1
|
Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
Collapse
Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
| |
Collapse
|
2
|
Paulikat M, Vitone D, Schackert FK, Schuth N, Barbanente A, Piccini G, Ippoliti E, Rossetti G, Clark AH, Nachtegaal M, Haumann M, Dau H, Carloni P, Geremia S, De Zorzi R, Quintanar L, Arnesano F. Molecular Dynamics and Structural Studies of Zinc Chloroquine Complexes. J Chem Inf Model 2023; 63:161-172. [PMID: 36468829 DOI: 10.1021/acs.jcim.2c01164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Chloroquine (CQ) is a first-choice drug against malaria and autoimmune diseases. It has been co-administered with zinc against SARS-CoV-2 and soon dismissed because of safety issues. The structural features of Zn-CQ complexes and the effect of CQ on zinc distribution in cells are poorly known. In this study, state-of-the-art computations combined with experiments were leveraged to solve the structural determinants of zinc-CQ interactions in solution and the solid state. NMR, ESI-MS, and X-ray absorption and diffraction methods were combined with ab initio molecular dynamics calculations to address the kinetic lability of this complex. Within the physiological pH range, CQ binds Zn2+ through the quinoline ring nitrogen, forming [Zn(CQH)Clx(H2O)3-x](3+)-x (x = 0, 1, 2, and 3) tetrahedral complexes. The Zn(CQH)Cl3 species is stable at neutral pH and at high chloride concentrations typical of the extracellular medium, but metal coordination is lost at a moderately low pH as in the lysosomal lumen. The pentacoordinate complex [Zn(CQH)(H2O)4]3+ may exist in the absence of chloride. This in vitro/in silico approach can be extended to other metal-targeting drugs and bioinorganic systems.
Collapse
Affiliation(s)
- Mirko Paulikat
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany
| | - Daniele Vitone
- Department of Chemistry, University of Bari "Aldo Moro", 70125Bari, Italy
| | - Florian K Schackert
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062Aachen, Germany
| | - Nils Schuth
- Department of Chemistry, Center for Research and Advanced Studies (Cinvestav), 07360Mexico City, Mexico
| | | | | | - Emiliano Ippoliti
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany
| | - Giulia Rossetti
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Neurology, RWTH Aachen University, 52062Aachen, Germany
| | - Adam H Clark
- Paul Scherrer Institute, 5232Villigen, Switzerland
| | | | - Michael Haumann
- Department of Physics, Freie Universität Berlin, 14195Berlin, Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin, 14195Berlin, Germany
| | - Paolo Carloni
- Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich GmbH, 52428Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062Aachen, Germany
| | - Silvano Geremia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127Trieste, Italy
| | - Liliana Quintanar
- Department of Chemistry, Center for Research and Advanced Studies (Cinvestav), 07360Mexico City, Mexico
| | - Fabio Arnesano
- Department of Chemistry, University of Bari "Aldo Moro", 70125Bari, Italy
| |
Collapse
|
3
|
Elveren B, Hribernik S, Kurečič M. Fabrication of Polysaccharide-Based Halochromic Nanofibers via Needle-Less Electrospinning and Their Characterization: A Study of the Leaching Effect. Polymers (Basel) 2022; 14:polym14194239. [PMID: 36236187 PMCID: PMC9571342 DOI: 10.3390/polym14194239] [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: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/25/2022] Open
Abstract
Responsive materials, i.e., smart materials, have the ability to change their physical or chemical properties upon certain external signals. The development of nanofibrous halochromic materials, specifically combining the pH-sensitive functionality and unique nanofiber properties, could yield interesting new applications, especially when the common problem of dye leaching is successfully tackled. Therefore, in this article, we studied the fabrication process of polysaccharide-based halochromic nanofibrous materials by using a combination of various halochromic dyes (bromothymol blue, bromocresol green, and thymol blue) and cellulose acetate in a spinning solution using a one-pot strategy. The inhibition of leaching was addressed by using a complexing agent: poly-diallyl-dimethylammonium chloride (PDADMAC). The preparation of hybrid spinning solutions, their characterization, and ability to form continuous nanofibers were studied using a high production needle-less electrospinning system. The produced hybrid solutions and nanofibers were characterized, in terms of their rheological properties, chemical structure, morphology, and functionality. Fabricated nanofibrous halochromic structures show a clear color change upon exposure to different pH values, as well as the reduced leaching of dyes, upon the addition of a complexing agent. The leaching decreased by 61% in the case of bromocresol green, while, in the case of bromothymol blue and thymol blue, the leaching was reduced by 95 and 99%, respectively.
Collapse
Affiliation(s)
- Beste Elveren
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
| | - Silvo Hribernik
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Institute of Automation, Faculty of Electrical Engineering and Computer Science, University of Maribor, Koroska cesta 46, 2000 Maribor, Slovenia
| | - Manja Kurečič
- Laboratory for Characterization and Processing of Polymers, Faculty of Mechanical Engineering, University of Maribor, Smetanova Ulica 17, 2000 Maribor, Slovenia
- Correspondence:
| |
Collapse
|
4
|
Shrestha R, Jia K, Khadka S, Eltis LD, Li P. Mechanistic Insights into DyPB from Rhodococcus jostii RHA1 Via Kinetic Characterization. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruben Shrestha
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Kaimin Jia
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Samiksha Khadka
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Lindsay D. Eltis
- Department of Microbiology and Immunology, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ping Li
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| |
Collapse
|
5
|
Hinterholzer A, Stanojlovic V, Regl C, Huber CG, Cabrele C, Schubert M. Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2021; 75:71-82. [PMID: 33475951 PMCID: PMC7897204 DOI: 10.1007/s10858-020-00356-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
The monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of + 18 Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pKa values of isoAsp and C-terminal Asp in short peptides. The characteristic 1H-13C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4-5) and 40 °C. The results show that the application of our 2D NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.
Collapse
Affiliation(s)
- Arthur Hinterholzer
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| |
Collapse
|
6
|
Prinz C, Starke L, Millward JM, Fillmer A, Delgado PR, Waiczies H, Pohlmann A, Rothe M, Nazaré M, Paul F, Niendorf T, Waiczies S. In vivo detection of teriflunomide-derived fluorine signal during neuroinflammation using fluorine MR spectroscopy. Theranostics 2021; 11:2490-2504. [PMID: 33456555 PMCID: PMC7806491 DOI: 10.7150/thno.47130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Magnetic resonance imaging (MRI) is indispensable for diagnosing neurological conditions such as multiple sclerosis (MS). MRI also supports decisions regarding the choice of disease-modifying drugs (DMDs). Determining in vivo tissue concentrations of DMDs has the potential to become an essential clinical tool for therapeutic drug monitoring (TDM). The aim here was to examine the feasibility of fluorine-19 (19F) MR methods to detect the fluorinated DMD teriflunomide (TF) during normal and pathological conditions. Methods: We used 19F MR spectroscopy to detect TF in the experimental autoimmune encephalomyelitis (EAE) mouse model of multiple sclerosis (MS) in vivo. Prior to the in vivo investigations we characterized the MR properties of TF in vitro. We studied the impact of pH and protein binding as well as MR contrast agents. Results: We could detect TF in vivo and could follow the 19F MR signal over different time points of disease. We quantified TF concentrations in different tissues using HPLC/MS and showed a significant correlation between ex vivo TF levels in serum and the ex vivo19F MR signal. Conclusion: This study demonstrates the feasibility of 19F MR methods to detect TF during neuroinflammation in vivo. It also highlights the need for further technological developments in this field. The ultimate goal is to add 19F MR protocols to conventional 1H MRI protocols in clinical practice to guide therapy decisions.
Collapse
|
7
|
Pravdivtsev AN, Sönnichsen FD, Hövener JB. In vitro singlet state and zero-quantum encoded magnetic resonance spectroscopy: Illustration with N-acetyl-aspartate. PLoS One 2020; 15:e0239982. [PMID: 33002045 PMCID: PMC7529218 DOI: 10.1371/journal.pone.0239982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Magnetic resonance spectroscopy (MRS) allows the analysis of biochemical processes non-invasively and in vivo. Still, its application in clinical diagnostics is rare. Routine MRS is limited to spatial, chemical and temporal resolutions of cubic centimetres, mM and minutes. In fact, the signal of many metabolites is strong enough for detection, but the resonances significantly overlap, exacerbating identification and quantification. Besides, the signals of water and lipids are much stronger and dominate the entire spectrum. To suppress the background and isolate selected signals, usually, relaxation times, J-coupling and chemical shifts are used. Here, we propose methods to isolate the signals of selected molecular groups within endogenous metabolites by using long-lived spin states (LLS). We exemplify the method by preparing the LLSs of coupled protons in the endogenous molecules N-acetyl-L-aspartic acid (NAA). First, we store polarization in long-lived, double spin states, followed by saturation pulses before the spin order is converted back to observable magnetization or double quantum filters to suppress background signals. We show that LLS and zero-quantum coherences can be used to selectively prepare and measure the signals of chosen metabolites or drugs in the presence of water, inhomogeneous field and highly concentrated fatty solutions. The strong suppression of unwanted signals achieved allowed us to measure pH as a function of chemical shift difference.
Collapse
Affiliation(s)
- Andrey N Pravdivtsev
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Kiel, Germany
| | - Frank D Sönnichsen
- Otto Diels Institute for Organic Chemistry, Kiel University, Kiel, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel University, Kiel, Germany
| |
Collapse
|
8
|
Pahari S, Sun L, Alexov E. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5359213. [PMID: 30805645 PMCID: PMC6389863 DOI: 10.1093/database/baz024] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/11/2019] [Accepted: 01/30/2019] [Indexed: 11/14/2022]
Abstract
Ionizable residues play key roles in many biological phenomena including protein folding, enzyme catalysis and binding. We present PKAD, a database of experimentally measured pKas of protein residues reported in the literature or taken from existing databases. The database contains pKa data for 1350 residues in 157 wild-type proteins and for 232 residues in 45 mutant proteins. Most of these values are for Asp, Glu, His and Lys amino acids. The database is available as downloadable file as well as a web server (http://compbio.clemson.edu/pkad). The PKAD database can be used as a benchmarking source for development and improvement of pKa's prediction methods. The web server provides additional information taken from the corresponding structures and amino acid sequences, which allows for easy search and grouping of the experimental pKas according to various biophysical characteristics, amino acid type and others.
Collapse
Affiliation(s)
- Swagata Pahari
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Lexuan Sun
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA
| |
Collapse
|
9
|
Artikis E, Brooks CL. Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides. Biophys J 2019; 117:258-268. [PMID: 31255294 DOI: 10.1016/j.bpj.2019.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/20/2019] [Accepted: 06/03/2019] [Indexed: 11/29/2022] Open
Abstract
Modeling the pH dependence of protein and peptide chemical shifts outside the range of physiological values (6.5-7) is key to understanding structure-function relationships of these systems. These capabilities are largely not available in current chemical shift prediction software. In this study, we utilize a combination of molecular dynamics and quantum mechanics to investigate the through-space and through-bond contributions of protonation-dependent chemical shift perturbations (CSPs) in model tripeptides. By altering the protonation state of the titratable group in the tripeptides, we observe a notable difference in the conformational ensembles and attendantly compute significant CSPs for all nuclei near the site of protonation. We thus demonstrate the ability to recapitulate experimental pH-dependent CSPs with good agreement (R = 0.85, 0.99, and 0.98 for 13C, 15N, and 1H, respectively). Broadly, we provide the groundwork for incorporating pH effects into empirical and semiempirical chemical shift predictors.
Collapse
Affiliation(s)
| | - Charles L Brooks
- Biophysics Program, University of Michigan, Ann Arbor, Michigan; Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
| |
Collapse
|
10
|
Drewniak M, Węglarz-Tomczak E, Ożga K, Rudzińska-Szostak E, Macegoniuk K, Tomczak JM, Bejger M, Rypniewski W, Berlicki Ł. Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics. Bioorg Chem 2018; 81:356-361. [PMID: 30195249 DOI: 10.1016/j.bioorg.2018.07.012] [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: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/18/2023]
Abstract
De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.
Collapse
Affiliation(s)
- Magda Drewniak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub M Tomczak
- Amsterdam Machine Learning Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| |
Collapse
|
11
|
Koppenol-Raab M, Harwig MC, Posey AE, Egner JM, MacKenzie KR, Hill RB. A Targeted Mutation Identified through pKa Measurements Indicates a Postrecruitment Role for Fis1 in Yeast Mitochondrial Fission. J Biol Chem 2016; 291:20329-44. [PMID: 27496949 DOI: 10.1074/jbc.m116.724005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Indexed: 12/25/2022] Open
Abstract
The tail-anchored protein Fis1 is implicated as a passive tether in yeast mitochondrial fission. We probed the functional role of Fis1 Glu-78, whose elevated side chain pKa suggests participation in protein interactions. Fis1 binds partners Mdv1 or Dnm1 tightly, but mutation E78A weakens Fis1 interaction with Mdv1, alters mitochondrial morphology, and abolishes fission in a growth assay. In fis1Δ rescue experiments, Fis1-E78A causes a novel localization pattern in which Dnm1 uniformly coats the mitochondria. By contrast, Fis1-E78A at lower expression levels recruits Dnm1 into mitochondrial punctate structures but fails to support normal fission. Thus, Fis1 makes multiple interactions that support Dnm1 puncta formation and may be essential after this step, supporting a revised model for assembly of the mitochondrial fission machinery. The insights gained by mutating a residue with a perturbed pKa suggest that side chain pKa values inferred from routine NMR sample pH optimization could provide useful leads for functional investigations.
Collapse
Affiliation(s)
| | - Megan Cleland Harwig
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Ammon E Posey
- From the Department of Biology and the Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218
| | - John M Egner
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| | - Kevin R MacKenzie
- the Department of Pathology, Baylor College of Medicine, Houston, Texas 77030
| | - R Blake Hill
- the Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, and
| |
Collapse
|
12
|
Højgaard C, Kofoed C, Espersen R, Johansson KE, Villa M, Willemoës M, Lindorff-Larsen K, Teilum K, Winther JR. A Soluble, Folded Protein without Charged Amino Acid Residues. Biochemistry 2016; 55:3949-56. [PMID: 27307139 DOI: 10.1021/acs.biochem.6b00269] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable side chains can maintain solubility, stability, and function. As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. We find that the protein shows a surprising resilience toward extremes of pH, demonstrating stability and function (cellulose binding) in the pH range from 2 to 11. To ask whether the four charged residues present were required for these properties of this protein, we altered them to nontitratable ones. Remarkably, this chargeless protein is produced reasonably well in Escherichia coli, retains its stable three-dimensional structure, and is still capable of strong cellulose binding. To further deprive this protein of charges, we removed the N-terminal charge by acetylation and studied the protein at pH 2, where the C-terminus is effectively protonated. Under these conditions, the protein retains its function and proved to be both soluble and have a reversible folding-unfolding transition. To the best of our knowledge, this is the first time a soluble, functional protein with no titratable side chains has been produced.
Collapse
Affiliation(s)
- Casper Højgaard
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Christian Kofoed
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Roall Espersen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kristoffer Enøe Johansson
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Mara Villa
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Martin Willemoës
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| | - Jakob R Winther
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , DK-2200 Copenhagen N, Denmark
| |
Collapse
|
13
|
Bodnarchuk MS, Heyes DM, Dini D, Chahine S, Edwards S. Role of Deprotonation Free Energies in pKa Prediction and Molecule Ranking. J Chem Theory Comput 2015; 10:2537-45. [PMID: 26580774 DOI: 10.1021/ct400914w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A computationally efficient classical molecular simulation technique is derived for ranking the pKa values of a set of chemically similar congeneric molecules in an implicit solvent model of water. This uses the deprotonation free energy of the titratable group in the gas and aqueous phases obtained by thermodynamic integration (TI). For a series of alcohols and acids a strong linear correlation is demonstrated between the experimental pKa and the deprotonation free energy difference in the gas and liquid phases. These calculations also show that classical TI is more efficient than slow-growth TI in calculating deprotonation free energies for the series of molecules considered herein.
Collapse
Affiliation(s)
- M S Bodnarchuk
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London, SW7 2AZ, U.K
| | - D M Heyes
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London, SW7 2AZ, U.K
| | - D Dini
- Department of Mechanical Engineering, Imperial College London , Exhibition Road, London, SW7 2AZ, U.K
| | - S Chahine
- BP Marine Limited, Marine Technology Centre , Whitchurch Hill, Pangbourne, RG8 7QR, U.K
| | - S Edwards
- BP Marine Limited, Marine Technology Centre , Whitchurch Hill, Pangbourne, RG8 7QR, U.K
| |
Collapse
|
14
|
Morrison EA, Robinson AE, Liu Y, Henzler-Wildman KA. Asymmetric protonation of EmrE. J Gen Physiol 2015; 146:445-61. [PMID: 26573622 PMCID: PMC4664823 DOI: 10.1085/jgp.201511404] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 10/13/2015] [Indexed: 01/26/2023] Open
Abstract
The small multidrug resistance transporter EmrE is a homodimer that uses energy provided by the proton motive force to drive the efflux of drug substrates. The pKa values of its "active-site" residues--glutamate 14 (Glu14) from each subunit--must be poised around physiological pH values to efficiently couple proton import to drug export in vivo. To assess the protonation of EmrE, pH titrations were conducted with (1)H-(15)N TROSY-HSQC nuclear magnetic resonance (NMR) spectra. Analysis of these spectra indicates that the Glu14 residues have asymmetric pKa values of 7.0 ± 0.1 and 8.2 ± 0.3 at 45°C and 6.8 ± 0.1 and 8.5 ± 0.2 at 25°C. These pKa values are substantially increased compared with typical pKa values for solvent-exposed glutamates but are within the range of published Glu14 pKa values inferred from the pH dependence of substrate binding and transport assays. The active-site mutant, E14D-EmrE, has pKa values below the physiological pH range, consistent with its impaired transport activity. The NMR spectra demonstrate that the protonation states of the active-site Glu14 residues determine both the global structure and the rate of conformational exchange between inward- and outward-facing EmrE. Thus, the pKa values of the asymmetric active-site Glu14 residues are key for proper coupling of proton import to multidrug efflux. However, the results raise new questions regarding the coupling mechanism because they show that EmrE exists in a mixture of protonation states near neutral pH and can interconvert between inward- and outward-facing forms in multiple different protonation states.
Collapse
Affiliation(s)
- Emma A Morrison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Anne E Robinson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Yongjia Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| | - Katherine A Henzler-Wildman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110
| |
Collapse
|
15
|
Kapitanov IV, Abakumov AA, Serdyuk AA. Identification of products in the reaction of 2-[(hydroxyimino)methyl]-1,3-dimethylimidazolium iodide with diethyl 4-nitrophenyl phosphate in alkaline medium. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2015. [DOI: 10.1134/s1070428015100024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Affiliation(s)
- Mathias A.S. Hass
- Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Frans A.A. Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark;
| |
Collapse
|
17
|
Jensen KS, Pedersen JT, Winther JR, Teilum K. The pKa value and accessibility of cysteine residues are key determinants for protein substrate discrimination by glutaredoxin. Biochemistry 2014; 53:2533-40. [PMID: 24673564 DOI: 10.1021/bi4016633] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The enzyme glutaredoxin catalyzes glutathione exchange, but little is known about its interaction with protein substrates. Very different proteins are substrates in vitro, and the enzyme seems to have low requirements for specific protein interactions. Here we present a systematic investigation of the interaction between human glutaredoxin 1 and glutathionylated variants of a single model protein. Thus, single cysteine variants of acyl-coenzyme A binding protein were produced creating a set of substrates in the same protein background. The rate constants for deglutathionylation differ by more than 2 orders of magnitude between the best (k1 = 1.75 × 10(5) M(-1) s(-1)) and the worst substrate (k1 = 4 × 10(2) M(-1) s(-1)). The pKa values of the substrate cysteine residues were determined by NMR spectroscopy and found to vary from 8.2 to 9.9. Rates of glutaredoxin 1-catalyzed deglutathionylation were assessed with respect to substrate cysteine pKa values, cysteine residue accessibility, local stability, and backbone dynamics. Good substrates are characterized by a combination of high accessibility of the glutathionylated site and low pKa of the cysteine residue.
Collapse
Affiliation(s)
- Kristine Steen Jensen
- Department of Biology, University of Copenhagen , Ole Maaleøs Vej 5, 2200 Copenhagen N, Denmark
| | | | | | | |
Collapse
|
18
|
Kukic P, Farrell D, McIntosh LP, García-Moreno E B, Jensen KS, Toleikis Z, Teilum K, Nielsen JE. Protein dielectric constants determined from NMR chemical shift perturbations. J Am Chem Soc 2013; 135:16968-76. [PMID: 24124752 DOI: 10.1021/ja406995j] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatic calculations are essential for this purpose, but their use has been limited by a long-standing discussion on which value to use for the dielectric constants (ε(eff) and ε(p)) required in Coulombic and Poisson-Boltzmann models. The currently used values for ε(eff) and ε(p) are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for ε(eff) and ε(p) by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in 14 proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (ε(eff)) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (ε(p)) ranged from 2 to 5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders and how different it is from the ε(p) of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of ε(p) = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pK(a) values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable ε(p) common to most folded proteins.
Collapse
Affiliation(s)
- Predrag Kukic
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin , Belfield, Dublin 4, Ireland
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Santambrogio C, Favretto F, D'Onofrio M, Assfalg M, Grandori R, Molinari H. Mass spectrometry and NMR analysis of ligand binding by human liver fatty acid binding protein. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:895-903. [PMID: 23893635 DOI: 10.1002/jms.3237] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/10/2013] [Accepted: 05/16/2013] [Indexed: 06/02/2023]
Abstract
Human liver fatty acid binding protein (hL-FABP) is the most abundant cytosolic protein in the liver. This protein plays important roles associated to partitioning of fatty acids (FAs) to specific metabolic pathways, nuclear signaling and protection against oxidative damage. The protein displays promiscuous binding properties and can bind two internal ligands, unlike FABPs from other tissues. Different topologies for the ligand located in the more accessible site have been reported, with either a 'head-in' or 'head-out' orientation of the carboxylate end. Electrospray-ionization mass spectrometry and nuclear magnetic resonance titrations are employed here in order to investigate in further detail the binding properties of this system, the equilibria established in solution and the pH dependence of the complexes. The results are consistent with two binding sites with different affinity and a unique head-out topology for the second molecule of either ligand. Competition experiments indicate a higher affinity for oleic acid relative to palmitic acid at each binding site.
Collapse
Affiliation(s)
- C Santambrogio
- Department of Biotechnology and Biosciences, Piazza della Scienza 2, University of Milano-Bicocca, 20126, Milan, Italy
| | | | | | | | | | | |
Collapse
|
20
|
|
21
|
1H CIDNP study of the kinetics and mechanism of the reversible photoinduced oxidation of tryptophyl-tryptophan dipeptide in aqueous solutions. Russ Chem Bull 2012. [DOI: 10.1007/s11172-011-0396-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
22
|
Farrell D, Webb H, Johnston MA, Poulsen TA, O’Meara F, Christensen LLH, Beier L, Borchert TV, Nielsen JE. Toward Fast Determination of Protein Stability Maps: Experimental and Theoretical Analysis of Mutants of a Nocardiopsis prasina Serine Protease. Biochemistry 2012; 51:5339-47. [DOI: 10.1021/bi201926f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Damien Farrell
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Helen Webb
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Michael A. Johnston
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Thomas A. Poulsen
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Fergal O’Meara
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Lars Beier
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Torben V. Borchert
- Protein Optimization, Novozymes A/S, Brudelysvej 26, 2880 Bagsværd,
Denmark
| | - Jens Erik Nielsen
- School of Biomolecular and Biomedical
Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
23
|
Johnston MA, Farrell D, Nielsen JE. A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. J Comput Aided Mol Des 2012; 26:387-96. [DOI: 10.1007/s10822-012-9564-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/18/2012] [Indexed: 11/29/2022]
|
24
|
Highly perturbed pKa values in the unfolded state of hen egg white lysozyme. Biophys J 2012; 102:1636-45. [PMID: 22500764 DOI: 10.1016/j.bpj.2012.02.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Revised: 01/28/2012] [Accepted: 02/13/2012] [Indexed: 11/21/2022] Open
Abstract
The majority of pK(a) values in protein unfolded states are close to the amino acid model pK(a) values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pK(a) values and the pH dependence of protein stability for this enzyme. The availability of accurate pK(a) values for the folded state of HEWL and separate measurements of mutant-induced effects on the folded state pK(a) values, allows us to estimate the pK(a) values of seven acidic residues in the unfolded state of HEWL. Asp-48 and Asp-66 display pK(a) values of 2.9 and 3.1 in our analysis, thus representing the most depressed unfolded state pK(a) values observed to date. We observe a strong correlation between the folded state pK(a) values and the unfolded state pK(a) values of HEWL, thus suggesting that the unfolded state of HEWL possesses a large degree of native state characteristics.
Collapse
|
25
|
Robertson IM, Holmes PC, Li MX, Pineda-Sanabria SE, Baryshnikova OK, Sykes BD. Elucidation of isoform-dependent pH sensitivity of troponin i by NMR spectroscopy. J Biol Chem 2011; 287:4996-5007. [PMID: 22179777 DOI: 10.1074/jbc.m111.301499] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Myocardial ischemia is characterized by reduced blood flow to cardiomyocytes, which can lead to acidosis. Acidosis decreases the calcium sensitivity and contractile efficiency of cardiac muscle. By contrast, skeletal and neonatal muscles are much less sensitive to changes in pH. The pH sensitivity of cardiac muscle can be reduced by replacing cardiac troponin I with its skeletal or neonatal counterparts. The isoform-specific response of troponin I is dictated by a single histidine, which is replaced by an alanine in cardiac troponin I. The decreased pH sensitivity may stem from the protonation of this histidine at low pH, which would promote the formation of electrostatic interactions with negatively charged residues on troponin C. In this study, we measured acid dissociation constants of glutamate residues on troponin C and of histidine on skeletal troponin I (His-130). The results indicate that Glu-19 comes in close contact with an ionizable group that has a pK(a) of ∼6.7 when it is in complex with skeletal troponin I but not when it is bound to cardiac troponin I. The pK(a) of Glu-19 is decreased when troponin C is bound to skeletal troponin I and the pK(a) of His-130 is shifted upward. These results strongly suggest that these residues form an electrostatic interaction. Furthermore, we found that skeletal troponin I bound to troponin C tighter at pH 6.1 than at pH 7.5. The data presented here provide insights into the molecular mechanism for the pH sensitivity of different muscle types.
Collapse
Affiliation(s)
- Ian M Robertson
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | | | | | | | | |
Collapse
|
26
|
Pantoja-Uceda D, Santoro J. Selective observation of Asp and Glu resonances in (13)CO detected experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49:558-561. [PMID: 21815211 DOI: 10.1002/mrc.2780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/03/2011] [Accepted: 05/16/2011] [Indexed: 05/31/2023]
Abstract
We present a filter element to observe exclusively the resonances of Asp and Glu residues in several (13)C detected experiments, CACO, CBCACO, and CCCO. As in these experiments the carboxylate resonances appear in the directly detected dimension, it is possible to measure their chemical shifts with a high precision. Therefore, the experiments can be of great utility in the accurate determination of the pKa 's of these residues. Furthermore, the experiments can be applied in the study of deuterated proteins, where the usual experiments for pKa determination cannot be used. Finally, the good resolution with which the carboxylate spectrum is obtained allows observing the coupling between the carboxyl carbon and the backbone CO in Asp residues, what provides information on their side chain conformation.
Collapse
Affiliation(s)
- David Pantoja-Uceda
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | | |
Collapse
|
27
|
McIntosh LP, Naito D, Baturin SJ, Okon M, Joshi MD, Nielsen JE. Dissecting electrostatic interactions in Bacillus circulans xylanase through NMR-monitored pH titrations. JOURNAL OF BIOMOLECULAR NMR 2011; 51:5-19. [PMID: 21947911 DOI: 10.1007/s10858-011-9537-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/25/2011] [Indexed: 05/31/2023]
Abstract
NMR-monitored pH titration curves of proteins provide a rich source of structural and electrostatic information. Although relatively straightforward to measure, interpreting pH-dependent chemical shift changes to obtain site-specific acid dissociation constants (pK (A) values) is challenging. In order to analyze the biphasic titrations exhibited by the side chain (13)C(γ) nuclei of the nucleophilic Glu78 and general acid/base Glu172 in Bacillus circulans xylanase, we have revisited the formalism for the ionization equilibria of two coupled acidic residues. In general, fitting NMR-monitored pH titration curves for such a system will only yield the two macroscopic pK (A) values that reflect the combined effects of both deprotonation reactions. However, through the use of mutations complemented with ionic strength-dependent measurements, we are able to extract the four microscopic pK (Ai) values governing the branched acid/base equilibria of Glu78 and Glu172 in BcX. These data, confirmed through theoretical calculations, help explain the pH-dependent mechanism of this model GH11 xylanase by demonstrating that the kinetically determined pK (A) values and hence catalytic roles of these two residues result from their electrostatic coupling.
Collapse
Affiliation(s)
- Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Michael Smith Laboratories, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
| | | | | | | | | | | |
Collapse
|
28
|
Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins 2011; 79:3287-98. [PMID: 21744393 DOI: 10.1002/prot.23091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/16/2011] [Accepted: 05/04/2011] [Indexed: 11/10/2022]
Abstract
Protein pK(a) calculation methods are developed partly to provide fast non-experimental estimates of the ionization constants of protein side chains. However, the most significant reason for developing such methods is that a good pK(a) calculation method is presumed to provide an accurate physical model of protein electrostatics, which can be applied in methods for drug design, protein design, and other structure-based energy calculation methods. We explore the validity of this presumption by simulating the development of a pK(a) calculation method using artificial experimental data derived from a human-defined physical reality. We examine the ability of an RMSD-guided development protocol to retrieve the correct (artificial) physical reality and find that a rugged optimization landscape and a huge parameter space prevent the identification of the correct physical reality. We examine the importance of the training set in developing pK(a) calculation methods and investigate the effect of experimental noise on our ability to identify the correct physical reality, and find that both effects have a significant and detrimental impact on the physical reality of the optimal model identified. Our findings are of relevance to all structure-based methods for protein energy calculations and simulation, and have large implications for all types of current pK(a) calculation methods. Our analysis furthermore suggests that careful and extensive validation on many types of experimental data can go some way in making current models more realistic.
Collapse
Affiliation(s)
- Tommy Carstensen
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | |
Collapse
|
29
|
Abstract
Accurate computational methods for predicting electrostatic energies are of major importance for our understanding of protein energetics in general for computer-aided drug design as well as for the design of novel biocatalysts and protein therapeutics. Electrostatic energies are of particular importance in such applications as virtual screening, drug design and protein-protein docking due to the high charge density of protein ligands and small-molecule drugs, and the frequent protonation state changes observed when drugs bind to their protein targets. Therefore, the development of a reliable and fast algorithm for the evaluation of electrostatic free energies, as an important contributor to the overall protein energy function, has been the focus for many scientists over the past three decades. In this review we describe the current state-of-the-art in modeling electrostatic effects in proteins and protein-ligand complexes. We focus mainly on the merits and drawbacks of the continuum methodology, and speculate on future directions in refining algorithms for calculating electrostatic energies in proteins using experimental data.
Collapse
|
30
|
Bjarnadottir U, Nielsen JE. Calculating pKa values in the cAMP-dependent protein kinase: the effect of conformational change and ligand binding. Protein Sci 2011; 19:2485-97. [PMID: 20954248 DOI: 10.1002/pro.530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The conformational change observed upon ligand binding and phosphorylation for the cAMP-dependent protein kinase (protein kinase A-PKA) is of high importance for the regulation of its activity. We calculate pKa values and net charges for 18 3D structures of PKA in various conformations and liganded states to examine the role of electrostatics in ligand binding and activation. We find that the conformational change of PKA takes place without any significant net proton uptake/release at all pH values, thus indicating that PKA has evolved to reduce any pH-dependent barriers to the conformational motion. We furthermore find that the binding of ligands induces large changes in the net charge of PKA at most pH values, but significantly, we find that the net charge difference at physiological pH is close to zero, thus indicating that the active-site pKa values have been preorganized for substrate binding. We are unable to unequivocally resolve the identity of the groups responsible for determining the pH-activity profile of PKA but speculate that the titration of Lys 168 or the titration of ATP itself could be responsible for the loss of activity at high pH values. Finally, we examine the effect of point mutations on the pKa values of the PKA catalytic residues and find these to be relatively insensitive to both noncharge-altering and charge-altering mutations.
Collapse
Affiliation(s)
- Una Bjarnadottir
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | |
Collapse
|
31
|
Wei L, Jiang P, Xu W, Li H, Zhang H, Yan L, Chan-Park MB, Liu XW, Tang K, Mu Y, Pervushin K. The molecular basis of distinct aggregation pathways of islet amyloid polypeptide. J Biol Chem 2011; 286:6291-300. [PMID: 21148563 PMCID: PMC3057848 DOI: 10.1074/jbc.m110.166678] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 12/09/2010] [Indexed: 11/06/2022] Open
Abstract
Abnormal aggregation of islet amyloid polypeptide (IAPP) into amyloid fibrils is a hallmark of type 2 diabetes. In this study, we investigated the initial oligomerization and subsequent addition of monomers to growing aggregates of human IAPP at the residue-specific level using NMR, atomic force microscopy, mass spectroscopy, and computational simulations. We found that in solution IAPPs rapidly associate into transient low-order oligomers such as dimers and trimers via interactions between histidine 18 and tyrosine 37. This initial event is proceeded by slow aggregation into higher-order spherical oligomers and elongated fibrils. In these two morphologically distinct types of aggregates IAPPs adopt structures with markedly different residual flexibility. Here we show that the anti-amyloidogenic compound resveratrol inhibits oligomerization and amyloid formation via binding to histidine 18, supporting the finding that this residue is crucial for on-pathway oligomer formation.
Collapse
Affiliation(s)
- Lei Wei
- From the Schools of Biological Sciences
| | | | - Weixin Xu
- From the Schools of Biological Sciences
| | - Hai Li
- Materials Science and Engineering
| | | | | | | | - Xue-Wei Liu
- Physical and Mathematical Sciences, Nanyang Technological University, Singapore 639798
| | - Kai Tang
- From the Schools of Biological Sciences
| | | | | |
Collapse
|
32
|
Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE. Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. Proteins 2010; 79:685-702. [PMID: 21287606 DOI: 10.1002/prot.22886] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 08/24/2010] [Accepted: 09/03/2010] [Indexed: 11/08/2022]
Abstract
Site-specific pK(a) values measured by NMR spectroscopy provide essential information on protein electrostatics, the pH-dependence of protein structure, dynamics and function, and constitute an important benchmark for protein pK(a) calculation algorithms. Titration curves can be measured by tracking the NMR chemical shifts of several reporter nuclei versus sample pH. However, careful analysis of these curves is needed to extract residue-specific pK(a) values since pH-dependent chemical shift changes can arise from many sources, including through-bond inductive effects, through-space electric field effects, and conformational changes. We have re-measured titration curves for all carboxylates and His 15 in Hen Egg White Lysozyme (HEWL) by recording the pH-dependent chemical shifts of all backbone amide nitrogens and protons, Asp/Glu side chain protons and carboxyl carbons, and imidazole protonated carbons and protons in this protein. We extracted pK(a) values from the resulting titration curves using standard fitting methods, and compared these values to each other, and with those measured previously by ¹H NMR (Bartik et al., Biophys J 1994;66:1180–1184). This analysis gives insights into the true accuracy associated with experimentally measured pK(a) values. We find that apparent pK(a) values frequently differ by 0.5–1.0 units depending upon the nuclei monitored, and that larger differences occasionally can be observed. The variation in measured pK(a) values, which reflects the difficulty in fitting and assigning pH-dependent chemical shifts to specific ionization equilibria, has significant implications for the experimental procedures used for measuring protein pK(a) values, for the benchmarking of protein pK(a) calculation algorithms, and for the understanding of protein electrostatics in general.
Collapse
Affiliation(s)
- Helen Webb
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Bowman SEJ, Bren KL. Variation and analysis of second-sphere interactions and axial histidinate character in c-type cytochromes. Inorg Chem 2010; 49:7890-7. [PMID: 20666367 PMCID: PMC2933145 DOI: 10.1021/ic100899k] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The electron-donating properties of the axial His ligand to heme iron in cytochromes c (cyts c) are found to be correlated with the midpoint reduction potential (E(m)) in variants of Hydrogenobacter thermophilus cytochrome c(552) (Ht cyt c(552)) in which mutations have been made in and near the Cys-X-X-Cys-His (CXXCH) heme-binding motif. To probe the strength of the His-Fe(III) interaction, we have measured (13)C nuclear magnetic resonance (NMR) chemical shifts for (13)CN(-) bound to heme iron trans to the axial His in Ht Fe(III) cyt c(552) variants. We observe a linear relationship between these (13)C chemical shifts and E(m), indicating that the His-Fe(III) bond strength correlates with E(m). To probe a conserved hydrogen bonding interaction between the axial His Hdelta1 and the backbone carbonyl of a Pro residue, we measured the pK(a) of the axial His Hdelta1 proton (pK(a(2))), which we propose to relate to the His-Fe(III) interaction, reduction potential, and local electrostatic effects. The observed linear relationship between the axial His (13)Cbeta chemical shift and E(m) is proposed to reflect histidinate (anionic) character of the ligand. A linear relationship also is seen between the average heme methyl (1)H chemical shift and E(m) which may reflect variation in axial His electron-donating properties or in the ruffling distortion of the heme plane. In summary, chemical shifts of the axial His and exogenous CN(-) bound trans to His are shown to be sensitive probes of the His-Fe(III) interaction in variants of Ht cyt c(552) and display trends that correlate with E(m).
Collapse
Affiliation(s)
- Sarah E. J. Bowman
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| |
Collapse
|
34
|
Farrell D, O'Meara F, Johnston M, Bradley J, Søndergaard CR, Georgi N, Webb H, Tynan-Connolly BM, Bjarnadottir U, Carstensen T, Nielsen JE. Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies. Nucleic Acids Res 2010; 38:e186. [PMID: 20724439 PMCID: PMC2978379 DOI: 10.1093/nar/gkq726] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Large amounts of data are being generated annually on the connection between the sequence, structure and function of proteins using site-directed mutagenesis, protein design and directed evolution techniques. These data provide the fundamental building blocks for our understanding of protein function, molecular biology and living organisms in general. However, much experimental data are never deposited in databases and is thus 'lost' in journal publications or in PhD theses. At the same time theoretical scientists are in need of large amounts of experimental data for benchmarking and calibrating novel predictive algorithms, and theoretical progress is therefore often hampered by the lack of suitable data to validate or disprove a theoretical assumption. We present PEAT (Protein Engineering Analysis Tool), an application that integrates data deposition, storage and analysis for researchers carrying out protein engineering projects or biophysical characterization of proteins. PEAT contains modules for DNA sequence manipulation, primer design, fitting of biophysical characterization data (enzyme kinetics, circular dichroism spectroscopy, NMR titration data, etc.), and facilitates sharing of experimental data and analyses for a typical university-based research group. PEAT is freely available to academic researchers at http://enzyme.ucd.ie/PEAT.
Collapse
Affiliation(s)
- Damien Farrell
- Centre for Synthesis and Chemical Biology, School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|