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Tarabarova A, Lopukhov A, Fedorov AN, Yurkova MS. Novel His-tag Variants for Insertion Inside Polypeptide Chain. ACS OMEGA 2024; 9:858-865. [PMID: 38222536 PMCID: PMC10785306 DOI: 10.1021/acsomega.3c06682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/23/2023] [Accepted: 12/06/2023] [Indexed: 01/16/2024]
Abstract
His-tags are protein affinity tags ubiquitously used due to their convenience and effectiveness. However, in some individual cases, the attachment of His-tags to a protein's N- or C-termini resulted in impairment of the protein's structure or function, which led to attempts to include His-tags inside of polypeptide chains. In this work, we describe newly designed internal His-tags, where two triplets of histidine residues are separated by glycine residues to avoid steric hindrances and consequently minimize their impact on the protein structure. The applicability of these His-tags was tested with eGFP, a multifaceted reference protein, and GrAD207, a modified apical domain of GroEL chaperone, designed to stabilize in soluble form initially insoluble proteins. Both proteins are used as fusion partners for different purposes, and providing them with His-tags introduced into their polypeptide chains should conveniently broaden their functionality without involving the termini. We conclude that the insertable tags may be adjusted for the purification of proteins belonging to different structural classes.
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Affiliation(s)
- Anastasiia
G. Tarabarova
- A
N Bach Institute of Biochemistry of the Russian Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
| | - Anton Lopukhov
- Chemistry
Department, Lomonosov Moscow State University, GSP-1, Leninskie Gory 1/3, Moscow 119991, Russian Federation
| | - Alexey N. Fedorov
- FSI
Federal Research Centre Fundamentals of Biotechnology of the Russian
Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
| | - Maria S. Yurkova
- A
N Bach Institute of Biochemistry of the Russian Academy of Sciences, Leninskii prosp 33/2, Moscow 119071, Russian Federation
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2
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Wa Tły J, Hecel A, Wieczorek R, Rowińska-Żyrek M, Kozłowski H. Poly-Gly Region Regulates the Accessibility of Metal Binding Sites in Snake Venom Peptides. Inorg Chem 2022; 61:14247-14251. [PMID: 36039984 PMCID: PMC9472272 DOI: 10.1021/acs.inorgchem.2c02584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
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It is supposed that the presence of poly-His regions
in close proximity
to poly-Gly domains in snake venoms is related to their biological
activity; poly-His/poly-Gly (pHpG) peptides inhibit the activity of
metalloproteinases during venom storage via the chelation metal ions,
necessary for their proper functioning. This work shows that only
the histidyl residues from the N-terminal VDHDHDH motif (but not from
the poly-His tag) were the primary Zn(II) binding sites and that the
poly-Gly domain situated in the proximity of a central proline residue
may play a regulatory role in venom gland protection. The proline
induces a kink of the peptide, resulting in steric hindrance, which
may modulate the accessibility of potential metal binding sites in
the poly-His domain and may, in turn, be one of the regulators of
Zn(II) accessibility in the venom gland and therefore a modulator
of metalloproteinase activity during venom storage. The proline induces a kink of the peptide, resulting in
a steric hindrance, which may modulate the accessibility of potential
metal binding sites in the poly-His domain and may, in turn, be one
of the regulators of Zn(II) accessibility in the venom gland and therefore
a modulator of metalloproteinase activity during venom storage.
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Affiliation(s)
- Joanna Wa Tły
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland
| | - Aleksandra Hecel
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland
| | - Robert Wieczorek
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland
| | | | - Henryk Kozłowski
- Faculty of Chemistry, University of Wrocław, F. Joliot-Curie 14, Wrocław 50-383, Poland.,Institute of Health Sciences, University of Opole, 68 Katowicka Street, Opole 45-060, Poland
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3
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Wasserberg D, Cabanas-Danés J, Prangsma J, O’Mahony S, Cazade PA, Tromp E, Blum C, Thompson D, Huskens J, Subramaniam V, Jonkheijm P. Controlling Protein Surface Orientation by Strategic Placement of Oligo-Histidine Tags. ACS NANO 2017; 11:9068-9083. [PMID: 28850777 PMCID: PMC5618149 DOI: 10.1021/acsnano.7b03717] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/29/2017] [Indexed: 05/24/2023]
Abstract
We report oriented immobilization of proteins using the standard hexahistidine (His6)-Ni2+:NTA (nitrilotriacetic acid) methodology, which we systematically tuned to give control of surface coverage. Fluorescence microscopy and surface plasmon resonance measurements of self-assembled monolayers (SAMs) of red fluorescent proteins (TagRFP) showed that binding strength increased by 1 order of magnitude for each additional His6-tag on the TagRFP proteins. All TagRFP variants with His6-tags located on only one side of the barrel-shaped protein yielded a 1.5 times higher surface coverage compared to variants with His6-tags on opposite sides of the so-called β-barrel. Time-resolved fluorescence anisotropy measurements supported by polarized infrared spectroscopy verified that the orientation (and thus coverage and functionality) of proteins on surfaces can be controlled by strategic placement of a His6-tag on the protein. Molecular dynamics simulations show how the differently tagged proteins reside at the surface in "end-on" and "side-on" orientations with each His6-tag contributing to binding. Also, not every dihistidine subunit in a given His6-tag forms a full coordination bond with the Ni2+:NTA SAMs, which varied with the position of the His6-tag on the protein. At equal valency but different tag positions on the protein, differences in binding were caused by probing for Ni2+:NTA moieties and by additional electrostatic interactions between different fractions of the β-barrel structure and charged NTA moieties. Potential of mean force calculations indicate there is no specific single-protein interaction mode that provides a clear preferential surface orientation, suggesting that the experimentally measured preference for the end-on orientation is a supra-protein, not a single-protein, effect.
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Affiliation(s)
- Dorothee Wasserberg
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jordi Cabanas-Danés
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jord Prangsma
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Shane O’Mahony
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Pierre-Andre Cazade
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Eldrich Tromp
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Christian Blum
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94 T9PX, Ireland
| | - Jurriaan Huskens
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- Free
University of Amsterdam, De Boelelaan 1105, 1081 HV Amsterdam, The Netherlands
| | - Pascal Jonkheijm
- Bioinspired
Molecular Engineering Laboratory, MIRA Biomedical Technology
and Technical Medicine Institute, Molecular nanoFabrication Group, MESA+ Institute
for Nanotechnology, and Nanobiophysics Group, MESA+ Institute for Nanotechnology,
and MIRA Biomedical Technology and Technical Medicine Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Watly J, Simonovsky E, Wieczorek R, Barbosa N, Miller Y, Kozlowski H. Insight into the coordination and the binding sites of Cu(2+) by the histidyl-6-tag using experimental and computational tools. Inorg Chem 2014; 53:6675-83. [PMID: 24905906 DOI: 10.1021/ic500387u] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
His-tags are specific sequences containing six to nine subsequent histydyl residues, and they are used for purification of recombinant proteins by use of IMAC chromatography. Such polyhistydyl tags, often used in molecular biology, can be also found in nature. Proteins containing histidine-rich domains play a critical role in many life functions in both prokaryote and eukaryote organisms. Binding mode and the thermodynamic properties of the system depend on the specific metal ion and the histidine sequence. Despite the wide application of the His-tag for purification of proteins, little is known about the properties of metal-binding to such tag domains. This inspired us to undertake detailed studies on the coordination of Cu(2+) ion to hexa-His-tag. Experiments were performed using the potentiometric, UV-visible, CD, and EPR techniques. In addition, molecular dynamics (MD) simulations and density functional theory (DFT) calculations were applied. The experimental studies have shown that the Cu(2+) ion binds most likely to two imidazoles and one, two, or three amide nitrogens, depending on the pH. The structures and stabilities of the complexes for the Cu(2+)-Ac-(His)6-NH2 system using experimental and computational tools were established. Polymorphic binding states are suggested, with a possibility of the formation of α-helix structure induced by metal ion coordination. Metal ion is bound to various pairs of imidazole moieties derived from the tag with different efficiencies. The coordination sphere around the metal ion is completed by molecules of water. Finally, the Cu(2+) binding by Ac-(His)6-NH2 is much more efficient compared to other multihistidine protein domains.
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Affiliation(s)
- Joanna Watly
- Faculty of Chemistry, University of Wroclaw , 50-383 Wroclaw, Poland
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7
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Tanner P, Ezhevskaya M, Nehring R, Van Doorslaer S, Meier W, Palivan C. Specific His6-tag Attachment to Metal-Functionalized Polymersomes Relies on Molecular Recognition. J Phys Chem B 2012; 116:10113-24. [DOI: 10.1021/jp305544v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Pascal Tanner
- Department of Physical Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
| | - Maria Ezhevskaya
- Spectroscopy
in Biophysics and
Catalysis (SIBAC), Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Rainer Nehring
- Department of Physical Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
| | - Sabine Van Doorslaer
- Spectroscopy
in Biophysics and
Catalysis (SIBAC), Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Wolfgang Meier
- Department of Physical Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
| | - Cornelia Palivan
- Department of Physical Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel,
Switzerland
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8
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Determination of copper(II) ion concentration by lifetime measurements of green fluorescent protein. J Fluoresc 2011; 21:2143-53. [PMID: 21773693 DOI: 10.1007/s10895-011-0916-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 07/04/2011] [Indexed: 10/18/2022]
Abstract
The understanding of cellular processes and functions and the elucidation of their physiological mechanisms is an important aim in the life sciences. One important aspect is the uptake and the release of essential substances as well as their interactions with the cellular environment. As green fluorescent protein (GFP) can be genetically encoded in cells it can be used as an internal sensor giving a deeper insight into biochemical pathways. Here we report that the presence of copper(II) ions leads to a decrease of the fluorescence lifetime (τ(fl)) of GFP and provide evidence for Förster resonance energy transfer (FRET) as the responsible quenching mechanism. We identify the His(6)-tag as the responsible binding site for Cu(2+) with a dissociation constant K(d) = 9 ± 2 μM and a Förster radius R(0) = 2.1 ± 0.1 nm. The extent of the lifetime quenching depends on [Cu(2+)] which is comprehended by a mathematical titration model. We envision that Cu(2+) can be quantified noninvasively and in real-time by measuring τ(fl) of GFP.
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