NMR thermal melt and DSC data, and by comparing these results to those obtained from the NMR relaxation dispersion experiments, we show that the native form of the protein undergoes two-state exchange with a small population of the thermally denatured form, well below the melting temperature. This result directly demonstrates the coexistence of distinct folded and unfolded forms and firmly establishes that folding of PBX-HD is cooperative. Further, we see evidence of large-scale structural and dynamical changes within the native state by NMR, which helps to explain the broad and shallow DSC profile. This study illustrates the potential of combining calorimetry with NMR dynamics experiments to dissect mechanisms of protein folding.
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Affiliation(s)
- Patrick Farber
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 2K6
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41
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Sirimulla S, Lerma M, Herndon WC. Prediction of Partial Molar Volumes of Amino Acids and Small Peptides: Counting Atoms versus Topological Indices. J Chem Inf Model 2010; 50:194-204. [PMID: 20058884 DOI: 10.1021/ci900318c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman Sirimulla
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
| | - Maricarmen Lerma
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
| | - William C. Herndon
- Department of Chemistry, University of Texas at El Paso, 500 West University Avenue, El Paso, Texas 79968
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42
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Kapłon TM, Michnik A, Drzazga Z, Richter K, Kochman M, Ożyhar A. The rod-shaped conformation of Starmaker. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1616-24. [DOI: 10.1016/j.bbapap.2009.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/14/2009] [Accepted: 07/16/2009] [Indexed: 12/13/2022]
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43
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The Partial Molar Heat Capacities and Expansions of Inosine, 2′-Deoxyinosine and 2′-Deoxyguanosine in Aqueous Solution at 298.15 K. J SOLUTION CHEM 2009. [DOI: 10.1007/s10953-009-9450-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Permyakov SE, Bakunts AG, Permyakova ME, Denesyuk AI, Uversky VN, Permyakov EA. Metal-controlled interdomain cooperativity in parvalbumins. Cell Calcium 2009; 46:163-75. [PMID: 19651438 DOI: 10.1016/j.ceca.2009.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 06/29/2009] [Accepted: 07/06/2009] [Indexed: 11/30/2022]
Abstract
Conformational behavior of five homologous proteins, parvalbumins (PAs) from northern pike (alpha and beta isoforms), Baltic cod, and rat (alpha and beta isoforms), was studied by scanning calorimetry, circular dichroism, and bis-ANS fluorescence. The mechanism of the temperature-induced denaturation of these proteins depends dramatically on both the peculiarities of their amino acid sequences and on their interaction with metal ions. For example, the pike alpha-PA melting can be described by two successive two-state transitions with mid-temperatures of 90 and 120 degrees C, suggesting the presence of two thermodynamic domains. The intermediate state populated at the end of the first transition was shown to bind Ca(2+) ions, and was characterized by the largely preserved secondary structure and increased solvent exposure of hydrophobic groups. Mg(2+)- and Na(+)-loaded forms of pike alpha-PA demonstrated a single two-state transition. Therefore, the mechanism of the PA thermal denaturation is controlled by metal binding. It ranged from the absence of detectable first-order transition (apo-form of pike PA), to the two-state transition (e.g., Mg(2+)- and Na(+)-loaded forms of pike alpha-PA), to the more complex mechanisms (Ca(2+)-loaded PAs) involving at least one partially folded intermediate. Analysis of isolated cavities in the protein structures revealed that the interface between the CD and EF subdomains of Ca(2+)-loaded pike alpha-PA is much more loosely packed compared with PAs manifesting single heat-sorption peak. The impairment of interactions between CD and EF subdomains may cause a loss of structural cooperativity and appearance of two separate thermodynamic domains. One more peculiar feature of pike alpha-PA is that depending on its interactions with metal ions, it can be an intrinsically disordered protein (apo-form), an ordered protein of mesophilic (Na(+)-bound state), thermophilic (Mg(2+)-form), or even of the hyperthermophilic origin (Ca(2+)-form).
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow, Russia.
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45
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Cul3-mediated Nrf2 ubiquitination and antioxidant response element (ARE) activation are dependent on the partial molar volume at position 151 of Keap1. Biochem J 2009; 422:171-80. [PMID: 19489739 DOI: 10.1042/bj20090471] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nrf2 (nuclear factor erythroid 2-related factor 2) is a transcription factor that activates transcription of a battery of cytoprotective genes by binding to the ARE (antioxidant response element). Nrf2 is repressed by the cysteine-rich Keap1 (kelch-like ECH-associated protein 1) protein, which targets Nrf2 for ubiquitination and subsequent degradation by a Cul3 (cullin 3)-mediated ubiquitination complex. We find that modification of Cys(151) of human Keap1, by mutation to a tryptophan, relieves the repression by Keap1 and allows activation of the ARE by Nrf2. The Keap1 C151W substitution has a decreased affinity for Cul3, and can no longer serve to target Nrf2 for ubiquitination, though it retains its affinity for Nrf2. A series of 12 mutant Keap1 proteins, each containing a different residue at position 151, was constructed to explore the chemistry required for this effect. The series reveals that the extent to which Keap1 loses the ability to target Nrf2 for degradation, and hence the ability to repress ARE activation, correlates well with the partial molar volume of the residue. Other physico-chemical properties do not appear to contribute significantly to the effect. Based on this finding, a structural model is proposed whereby large residues at position 151 cause steric clashes that lead to alteration of the Keap1-Cul3 interaction. This model has significant implications for how electrophiles which modify Cys(151), disrupt the repressive function of Keap1.
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46
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Mitra L, Rouget JB, Garcia-Moreno B, Royer CA, Winter R. Towards a quantitative understanding of protein hydration and volumetric properties. Chemphyschem 2009; 9:2715-21. [PMID: 18814170 DOI: 10.1002/cphc.200800405] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Herein, we probe by pressure perturbation calorimetry (PPC) the coefficient of thermal expansion, the volumetric and the hydration properties of variants of a hyperstable variant of staphylococcal nuclease (SNase), Delta+PHS. The temperature-dependent volumetric properties of the folded and unfolded states of the wild-type protein are calculated with previously published data. The present PPC results are used to interpret the volume diagram and expansivity at a molecular level. We conclude that the expansivity of the unfolded state is, to a first approximation, temperature independent, while that of the folded state decreases with increasing temperature. Our data suggest that at low temperature the defining contribution to DeltaV comes mainly from excluded volume differences and DeltaV for unfolding is negative. In contrast, at high temperatures, differential solvation due to the increased exposed surface area of the unfolded state and, in particular, its larger thermal volume linked to the increased conformational dynamics of the unfolded state ensemble takes over and DeltaV for unfolding eventually becomes positive.
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Affiliation(s)
- Lally Mitra
- Dortmund University of Technology, Department of Chemistry, Physical Chemistry I-Biophysical Chemistry, Otto-Hahn Str. 6, 44227 Dortmund, Germany
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47
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Stewart AK, Kurschat CE, Vaughan-Jones RD, Alper SL. Putative re-entrant loop 1 of AE2 transmembrane domain has a major role in acute regulation of anion exchange by pH. J Biol Chem 2008; 284:6126-39. [PMID: 19103596 DOI: 10.1074/jbc.m802051200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Normal pH sensitivity of the SLC4A2/AE2 anion exchanger requires transmembrane domain (TMD) amino acid (aa) residues not conserved in the homologous but relatively pH-insensitive SLC4A1/AE1 polypeptide. We tested the hypothesis that the nonconserved aa cluster 1075DKPK1078 within the first putative re-entrant loop (RL1) of AE2 TMD contributes to pH sensor function by studying anion exchange function of AE2 mutants in which these and other RL1 aa were systematically substituted with corresponding RL1 aa from AE1. Regulation of Cl-/Cl- and Cl-/HCO(-)3 exchange by intracellular pH (pHi) or extracellular pH (pHo) was measured as 4,4'-di-isothiocyanatostilbene-2,2' disulfonic acid-sensitive 36Cl- efflux from Xenopus oocytes. AE2 RL1 mutants 1075AAAQ1078 and 1075AAAQN1079 showed reduced pHi sensitivity and pHo sensitivity was acid-shifted by approximately 1 pH unit. Individual mutants D1075A and P1077A exhibited moderately altered pH sensitivity, whereas a range of substitutions at conserved AE2 Ile-1079 substantially altered sensitivity to pHo and/or pHi. Substitution of the complete AE1 RL1 with AE2 RL1 failed to confer AE2-like pH sensitivity onto AE1. Replacement, however, of AE1 RL1 763SGPGAAAQ770 with AE2 1071VAPGDKPK1078 restored pHi sensitivity to the chimera AE2(1-920)/AE1(613-929) without affecting its low sensitivity to pHo. The results show that acute regulation of AE2 by pH requires RL1 of the TMD. We propose that critical segments of RL1 constitute part of an AE2 pH sensor that, together with residues within the N-terminal half of the TMD, constrain the AE2 polypeptide in a conformation required for regulation of anion exchange by pHi.
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Affiliation(s)
- Andrew K Stewart
- Department of Medicine, Harvard Medical School, and Molecular and Vascular Medicine Unit, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
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48
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Permyakov SE, Bakunts AG, Denesyuk AI, Knyazeva EL, Uversky VN, Permyakov EA. Apo-parvalbumin as an intrinsically disordered protein. Proteins 2008; 72:822-36. [PMID: 18260106 DOI: 10.1002/prot.21974] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recently defined family of intrinsically disordered proteins (IDP) includes proteins lacking rigid tertiary structure meanwhile fulfilling essential biological functions. Here we show that apo-state of pike parvalbumin (alpha- and beta-isoforms, pI 5.0 and 4.2, respectively) belongs to the family of IDP, which is in accord with theoretical predictions. Parvalbumin (PA) is a 12-kDa calcium-binding protein involved into regulation of relaxation of fast muscles. Differential scanning calorimetry measurements of metal-depleted form of PA revealed the absence of any thermally induced transitions with measurable denaturation enthalpy along with elevated specific heat capacity, implying the lack of rigid tertiary structure and exposure of hydrophobic protein groups to the solvent. Calcium removal from the PAs causes more than 10-fold increase in fluorescence intensity of hydrophobic probe bis-ANS and is accompanied by a decrease in alpha-helical content and a marked increase in mobility of aromatic residues environment, as judged by circular dichroism spectroscopy (CD). Guanidinium chloride-induced unfolding of the apo-parvalbumins monitored by CD showed the lack of fixed tertiary structure. Theoretical estimation of energetics of the charge-charge interactions in the PAs indicated their pronounced destabilization upon calcium removal, which is in line with sequence-based predictions of disordered protein chain regions. Far-UV CD studies of apo-alpha-PA revealed hallmarks of cold denaturation of the protein at temperatures below 20 degrees C. Moreover, a cooperative thermal denaturation transition with mid-temperature at 10-15 degrees C is revealed by near-UV CD for both PAs. The absence of detectable enthalpy change in this temperature region suggests continuous nature of the transition. Overall, the theoretical and experimental data obtained show that PA in apo-state is essentially disordered nevertheless demonstrates complex denaturation behavior. The native rigid tertiary structure of PA is attained upon association of one (alpha-PA) or two (beta-PA) calcium ions per protein molecule, as follows from calorimetric and calcium titration data.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
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49
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Auton M, Bolen DW, Rösgen J. Structural thermodynamics of protein preferential solvation: Osmolyte solvation of proteins, aminoacids, and peptides. Proteins 2008; 73:802-13. [DOI: 10.1002/prot.22103] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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Partial molar volumes and adiabatic compressibilities of unfolded protein states. Biophys Chem 2008; 134:185-99. [PMID: 18342425 DOI: 10.1016/j.bpc.2008.02.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 02/12/2008] [Accepted: 02/12/2008] [Indexed: 11/22/2022]
Abstract
We determined the partial molar volumes, V degrees , and adiabatic compressibilities, K degrees (S), of N-acetyl amino acids with neutralized carboxyl termini, N-acetyl amino acid amides, and N-acetyl amino acid methylamides between 18 and 55 degrees C. The individual compounds in the three classes have been selected so as to collectively cover the 20 naturally occurring amino acid side chains. We interpret our experimental results in terms of the volumetric contributions and hydration properties of individual amino acid side chains and their constituent atomic groups. We also conducted pH-dependent densimetric and acoustic measurements to determine changes in volume and compressibility accompanying protonation of the aspartic acid, glutamic acid, histidine, lysine, and arginine side chains. We use our resulting data to develop an additive scheme for calculating the partial molar (specific) volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We discuss the differences and similarities between our proposed scheme and the reported additive approaches. We compare our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in water (for apocytochrome c) or acidic pH (for apomyoglobin). At these respective experimental conditions, the two proteins are unfolded. However, the comparison between the calculated and experimental volumetric characteristics suggests that neither apocytochrome c nor apomyoglobin are fully unfolded and retain a sizeable core of solvent-inaccessible groups.
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