1
|
Zeppilli D, Madabeni A, Nogara PA, Rocha JBT, Orian L. Reactivity of Zinc Fingers in Oxidizing Environments: Insight from Molecular Models Through Activation Strain Analysis. Chempluschem 2024:e202400252. [PMID: 38842473 DOI: 10.1002/cplu.202400252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/07/2024]
Abstract
The reactivity of Zn2+ tetrahedral complexes with H2O2 was investigated in silico, as a first step in their disruption process. The substrates were chosen to represent the cores of three different zinc finger protein motifs, i. e., a Zn2+ ion coordinated to four cysteines (CCCC), to three cysteines and one histidine (CCCH), and to two cysteines and two histidines (CCHH). The cysteine and histidine ligands were further simplified to methyl thiolate and imidazole, respectively. H2O2 was chosen as an oxidizing agent due to its biological role as a metabolic product and species involved in signaling processes. The mechanism of oxidation of a coordinated cysteinate to sulfenate-κS and the trends for the different substrates were rationalized through activation strain analysis and energy decomposition analysis in the framework of scalar relativistic Density Functional Theory (DFT) calculations at ZORA-M06/TZ2P ae // ZORA-BLYP-D3(BJ)/TZ2P. CCCC is oxidized most easily, an outcome explained considering both electrostatic and orbital interactions. The isomerization to sulfenate-κO was attempted to assess whether this step may affect the ligand dissociation; however, it was found to introduce a kinetic barrier without improving the energetics of the dissociation. Lastly, ligand exchange with free thiolates and selenolates was investigated as a trigger for ligand dissociation, possibly leading to metal ejection; molecular docking simulations also support this hypothesis.
Collapse
Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Pablo A Nogara
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia Sul-rio-grandense (IFSul), Av. Leonel de Moura Brizola, 2501, 96418-400, Bagé, RS, Brasil
| | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecolar, Universidade Federal de Santa Maria (UFSM), 97105-900, Santa Maria, RS, Brazil
| | - Laura Orian
- Dipartimento di Scienze Chimiche Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| |
Collapse
|
2
|
Scrima S, Tiberti M, Ryde U, Lambrughi M, Papaleo E. Comparison of force fields to study the zinc-finger containing protein NPL4, a target for disulfiram in cancer therapy. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140921. [PMID: 37230374 DOI: 10.1016/j.bbapap.2023.140921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
Molecular dynamics (MD) simulations are a powerful approach to studying the structure and dynamics of proteins related to health and disease. Advances in the MD field allow modeling proteins with high accuracy. However, modeling metal ions and their interactions with proteins is still challenging. NPL4 is a zinc-binding protein and works as a cofactor for p97 to regulate protein homeostasis. NPL4 is of biomedical importance and has been proposed as the target of disulfiram, a drug recently repurposed for cancer treatment. Experimental studies proposed that the disulfiram metabolites, bis-(diethyldithiocarbamate)‑copper and cupric ions, induce NPL4 misfolding and aggregation. However, the molecular details of their interactions with NPL4 and consequent structural effects are still elusive. Here, biomolecular simulations can help to shed light on the related structural details. To apply MD simulations to NPL4 and its interaction with copper the first important step is identifying a suitable force field to describe the protein in its zinc-bound states. We examined different sets of non-bonded parameters because we want to study the misfolding mechanism and cannot rule out that the zinc may detach from the protein during the process and copper replaces it. We investigated the force-field ability to model the coordination geometry of the metal ions by comparing the results from MD simulations with optimized geometries from quantum mechanics (QM) calculations using model systems of NPL4. Furthermore, we investigated the performance of a force field including bonded parameters to treat copper ions in NPL4 that we obtained based on QM calculations.
Collapse
Affiliation(s)
- Simone Scrima
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Ulf Ryde
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Matteo Lambrughi
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, 2100 Copenhagen, Denmark; Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark.
| |
Collapse
|
3
|
Wu H, Hegde RS. Mechanism of signal-anchor triage during early steps of membrane protein insertion. Mol Cell 2023; 83:961-973.e7. [PMID: 36764302 PMCID: PMC10155758 DOI: 10.1016/j.molcel.2023.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 12/08/2022] [Accepted: 01/18/2023] [Indexed: 02/11/2023]
Abstract
Most membrane proteins use their first transmembrane domain, known as a signal anchor (SA), for co-translational targeting to the endoplasmic reticulum (ER) via the signal recognition particle (SRP). The SA then inserts into the membrane using either the Sec61 translocation channel or the ER membrane protein complex (EMC) insertase. How EMC and Sec61 collaborate to ensure SA insertion in the correct topology is not understood. Using site-specific crosslinking, we detect a pre-insertion SA intermediate adjacent to EMC. This intermediate forms after SA release from SRP but before ribosome transfer to Sec61. The polypeptide's N-terminal tail samples a cytosolic vestibule bordered by EMC3, from where it can translocate across the membrane concomitant with SA insertion. The ribosome then docks on Sec61, which has an opportunity to insert those SAs skipped by EMC. These results suggest that EMC acts between SRP and Sec61 to triage SAs for insertion during membrane protein biogenesis.
Collapse
Affiliation(s)
- Haoxi Wu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | |
Collapse
|
4
|
Interactions of an Artificial Zinc Finger Protein with Cd(II) and Hg(II): Competition and Metal and DNA Binding. INORGANICS 2023. [DOI: 10.3390/inorganics11020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cys2His2 zinc finger proteins are important for living organisms, as they—among other functions—specifically recognise DNA when Zn(II) is coordinated to the proteins, stabilising their ββα secondary structure. Therefore, competition with other metal ions may alter their original function. Toxic metal ions such as Cd(II) or Hg(II) might be especially dangerous because of their similar chemical properties to Zn(II). Most competition studies carried out so far have involved small zinc finger peptides. Therefore, we have investigated the interactions of toxic metal ions with a zinc finger proteins consisting of three finger units and the consequences on the DNA binding properties of the protein. Binding of one Cd(II) per finger subunit of the protein was shown by circular dichroism spectroscopy, fluorimetry and electrospray ionisation mass spectrometry. Cd(II) stabilised a similar secondary structure to that of the Zn(II)-bound protein but with a slightly lower affinity. In contrast, Hg(II) could displace Zn(II) quantitatively (logβ′ ≥ 16.7), demolishing the secondary structure, and further Hg(II) binding was also observed. Based on electrophoretic gel mobility shift assays, the Cd(II)-bound zinc finger protein could recognise the specific DNA target sequence similarly to the Zn(II)-loaded form but with a ~0.6 log units lower stability constant, while Hg(II) could destroy DNA binding completely.
Collapse
|
5
|
Moulick D, Bhutia KL, Sarkar S, Roy A, Mishra UN, Pramanick B, Maitra S, Shankar T, Hazra S, Skalicky M, Brestic M, Barek V, Hossain A. The intertwining of Zn-finger motifs and abiotic stress tolerance in plants: Current status and future prospects. FRONTIERS IN PLANT SCIENCE 2023; 13:1083960. [PMID: 36684752 PMCID: PMC9846276 DOI: 10.3389/fpls.2022.1083960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Environmental stresses such as drought, high salinity, and low temperature can adversely modulate the field crop's ability by altering the morphological, physiological, and biochemical processes of the plants. It is estimated that about 50% + of the productivity of several crops is limited due to various types of abiotic stresses either presence alone or in combination (s). However, there are two ways plants can survive against these abiotic stresses; a) through management practices and b) through adaptive mechanisms to tolerate plants. These adaptive mechanisms of tolerant plants are mostly linked to their signalling transduction pathway, triggering the action of plant transcription factors and controlling the expression of various stress-regulated genes. In recent times, several studies found that Zn-finger motifs have a significant function during abiotic stress response in plants. In the first report, a wide range of Zn-binding motifs has been recognized and termed Zn-fingers. Since the zinc finger motifs regulate the function of stress-responsive genes. The Zn-finger was first reported as a repeated Zn-binding motif, comprising conserved cysteine (Cys) and histidine (His) ligands, in Xenopus laevis oocytes as a transcription factor (TF) IIIA (or TFIIIA). In the proteins where Zn2+ is mainly attached to amino acid residues and thus espousing a tetrahedral coordination geometry. The physical nature of Zn-proteins, defining the attraction of Zn-proteins for Zn2+, is crucial for having an in-depth knowledge of how a Zn2+ facilitates their characteristic function and how proteins control its mobility (intra and intercellular) as well as cellular availability. The current review summarized the concept, importance and mechanisms of Zn-finger motifs during abiotic stress response in plants.
Collapse
Affiliation(s)
- Debojyoti Moulick
- Department of Environmental Science, University of Kalyani, Nadia, West Bengal, India
| | - Karma Landup Bhutia
- Department of Agricultural Biotechnology & Molecular Breeding, College of Basic Science and Humanities, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
| | - Sukamal Sarkar
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Anirban Roy
- School of Agriculture and Rural Development, Faculty Centre for Integrated Rural Development and Management (IRDM), Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India
| | - Udit Nandan Mishra
- Department of Crop Physiology and Biochemistry, Sri University, Cuttack, Odisha, India
| | - Biswajit Pramanick
- Department of Agronomy, Dr. Rajendra Prasad Central Agricultural University, PUSA, Samastipur, Bihar, India
- Department of Agronomy and Horticulture, University of Nebraska Lincoln, Scottsbluff, NE, United States
| | - Sagar Maitra
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Tanmoy Shankar
- Department of Agronomy and Agroforestry, Centurion University of Technology and Management, Paralakhemundi, Odisha, India
| | - Swati Hazra
- School of Agricultural Sciences, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia
- Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Slovakia
| | - Viliam Barek
- Department of Water Resources and Environmental Engineering, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Nitra, Slovakia
| | - Akbar Hossain
- Division of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, Bangladesh
| |
Collapse
|
6
|
Said M, Kang CS, Wang S, Sheffler W, Salveson PJ, Bera AK, Kang A, Nguyen H, Ballard R, Li X, Bai H, Stewart L, Levine P, Baker D. Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2022; 34:9736-9744. [PMID: 36397834 PMCID: PMC9648172 DOI: 10.1021/acs.chemmater.2c02597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Despite remarkable advances in the assembly of highly structured coordination polymers and metal-organic frameworks, the rational design of such materials using more conformationally flexible organic ligands such as peptides remains challenging. In an effort to make the design of such materials fully programmable, we first developed a computational design method for generating metal-mediated 3D frameworks using rigid and symmetric peptide macrocycles with metal-coordinating sidechains. We solved the structures of six crystalline networks involving conformationally constrained 6 to 12 residue cyclic peptides with C2, C3, and S2 internal symmetry and three different types of metals (Zn2+, Co2+, or Cu2+) by single-crystal X-ray diffraction, which reveals how the peptide sequences, backbone symmetries, and metal coordination preferences drive the assembly of the resulting structures. In contrast to smaller ligands, these peptides associate through peptide-peptide interactions without full coordination of the metals, contrary to one of the assumptions underlying our computational design method. The cyclic peptides are the largest peptidic ligands reported to form crystalline coordination polymers with transition metals to date, and while more work is required to develop methods for fully programming their crystal structures, the combination of high chemical diversity with synthetic accessibility makes them attractive building blocks for engineering a broader set of new crystalline materials for use in applications such as sensing, asymmetric catalysis, and chiral separation.
Collapse
Affiliation(s)
- Meerit
Y. Said
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Christine S. Kang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Shunzhi Wang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - William Sheffler
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Patrick J. Salveson
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Asim K. Bera
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Alex Kang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Hannah Nguyen
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Ryanne Ballard
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Xinting Li
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Hua Bai
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Lance Stewart
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Paul Levine
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - David Baker
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
| |
Collapse
|
7
|
Hoffnagle AM, Eng VH, Markel U, Tezcan F. Computationally Guided Redesign of a Heme-free Cytochrome with Native-like Structure and Stability. Biochemistry 2022; 61:2063-2072. [PMID: 36106943 PMCID: PMC9949987 DOI: 10.1021/acs.biochem.2c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metals can play key roles in stabilizing protein structures, but ensuring their proper incorporation is a challenge when a metalloprotein is overexpressed in a non-native cellular environment. Here, we have used computational protein design tools to redesign cytochrome b562 (cyt b562), which relies on the binding of its heme cofactor to achieve its proper fold, into a stable, heme-free protein. The resulting protein, ApoCyt, features only four mutations and no metal-ligand or covalent bonds, yet displays improved stability over cyt b562. Mutagenesis studies and X-ray crystal structures reveal that the increase in stability is due to the computationally prescribed mutations, which stabilize the protein fold through a combination of hydrophobic packing interactions, hydrogen bonds, and cation-π interactions. Upon installation of the relevant mutations, ApoCyt is capable of assembling into previously reported, cytochrome-based trimeric and tetrameric assemblies, demonstrating that ApoCyt retains the structure and assembly properties of cyt b562. The successful design of ApoCyt therefore enables further functional diversification of cytochrome-based assemblies and demonstrates that structural metal cofactors can be replaced by a small number of well-designed, non-covalent interactions.
Collapse
Affiliation(s)
| | | | | | - F.Akif Tezcan
- Corresponding Author: F. Akif Tezcan, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States.
| |
Collapse
|
8
|
Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
Collapse
Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| |
Collapse
|
9
|
Wruck F, Tian P, Kudva R, Best RB, von Heijne G, Tans SJ, Katranidis A. The ribosome modulates folding inside the ribosomal exit tunnel. Commun Biol 2021; 4:523. [PMID: 33953328 PMCID: PMC8100117 DOI: 10.1038/s42003-021-02055-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Proteins commonly fold co-translationally at the ribosome, while the nascent chain emerges from the ribosomal exit tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is not well understood. Here, we combine optical tweezers with single-molecule FRET and molecular dynamics simulations to investigate folding of the small zinc-finger domain ADR1a inside and at the vestibule of the ribosomal tunnel. The tunnel is found to accelerate folding and stabilize the folded state, reminiscent of the effects of chaperonins. However, a simple mechanism involving stabilization by confinement does not explain the results. Instead, it appears that electrostatic interactions between the protein and ribosome contribute to the observed folding acceleration and stabilization of ADR1a.
Collapse
Affiliation(s)
- Florian Wruck
- AMOLF, Amsterdam, The Netherlands.,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands.,Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Pengfei Tian
- Protein Engineering, Novozymes A/S, Lyngby, Denmark
| | - Renuka Kudva
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Sander J Tans
- AMOLF, Amsterdam, The Netherlands. .,Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, The Netherlands. .,Kavli Institute of Nanoscience, Delft, The Netherlands.
| | - Alexandros Katranidis
- Institute of Biological Information Processing IBI-6, Forschungszentrum Jülich (FZJ), Jülich, Germany.
| |
Collapse
|
10
|
Zhang J, Yuan Y, Ye T, Tan S, Liu N, Qian J, Huang S, Xia F. Highly efficient zinc finger peptide detection with ZIF-8-modified micropipets. Chem Commun (Camb) 2021; 56:10855-10858. [PMID: 32895684 DOI: 10.1039/d0cc04683c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Zeolitic imidazolate framework-8 (ZIF-8)-modified micropipets can be an effective sensing platform for zinc finger peptides, the limit of detection of which reaches 10-2 μg ml-1. A series of techniques for detecting biomolecules are expected to emerge because of its simplicity, low cost, and universality by modifying other functional materials into the micropipets.
Collapse
Affiliation(s)
- Jinzheng Zhang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Yuqi Yuan
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Tingyan Ye
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Shiyi Tan
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Nannan Liu
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Jinjie Qian
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China
| | - Shaoming Huang
- Key Laboratory of Carbon Materials of Zhejiang Province, College of Chemistry & Materials Engineering, Wenzhou University, Wenzhou 325027, P. R. China and School of Materials and Energy, Guangzhou Key Laboratory of Low-Dimensional Materials and Energy Storage Devices, Guangdong University of Technology, Guangzhou 510006, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
| |
Collapse
|
11
|
Sargsyan K, Lin CC, Chen T, Grauffel C, Chen YP, Yang WZ, Yuan HS, Lim C. Multi-targeting of functional cysteines in multiple conserved SARS-CoV-2 domains by clinically safe Zn-ejectors. Chem Sci 2020; 11:9904-9909. [PMID: 34094251 PMCID: PMC8162115 DOI: 10.1039/d0sc02646h] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 04/22/2021] [Accepted: 08/29/2020] [Indexed: 11/21/2022] Open
Abstract
We present a near-term treatment strategy to tackle pandemic outbreaks of coronaviruses with no specific drugs/vaccines by combining evolutionary and physical principles to identify conserved viral domains containing druggable Zn-sites that can be targeted by clinically safe Zn-ejecting compounds. By applying this strategy to SARS-CoV-2 polyprotein-1ab, we predicted multiple labile Zn-sites in papain-like cysteine protease (PLpro), nsp10 transcription factor, and nsp13 helicase. These are attractive drug targets because they are highly conserved among coronaviruses and play vital structural/catalytic roles in viral proteins indispensable for virus replication. We show that five Zn-ejectors can release Zn2+ from PLpro and nsp10, and clinically-safe disulfiram and ebselen can not only covalently bind to the Zn-bound cysteines in both proteins, but also inhibit PLpro protease. We propose combining disulfiram/ebselen with broad-spectrum antivirals/drugs to target different conserved domains acting at various stages of the virus life cycle to synergistically inhibit SARS-CoV-2 replication and reduce the emergence of drug resistance.
Collapse
Affiliation(s)
- Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
| | - Chien-Chu Lin
- Institute of Molecular Biology, Academia Sinica Taipei 115 Taiwan
| | - Ting Chen
- Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
| | - Yi-Ping Chen
- Institute of Molecular Biology, Academia Sinica Taipei 115 Taiwan
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica Taipei 115 Taiwan
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica Taipei 115 Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica Taipei 115 Taiwan
- Department of Chemistry, National Tsing Hua University Hsinchu 300 Taiwan
| |
Collapse
|
12
|
Dukes MP, Rowe RK, Harvey T, Rangel W, Pedigo S. Nickel reduces calcium dependent dimerization in neural cadherin. Metallomics 2020; 11:475-482. [PMID: 30624456 DOI: 10.1039/c8mt00349a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cadherins are the transmembrane component in adherens junctions, structures that link the actin cytoskeletons in adjacent cells within solid tissues including neurological synapses, epithelium and endothelium. Cell-cell adhesion by cadherins requires the binding of calcium ions to specific sites in the extracellular region. Given the complexity of the cell adhesion microenvironment, we are investigating whether other divalent cations might affect calcium-dependent dimerization of neural (N) cadherin. The studies reported herein characterize the impact of binding physiological magnesium(ii) or neurotoxic nickel(ii) on calcium-dependent N-cadherin function. Physiological levels of magnesium have only a small effect on the calcium-binding affinity and calcium-induced dimerization of N-cadherin. However, a tenfold lower concentration of nickel decreases the apparent calcium-binding affinity and calcium-induced dimerization of N-cadherin. Competitive binding studies indicate that the apparent dissociation constants for nickel and magnesium are 0.2 mM and 2.5 mM, respectively. These Kd values are consistent with concentrations observed for a range of divalent cations in the extracellular space. Results from these studies indicate that calcium-induced dimerization by N-cadherin is attenuated by natural and non-physiological divalent cations in the extracellular microenvironment.
Collapse
Affiliation(s)
- M P Dukes
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA.
| | | | | | | | | |
Collapse
|
13
|
Padjasek M, Kocyła A, Kluska K, Kerber O, Tran JB, Krężel A. Structural zinc binding sites shaped for greater works: Structure-function relations in classical zinc finger, hook and clasp domains. J Inorg Biochem 2020; 204:110955. [DOI: 10.1016/j.jinorgbio.2019.110955] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/08/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022]
|
14
|
Su X, Meng T, Zhao Y, Li G, Cheng X, Abdullah M, Sun X, Cai Y, Lin Y. Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear ( Pyrus bretschneideri). PeerJ 2019; 7:e6628. [PMID: 30941270 PMCID: PMC6440465 DOI: 10.7717/peerj.6628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 12/12/2022] Open
Abstract
The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD genes.
Collapse
Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Tiankai Meng
- School of Life Sciences and Technology, TongJi University, Shanghai, China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, China
| | | | - Xu Sun
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Science, Anhui Agricultural University, Hefei, China
| |
Collapse
|
15
|
Owen CJ, Boles GC, Berden G, Oomens J, Armentrout PB. Experimental and theoretical investigations of infrared multiple photon dissociation spectra of lysine complexes with Zn 2+ and Cd 2. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:97-111. [PMID: 30526028 DOI: 10.1177/1469066718792902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The gas-phase structures of zinc and cadmium complexes of lysine (Lys) are investigated via a combination of infrared multiple photon dissociation action spectroscopy and ab initio quantum chemical calculations. In order to unambiguously identify the experimentally observed species, [Zn(Lys-H)]+ and CdCl+(Lys), the action spectra were compared to linear absorption spectra calculated at the B3LYP level of theory, using 6-311+G(d,p) and def2-TVZP basis sets for the zinc and cadmium systems, respectively. Single point energies were also calculated at the B3LYP, B3P86, MP2, and B3LYP-GD3BJ (accounting for empirical dispersion) levels of theory using larger basis sets. Identification of the experimentally formed isomers is possible through good agreement between infrared multiple photon dissociation action spectra and the theoretically predicted spectra. The [Zn(Lys-H)]+ complex adopts a tridentate orientation involving the amino acid backbone amine and deprotonated carboxylic acid groups as well as the side-chain amine group, [Nα,CO-,Nɛ]. The CdCl+(Lys) complex similarly adopts a tridentate chelation involving the amino acid backbone amine and carbonyl groups, as well as the side-chain amine group, [Nα,CO,Nɛ]. In both cases, the identified complexes are the lowest energy gas-phase structures at all levels of theory.
Collapse
Affiliation(s)
- Cameron J Owen
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Georgia C Boles
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| | - Giel Berden
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Jos Oomens
- 2 FELIX Laboratory, Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
- 3 Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - P B Armentrout
- 1 Department of Chemistry, University of Utah, Salt Lake City, USA
| |
Collapse
|
16
|
Kluska K, Adamczyk J, Krężel A. Metal binding properties, stability and reactivity of zinc fingers. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
17
|
Wang X, Ning Y, Yang L, Yu F, Guo X. Zinc: the Other Suspected Environmental Factor in Kashin-Beck Disease in Addition to Selenium. Biol Trace Elem Res 2017; 179:178-184. [PMID: 28224461 DOI: 10.1007/s12011-017-0964-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 02/08/2017] [Indexed: 12/19/2022]
Abstract
Kashin-Beck disease (KBD) is an endemic chronic osteochondral disease characterized by high prevalence, disability, and morbidity and is distributed from the northeast to the southwest in China, in some regions of Eastern Siberia in Russia, and in North Korea. Although the selenium deficiency etiological hypothesis for KBD has been proposed by scientists for decades, the idea that selenium deficiency is one of the most important environmental factors but not the primary and sole pathogenic factor for KBD has been widely accepted. Zn2+, which is closely involved in the synthesis of enzymes, nucleic acids, and proteins, is an essential microelement in vivo. A conundrum still exists in research on the relationship between Zn2+ and KBD due to inconsistent results, but it has been confirmed that Zn2+ can help repair metaphyseal lesions in patients with KBD, indicating that Zn2+ might play a key role in the pathogenesis of KBD, although the mechanism is unknown. The zinc-ZIP8-MTF1 axis in chondrocytes forms a catabolic cascade that promotes upregulation of the crucial effector matrix-degrading enzymes MMP3, MMP13, and ADAMTS5, thereby leading to osteoarthritis (OA) cartilage destruction. Zinc finger protein-related genes, the ZNT family, and the ZIP family of Zn2+ transporter genes have been found to be differentially expressed in KBD by high-throughput screening. Therefore, Zn2+ could play a key role in the pathogenesis of KBD.
Collapse
Affiliation(s)
- Xi Wang
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Yujie Ning
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Lei Yang
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Fangfang Yu
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xiong Guo
- School of Public Health, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an Jiaotong University Health Science Center, No.76 Yanta West Road, Xi'an, Shaanxi, 710061, People's Republic of China.
| |
Collapse
|
18
|
Koubek J, Chang YC, Yang SYC, Huang JJT. Trigger Factor-Induced Nascent Chain Dynamics Changes Suggest Two Different Chaperone-Nascent Chain Interactions during Translation. J Mol Biol 2017; 429:1733-1745. [PMID: 28385637 DOI: 10.1016/j.jmb.2017.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 11/25/2022]
Abstract
Protein biogenesis is poorly understood due to the ribosome that perturbs measurement attempted on the ribosome-bound nascent chain (RNC). Investigating nascent chain dynamics may provide invaluable insight into the co-translational processes such as structure formation or interaction with a chaperone [e.g., the bacterial trigger factor (TF)]. In this study, we aim to establish a platform for studying nascent chain dynamics by exploring the local environment near the fluorescent dye on site-specifically labeled RNCs with time-resolved fluorescence anisotropy. To prepare a quantitative model of fluorescence depolarization, we utilized intrinsically disordered protein bound to ribosome, which helped us couple the sub-nanosecond depolarization with the motion of the nascent chain backbone. This was consistent with zinc-finger-domain-containing RNCs, where the extent of sub-nanosecond motion decreased upon the addition of zinc when the fluorophore was in close proximity of the domain. After the characterization of disordered nascent chain dynamics, we investigated the synthesis of a model cytosolic protein, Entner-Doudoroff aldolase, labeled at different sites during various stages of translation. Depending on the stage of translation, the addition of the TF to the nascent chain led to two different responses in the nascent chain dynamics serendipitously, suggesting steric hindrance between the nascent chain and the chaperone as a mechanism for TF dissociation from the ribosome during translation. Overall, our study demonstrates the possible use of site-specific labeling and time-resolved anisotropy to gain insight on chaperone binding event at various stages of translation and hints on TF co-translational mechanism.
Collapse
Affiliation(s)
- Jiří Koubek
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
| | - Yi-Che Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan, 11529, R.O.C
| | | | | |
Collapse
|
19
|
Phylogenetic analysis of IDD gene family and characterization of its expression in response to flower induction in Malus. Mol Genet Genomics 2017; 292:755-771. [DOI: 10.1007/s00438-017-1306-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 03/02/2017] [Indexed: 11/27/2022]
|
20
|
Farías-Rico JA, Goetz SK, Marino J, von Heijne G. Mutational analysis of protein folding inside the ribosome exit tunnel. FEBS Lett 2016; 591:155-163. [DOI: 10.1002/1873-3468.12504] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 11/18/2016] [Accepted: 11/22/2016] [Indexed: 12/23/2022]
Affiliation(s)
- José Arcadio Farías-Rico
- Department of Biochemistry and Biophysics; Center for Biomembrane Research; Stockholm University; Sweden
| | - Sara Kathrin Goetz
- Department of Biochemistry and Biophysics; Center for Biomembrane Research; Stockholm University; Sweden
| | - Jacopo Marino
- Gene Center and Center for Integrated Protein Science Munich; CiPS-M; University of Munich; Germany
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics; Center for Biomembrane Research; Stockholm University; Sweden
- Science for Life Laboratory; Stockholm University; Solna Sweden
| |
Collapse
|
21
|
Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases. Cell Chem Biol 2016; 23:57-73. [PMID: 26933736 DOI: 10.1016/j.chembiol.2015.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 12/28/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
Programmable DNA nucleases have provided scientists with the unprecedented ability to probe, regulate, and manipulate the human genome. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat-Cas9 system (CRISPR-Cas9) represent a powerful array of tools that can bind to and cleave a specified DNA sequence. In their canonical forms, these nucleases induce double-strand breaks at a DNA locus of interest that can trigger cellular DNA repair processes that disrupt or replace genes. The fusion of these programmable nucleases with a variety of other protein domains has led to a rapidly growing suite of tools for activating, repressing, visualizing, and modifying loci of interest. Maximizing the usefulness and therapeutic relevance of these tools, however, requires precisely controlling their activity and specificity to minimize potentially toxic side effects arising from off-target activities. This need has motivated the application of chemical biology principles and methods to genome-editing proteins, including the engineering of variants of these proteins with improved or altered specificities, and the development of genetic, chemical, optical, and protein delivery methods that control the activity of these agents in cells. Advancing the capabilities, safety, effectiveness, and therapeutic relevance of genome-engineering proteins will continue to rely on chemical biology strategies that manipulate their activity, specificity, and localization.
Collapse
|
22
|
Desaki R, Sawada G, Okumura H, Ikeda R, Tanabe K, Komatsu H, Mimori K, Mori M, Kita Y, Uchikado Y, Arigami T, Uenosono Y, Owaki T, Ishigami S, Natsugoe S. As a Novel Prognostic Marker, Cysteine/histidine-rich 1 (CYHR1) is a Therapeutic Target in Patients with Esophageal Squamous Cell Carcinoma. Ann Surg Oncol 2015; 24:586-593. [PMID: 26676980 DOI: 10.1245/s10434-015-5031-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 01/02/2023]
Abstract
BACKGROUND Cysteine/histidine-rich 1 (CYHR1) was first discovered in a yeast two-hybrid screen with murine galectin-3, and no previous reports have described a relationship between the CYHR1 gene and human cancer. The current study evaluated the role and significance of CYHR1 in esophageal cancer. METHODS The human esophageal squamous cell carcinoma (ESCC) cell line TE-8 and the CYHR1 knock-down cell line TE-8/small interfering (si)-CYHR1 were used for in vitro and in vivo assays. For clinical study, ESCC tissues (n = 104) were used. RESULTS Compared with parental cells, TE-8/si-CYHR1 cells had suppressed proliferation and invasion activities. In the in vivo assay, the tumors from TE-8 cells treated with si-CYHR1 had abrogated tumorigenicity. In the clinical study, the expression of CYHR1 mRNA was associated with lymph node metastasis and stage and shown to be an independent prognostic factor. CONCLUSIONS As the findings show, CYHR1 may represent not only a valuable prognostic marker but also a therapeutic target for ESCC patients.
Collapse
Affiliation(s)
- Ryosuke Desaki
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Genta Sawada
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita, Japan
| | - Hiroshi Okumura
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan.
| | - Ryuji Ikeda
- Department of Clinical Pharmacy and Pharmacology, Graduate School of Medicine, Kagoshima University, Kagoshima, Japan
| | - Kan Tanabe
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Hisateru Komatsu
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yoshiaki Kita
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yasuto Uchikado
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Takaaki Arigami
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Yoshikazu Uenosono
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Tetsuhiro Owaki
- Education Center for Doctors in Remote Islands and Rural Areas, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Sumiya Ishigami
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| | - Shoji Natsugoe
- Department of Surgical Oncology, Digestive Surgery, Graduate School of Medical Sciences, Kagoshima University, Kagoshima, Japan
| |
Collapse
|
23
|
Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G. Cotranslational Protein Folding inside the Ribosome Exit Tunnel. Cell Rep 2015; 12:1533-40. [PMID: 26321634 PMCID: PMC4571824 DOI: 10.1016/j.celrep.2015.07.065] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 07/17/2015] [Accepted: 07/29/2015] [Indexed: 12/25/2022] Open
Abstract
At what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins. Cotranslational folding is studied by arrest-peptide-mediated force measurements Single-molecule measurements show that a pulling force prevents ribosome stalling A ribosome-tethered zinc-finger domain is visualized by cryo-EM (electron microscopy) The zinc-finger domain is shown to fold deep inside the ribosome exit tunnel
Collapse
Affiliation(s)
- Ola B Nilsson
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Rickard Hedman
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Jacopo Marino
- Gene Center and Center for Integrated Protein Science Munich, CiPS-M, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Stephan Wickles
- Gene Center and Center for Integrated Protein Science Munich, CiPS-M, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Lukas Bischoff
- Gene Center and Center for Integrated Protein Science Munich, CiPS-M, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Magnus Johansson
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Annika Müller-Lucks
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabio Trovato
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Stanford Magnetic Resonance Laboratory, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Edward P O'Brien
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Roland Beckmann
- Gene Center and Center for Integrated Protein Science Munich, CiPS-M, Feodor-Lynen-Strasse 25, University of Munich, 81377 Munich, Germany
| | - Gunnar von Heijne
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, 106 91 Stockholm, Sweden; Science for Life Laboratory, Stockholm University, Box 1031, 171 21 Solna, Sweden.
| |
Collapse
|
24
|
Reddi AR, Pawlowska M, Gibney BR. Evaluation of the Intrinsic Zn(II) Affinity of a Cys3His1 Site in the Absence of Protein Folding Effects. Inorg Chem 2015; 54:5942-8. [PMID: 26016528 DOI: 10.1021/acs.inorgchem.5b00718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Zinc finger transcription factors are the largest class of metalloproteins in the human genome. Binding of Zn(II) to their canonical Cys2His2, Cys3His1, or Cys4 sites results in metal-induced protein folding events required to achieve their biologically active structures. However, the coupled nature of metal binding and protein folding obscures the individual free energy contributions of each process toward overall zinc finger stabilization. Herein, we separate the energetic contributions of metal-ligand interactions from those of protein-protein interactions using a natural protein scaffold that retains essentially identical structures with and without Zn(II) bound, the 59 amino acid zinc binding domain of human transcription factor IIB (ZBD-TFIIB). The formation constant of Zn(II)-ZBD-TFIIB, which contains a single Cys3His1 site, was determined to be 1.5 × 10(15) M(-1) via fluorimetry and isothermal titration calorimetry. Isothermal titration calorimetry showed that Zn(II) binding is entropically favored at pH 5.5, 7.0, and 8.0 and enthalpically favored at pH 8.0 but slightly enthalpically disfavored at pH 5.5 and 7.0. The conditional dissociation constants of Zn(II)-ZBD-TFIIB and natural Cys3His1 zinc finger proteins were compared to determine the free energy cost of protein folding in the latter. Our analysis reveals that the energetic cost to fold zinc finger proteins is minimal relative to the contribution of Zn(II) binding and suggests that the true role of Zn(II) binding may be to modulate protein dynamics and/or kinetically template the protein folding process.
Collapse
Affiliation(s)
| | - Malgorzata Pawlowska
- ‡Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
| | - Brian R Gibney
- ‡Department of Chemistry, Brooklyn College, 2900 Bedford Avenue, Brooklyn, New York 11210, United States
- §Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| |
Collapse
|
25
|
Besold AN, Amick DL, Michel SLJ. A role for hydrogen bonding in DNA recognition by the non-classical CCHHC type zinc finger, NZF-1. MOLECULAR BIOSYSTEMS 2014; 10:1753-6. [PMID: 24820620 DOI: 10.1039/c4mb00246f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally important hydrogen bonding interaction.
Collapse
Affiliation(s)
- Angelique N Besold
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA.
| | | | | |
Collapse
|
26
|
Conti BJ, Elferich J, Yang Z, Shinde U, Skach WR. Cotranslational folding inhibits translocation from within the ribosome-Sec61 translocon complex. Nat Struct Mol Biol 2014; 21:228-35. [PMID: 24561504 PMCID: PMC4351553 DOI: 10.1038/nsmb.2779] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/27/2014] [Indexed: 12/31/2022]
Abstract
Eukaryotic secretory proteins cross the endoplasmic reticulum (ER) membrane through a protein-conducting channel contained within the ribosome-Sec61translocon complex (RTC). Using a zinc-finger sequence as a folding switch, we show that cotranslational folding of a secretory passenger inhibits translocation in canine ER microsomes and in human cells. Folding occurs within a cytosolically inaccessible environment, after ER targeting but before initiation of translocation, and it is most effective when the folded domain is 15-54 residues beyond the signal sequence. Under these conditions, substrate is diverted into cytosol at the stage of synthesis in which unfolded substrate enters the ER lumen. Moreover, the translocation block is reversed by passenger unfolding even after cytosol emergence. These studies identify an enclosed compartment within the assembled RTC that allows a short span of nascent chain to reversibly abort translocation in a substrate-specific manner.
Collapse
Affiliation(s)
- Brian J Conti
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Johannes Elferich
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Zhongying Yang
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Ujwal Shinde
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - William R Skach
- Department of Biochemistry and Molecular Biology, Oregon Health and Sciences University, Portland, Oregon, USA
| |
Collapse
|
27
|
Accelerated alcoholic fermentation caused by defective gene expression related to glucose derepression in Saccharomyces cerevisiae. Biosci Biotechnol Biochem 2013; 77:2255-62. [PMID: 24200791 DOI: 10.1271/bbb.130519] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sake yeast strains maintain high fermentation rates, even after the stationary growth phase begins. To determine the molecular mechanisms underlying this advantageous brewing property, we compared the gene expression profiles of sake and laboratory yeast strains of Saccharomyces cerevisiae during the stationary growth phase. DNA microarray analysis revealed that the sake yeast strain examined had defects in expression of the genes related to glucose derepression mediated by transcription factors Adr1p and Cat8p. Furthermore, deletion of the ADR1 and CAT8 genes slightly but statistically significantly improved the fermentation rate of a laboratory yeast strain. We also identified two loss-of-function mutations in the ADR1 gene of existing sake yeast strains. Taken together, these results indicate that the gene expression program associated with glucose derepression for yeast acts as an impediment to effective alcoholic fermentation under glucose-rich fermentative conditions.
Collapse
|
28
|
Jacques A, Mettra B, Lebrun V, Latour JM, Sénèque O. On the design of zinc-finger models with cyclic peptides bearing a linear tail. Chemistry 2013; 19:3921-31. [PMID: 23436718 DOI: 10.1002/chem.201204167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Indexed: 11/07/2022]
Abstract
Cyclic peptides with a linear tail (CPLT) have been successfully used to model two zinc fingers (ZFs) adopting the treble-clef- and loosened zinc-ribbon folds. In this article, we examine the factors that may influence the design of such ZF models: mutations in the sequence, size of the cycle, and size of the tail. For this purpose, several peptides derived from the CPLT-based models of the treble-clef- and loosened zinc-ribbon ZF were synthesized and studied. CPLT-based models appear to be robust toward mutations, accommodate various cycle sizes, and are sensible to the size of the linking region of the tail located between the cycle and the coordinating amino acids. Based on these criteria, we describe the design of a new CPLT-based model for the zinc-ribbon ZFs, LZR , and compare it to a linear analogue, LZR(lin) . The model complex Zn⋅LZR is able to fold correctly around the metal ion contrary to Zn⋅LZR(lin) , suggesting that CPLT-based models are more likely to yield structurally meaningful models of ZF sites than linear peptide models. Finally, we draw some rules that could allow the design of new CPLT-based metallopeptides with a controlled fold.
Collapse
Affiliation(s)
- Aurélie Jacques
- Laboratoire de Chimie et Biologie des Métaux, Equipe de Physicochimie des Métaux en Biologie, UMR 5249 CNRS/CEA-DSV-iRTSV/, Université Joseph Fourier, 17 rue des Martyrs, Grenoble 38054, France
| | | | | | | | | |
Collapse
|
29
|
Raspor P, Russell I, Stewart GG. AN UPDATE OF ZINC ION AS AN EFFECTOR OF FLOCCULATION IN BREWER'S YEAST STRAINS. JOURNAL OF THE INSTITUTE OF BREWING 2013. [DOI: 10.1002/j.2050-0416.1990.tb01035.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
30
|
Engineered Zinc Finger Nucleases for Targeted Genome Editing. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
31
|
Bitar M, Drummond MG, Costa MGS, Lobo FP, Calzavara-Silva CE, Bisch PM, Machado CR, Macedo AM, Pierce RJ, Franco GR. Modeling the zing finger protein SmZF1 from Schistosoma mansoni: Insights into DNA binding and gene regulation. J Mol Graph Model 2012; 39:29-38. [PMID: 23220279 DOI: 10.1016/j.jmgm.2012.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 10/27/2022]
Abstract
Zinc finger proteins are widely found in eukaryotes, representing an important class of DNA-binding proteins frequently involved in transcriptional regulation. Zinc finger motifs are composed by two antiparallel β-strands and one α-helix, stabilized by a zinc ion coordinated by conserved histidine and cysteine residues. In Schistosoma mansoni, these regulatory proteins are known to modulate morphological and physiological changes, having crucial roles in parasite development. A previously described C(2)H(2) zinc finger protein, SmZF1, was shown to be present in cell nuclei of different life stages of S. mansoni and to activate gene transcription in a heterologous system. A high-quality SmZF1 tridimensional structure was generated using comparative modeling. Molecular dynamics simulations of the obtained structure revealed stability of the zinc fingers motifs and high flexibility on the terminals, comparable to the profile observed on the template X-ray structure based on thermal b-factors. Based on the protein tridimensional features and amino acid composition, we were able to characterize four C(2)H(2) zinc finger motifs, the first involved in protein-protein interactions while the three others involved in DNA binding. We defined a consensus DNA binding sequence using three distinct algorithms and further carried out docking calculations, which revealed the interaction of fingers 2-4 with the predicted DNA. A search for S. mansoni genes presenting putative SmZF1 binding sites revealed 415 genes hypothetically under SmZF1 control. Using an automatic annotation and GO assignment approach, we found that the majority of those genes code for proteins involved in developmental processes. Taken together, these results present a consistent base to the structural and functional characterization of SmZF1.
Collapse
Affiliation(s)
- Mainá Bitar
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Rich AM, Bombarda E, Schenk AD, Lee PE, Cox EH, Spuches AM, Hudson LD, Kieffer B, Wilcox DE. Thermodynamics of Zn2+ binding to Cys2His2 and Cys2HisCys zinc fingers and a Cys4 transcription factor site. J Am Chem Soc 2012; 134:10405-18. [PMID: 22591173 DOI: 10.1021/ja211417g] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thermodynamics of Zn(2+) binding to three peptides corresponding to naturally occurring Zn-binding sequences in transcription factors have been quantified with isothermal titration calorimetry (ITC). These peptides, the third zinc finger of Sp1 (Sp1-3), the second zinc finger of myelin transcription factor 1 (MyT1-2), and the second Zn-binding sequence of the DNA-binding domain of glucocorticoid receptor (GR-2), bind Zn(2+) with Cys(2)His(2), Cys(2)HisCys, and Cys(4) coordination, respectively. Circular dichroism confirms that Sp1-3 and MyT1-2 have considerable and negligible Zn-stabilized secondary structure, respectively, and indicate only a small amount for GR-2. The pK(a)'s of the Sp1-3 cysteines and histidines were determined by NMR and used to estimate the number of protons displaced by Zn(2+) at pH 7.4. ITC was also used to determine this number, and the two methods agree. Subtraction of buffer contributions to the calorimetric data reveals that all three peptides have a similar affinity for Zn(2+), which has equal enthalpy and entropy components for Sp1-3 but is more enthalpically disfavored and entropically favored with increasing Cys ligands. The resulting enthalpy-entropy compensation originates from the Zn-Cys coordination, as subtraction of the cysteine deprotonation enthalpy results in a similar Zn(2+)-binding enthalpy for all three peptides, and the binding entropy tracks with the number of displaced protons. Metal and protein components of the binding enthalpy and entropy have been estimated. While dominated by Zn(2+) coordination to the cysteines and histidines, other residues in the sequence affect the protein contributions that modulate the stability of these motifs.
Collapse
Affiliation(s)
- Anne M Rich
- Department of Chemistry, Dartmouth College Hanover, New Hampshire 03755, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Michalek JL, Besold AN, Michel SLJ. Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function. Dalton Trans 2011; 40:12619-32. [PMID: 21952363 DOI: 10.1039/c1dt11071c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.
Collapse
Affiliation(s)
- Jamie L Michalek
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, USA
| | | | | |
Collapse
|
34
|
Scheck RA, Schepartz A. Surveying protein structure and function using bis-arsenical small molecules. Acc Chem Res 2011; 44:654-65. [PMID: 21766813 DOI: 10.1021/ar2001028] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exploration across the fields of biology, chemical biology, and medicine has led to an increasingly complex, albeit incomplete, view of the interactions that drive life's processes. The ability to monitor and track the movement, activity, and interactions of biomolecules in living cells is an essential part of this investigation. In our laboratory, we have endeavored to develop tools that are capable not only of monitoring protein localization but also reporting on protein structure and function. Central to our efforts is a new strategy, bipartite tetracysteine display, that relies on the specific and high-affinity interaction between a fluorogenic, bis-arsenical small molecule and a unique protein sequence, conformation, or assembly. In 1998, a small-molecule analogue of fluorescein with two arsenic atoms, FlAsH, was shown by Tsien and coworkers to fluoresce upon binding to a linear amino acid sequence, Cys-Cys-Arg-Glu-Cys-Cys. Later work demonstrated that substituting Pro-Gly for Arg-Glu optimized both binding and fluorescence yield. Our strategy of bipartite tetracysteine display emanated from the idea that it would be possible to replace the intervening Pro-Gly dipeptide in this sequence with a protein or protein partnership, provided the assembled protein fold successfully reproduced the approximate placement of the two Cys-Cys pairs. In this Account, we describe our recent progress in this area, with an emphasis on the fundamental concepts that underlie the successful use of bis-arsenicals such as FlAsH and the related ReAsH for bipartite display experiments. In particular, we highlight studies that have explored how broadly bipartite tetracysteine display can be employed and that have navigated the conformational boundary conditions favoring success. To emphasize the utility of these principles, we outline two recently reported applications of bipartite tetracysteine display. The first is a novel, encodable, selective, Src kinase sensor that lacks fluorescent proteins but possesses a fluorescent readout exceeding that of most sensors based on Förster resonance energy transfer (FRET). The second is a unique method, called complex-edited electron microscopy (CE-EM), that facilitates visualization of protein-protein complexes with electron microscopy. Exciting as these applications may be, the continued development of small-molecule tools with improved utility in living cells, let alone in vivo, will demand a more nuanced understanding of the fundamental photophysics that lead to fluorogenicity, as well as creative approaches toward the synthesis and identification of new and orthogonal dye-tag pairs that can be applied facilely in tandem. We describe one example of a dye-sequence tag pair that is chemically distinct from bis-arsenical chemistry. Through further effort, we expect that that bipartite tetracysteine display will find successful use in the study of sophisticated biological questions that are essential to the fields of biochemistry and biology as well as to our progressive understanding of human disease.
Collapse
Affiliation(s)
- Rebecca A. Scheck
- Departments of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Departments of Chemistry and Molecular, Cellular and Developmental Biology, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
35
|
Abstract
Proteins provide much of the scaffolding for life, as well as undertaking a variety of essential catalytic reactions. These characteristic functions have led us to presuppose that proteins are in general functional only when well structured and correctly folded. As we begin to explore the repertoire of possible protein sequences inherent in the human and other genomes, two stark facts that belie this supposition become clear: firstly, the number of apparent open reading frames in the human genome is significantly smaller than appears to be necessary to code for all of the diverse proteins in higher organisms, and secondly that a significant proportion of the protein sequences that would be coded by the genome would not be expected to form stable three-dimensional (3D) structures. Clearly the genome must include coding for a multitude of alternative forms of proteins, some of which may be partly or fully disordered or incompletely structured in their functional states. At the same time as this likelihood was recognized, experimental studies also began to uncover examples of important protein molecules and domains that were incompletely structured or completely disordered in solution, yet remained perfectly functional. In the ensuing years, we have seen an explosion of experimental and genome-annotation studies that have mapped the extent of the intrinsic disorder phenomenon and explored the possible biological rationales for its widespread occurrence. Answers to the question 'why would a particular domain need to be unstructured?' are as varied as the systems where such domains are found. This review provides a survey of recent new directions in this field, and includes an evaluation of the role not only of intrinsically disordered proteins but also of partially structured and highly dynamic members of the disorder-order continuum.
Collapse
|
36
|
Nomura A, Okamoto A. Phosphopeptides Designed for 5-Methylcytosine Recognition. Biochemistry 2011; 50:3376-85. [DOI: 10.1021/bi102053d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Akiko Nomura
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
| | - Akimitsu Okamoto
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
37
|
Berezovskaya Y, Armstrong CT, Boyle AL, Porrini M, Woolfson DN, Barran PE. Metal binding to a zinc-finger peptide: a comparison between solution and the gas phase. Chem Commun (Camb) 2011; 47:412-4. [DOI: 10.1039/c0cc02445g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
38
|
Kishore S, Luber S, Zavolan M. Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics 2010; 9:391-404. [PMID: 21127008 DOI: 10.1093/bfgp/elq028] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells express a large variety of ribonucleic acid-(RNA)-binding proteins (RBPs) with diverse affinity and specificity towards target RNAs that play a crucial role in almost every aspect of RNA metabolism. In addition, specific domains in RBPs impart catalytic activity or mediate protein-protein interactions, making RBPs versatile regulators of gene expression. In this review, we elaborate on recent experimental and computational approaches that have increased our understanding of RNA-protein interactions and their role in cellular function. We review aspects of gene expression that are modulated post-transcriptionally by RBPs, namely the stability of polymerase II-derived mRNA transcripts and their rate of translation into proteins. We further highlight the extensive regulatory networks of RBPs that implement a combinatorial control of gene expression. Taking cues from the recent development in the field, we argue that understanding spatio-temporal RNA-protein association on a transcriptome level will provide invaluable and unexpected insights into the regulatory codes that define growth, differentiation and disease.
Collapse
|
39
|
Parua PK, Ratnakumar S, Braun KA, Dombek KM, Arms E, Ryan PM, Young ET. 14-3-3 (Bmh) proteins inhibit transcription activation by Adr1 through direct binding to its regulatory domain. Mol Cell Biol 2010; 30:5273-83. [PMID: 20855531 PMCID: PMC2976377 DOI: 10.1128/mcb.00715-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Revised: 08/10/2010] [Accepted: 09/02/2010] [Indexed: 11/20/2022] Open
Abstract
14-3-3 proteins, known as Bmh in yeast, are ubiquitous, highly conserved proteins that function as adaptors in signal transduction pathways by binding to phosphorylated proteins to activate, inactivate, or sequester their substrates. Bmh proteins have an important role in glucose repression by binding to Reg1, the regulatory subunit of Glc7, a protein phosphatase that inactivates the AMP-activated protein kinase Snf1. We describe here another role for Bmh in glucose repression. We show that Bmh binds to the Snf1-dependent transcription factor Adr1 and inhibits its transcriptional activity. Bmh binds within the regulatory domain of Adr1 between amino acids 215 and 260, the location of mutant ADR1(c) alleles that deregulate Adr1 activity. This provides the first explanation for the phenotype resulting from these mutations. Bmh inhibits Gal4-Adr1 fusion protein activity by binding to the Ser230 region and blocking the function of a nearby cryptic activating region. ADR1(c) alleles, or the inactivation of Bmh, relieve the inhibition and Snf1 dependence of this activating region, indicating that the phosphorylation of Ser230 and Bmh are important for the inactivation of Gal4-Adr1. The Bmh binding domain is conserved in orthologs of Adr1, suggesting that it acquired an important biological function before the whole-genome duplication of the ancestor of S. cerevisiae.
Collapse
Affiliation(s)
- P. K. Parua
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - S. Ratnakumar
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - K. A. Braun
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - K. M. Dombek
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - E. Arms
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - P. M. Ryan
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| | - E. T. Young
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, Washington 98195-7350
| |
Collapse
|
40
|
Eklund DM, Ståldal V, Valsecchi I, Cierlik I, Eriksson C, Hiratsu K, Ohme-Takagi M, Sundström JF, Thelander M, Ezcurra I, Sundberg E. The Arabidopsis thaliana STYLISH1 protein acts as a transcriptional activator regulating auxin biosynthesis. THE PLANT CELL 2010; 22:349-63. [PMID: 20154152 PMCID: PMC2845406 DOI: 10.1105/tpc.108.064816] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 12/08/2009] [Accepted: 01/27/2010] [Indexed: 05/17/2023]
Abstract
The establishment and maintenance of auxin maxima in vascular plants is regulated by auxin biosynthesis and polar intercellular auxin flow. The disruption of normal auxin biosynthesis in mouse-ear cress (Arabidopsis thaliana) leads to severe abnormalities, suggesting that spatiotemporal regulation of auxin biosynthesis is fundamental for normal growth and development. We have shown previously that the induction of the SHORT-INTERNODES/STYLISH (SHI/STY) family member STY1 results in increased transcript levels of the YUCCA (YUC) family member YUC4 and also higher auxin levels and auxin biosynthesis rates in Arabidopsis seedlings. We have also shown previously that SHI/STY family members redundantly affect development of flowers and leaves. Here, we further examine the function of STY1 by analyzing its DNA and protein binding properties. Our results suggest that STY1, and most likely other SHI/STY members, are DNA binding transcriptional activators that target genes encoding proteins mediating auxin biosynthesis. This suggests that the SHI/STY family members are essential regulators of auxin-mediated leaf and flower development. Furthermore, the lack of a shoot apical meristem in seedlings carrying a fusion construct between STY1 and a repressor domain, SRDX, suggests that STY1, and other SHI/STY members, has a role in the formation and/or maintenance of the shoot apical meristem, possibly by regulating auxin levels in the embryo.
Collapse
Affiliation(s)
- D. Magnus Eklund
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Veronika Ståldal
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Isabel Valsecchi
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Izabela Cierlik
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Caitriona Eriksson
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Keiichiro Hiratsu
- Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8562, Japan
| | - Masaru Ohme-Takagi
- Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8562, Japan
| | - Jens F. Sundström
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Mattias Thelander
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Inés Ezcurra
- Department of Wood Biotechnology, Royal Institute of Technology, AlbaNova University Center, S-106 91 Stockholm, Sweden
| | - Eva Sundberg
- Department of Plant Biology and Forest Genetics, Uppsala BioCenter Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| |
Collapse
|
41
|
Tian Y, Hou X, Wen L, Guo W, Song Y, Sun H, Wang Y, Jiang L, Zhu D. A biomimetic zinc activated ion channel. Chem Commun (Camb) 2010; 46:1682-4. [DOI: 10.1039/b918006k] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
42
|
Dhanasekaran M, Negi S, Imanishi M, Suzuki M, Sugiura Y. Effects of Bulkiness and Hydrophobicity of an Aliphatic Amino Acid in the Recognition Helix of the GAGA Zinc Finger on the Stability of the Hydrophobic Core and DNA Binding Affinity. Biochemistry 2008; 47:11717-24. [DOI: 10.1021/bi801306d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Muthu Dhanasekaran
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan, and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Shigeru Negi
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan, and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Miki Imanishi
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan, and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Michiko Suzuki
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan, and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Yukio Sugiura
- Faculty of Pharmaceutical Sciences, Doshisha Women’s University, Koudo, Kyotanabe-Shi 610-0395, Japan, and Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| |
Collapse
|
43
|
Stefureac RI, Lee JS. Nanopore analysis of the folding of zinc fingers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2008; 4:1646-1650. [PMID: 18819138 DOI: 10.1002/smll.200800585] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Radu I Stefureac
- Department of Biochemistry, University of Saskatchewan, Saskatoon Saskatchewan, S7N 5E5, Canada
| | | |
Collapse
|
44
|
Transactivation, dimerization, and DNA-binding activity of white spot syndrome virus immediate-early protein IE1. J Virol 2008; 82:11362-73. [PMID: 18768963 DOI: 10.1128/jvi.01244-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Immediate-early proteins from many viruses function as transcriptional regulators and exhibit transactivation activity, DNA binding activity, and dimerization. In this study, we investigated these characteristics in white spot syndrome virus (WSSV) immediate-early protein 1 (IE1) and attempted to map the corresponding functional domains. Transactivation was investigated by transiently expressing a protein consisting of the DNA binding domain of the yeast transactivator GAL4 fused to full-length IE1. This GAL4-IE1 fusion protein successfully activated the Autographa californica multicapsid nucleopolyhedrovirus p35 basal promoter when five copies of the GAL4 DNA binding site were inserted upstream of the TATA box. A deletion series of GAL4-IE1 fusion proteins suggested that the transactivation domain of WSSV IE1 was carried within its first 80 amino acids. A point mutation assay further showed that all 12 of the acidic residues in this highly acidic domain were important for IE1's transactivation activity. DNA binding activity was confirmed by an electrophoresis mobility shift assay using a probe with (32)P-labeled random oligonucleotides. The DNA binding region of WSSV IE1 was located in its C-terminal end (amino acids 81 to 224), but mutation of a putative zinc finger motif in this C-terminal region suggested that this motif was not directly involved in the DNA binding activity. A homotypic interaction between IE1 molecules was demonstrated by glutathione S-transferase pull-down assay and a coimmunoprecipitation analysis. A glutaraldehyde cross-linking experiment and gel filtration analysis showed that this self-interaction led to the formation of stable IE1 dimers.
Collapse
|
45
|
Hatayama M, Tomizawa T, Sakai-Kato K, Bouvagnet P, Kose S, Imamoto N, Yokoyama S, Utsunomiya-Tate N, Mikoshiba K, Kigawa T, Aruga J. Functional and structural basis of the nuclear localization signal in the ZIC3 zinc finger domain. Hum Mol Genet 2008; 17:3459-73. [PMID: 18716025 PMCID: PMC2572694 DOI: 10.1093/hmg/ddn239] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Disruptions in ZIC3 cause heterotaxy, a congenital anomaly of the left–right axis. ZIC3 encodes a nuclear protein with a zinc finger (ZF) domain that contains five tandem C2H2 ZF motifs. Missense mutations in the first ZF motif (ZF1) result in defective nuclear localization, which may underlie the pathogenesis of heterotaxy. Here we revealed the structural and functional basis of the nuclear localization signal (NLS) of ZIC3 and investigated its relationship to the defect caused by ZF1 mutation. The ZIC3 NLS was located in the ZF2 and ZF3 regions, rather than ZF1. Several basic residues interspersed throughout these regions were responsible for the nuclear localization, but R320, K337 and R350 were particularly important. NMR structure analysis revealed that ZF1–4 had a similar structure to GLI ZF, and the basic side chains of the NLS clustered together in two regions on the protein surface, similar to classical bipartite NLSs. Among the residues for the ZF1 mutations, C253 and H286 were positioned for the metal chelation, whereas W255 was positioned in the hydrophobic core formed by ZF1 and ZF2. Tryptophan 255 was a highly conserved inter-finger connector and formed part of a structural motif (tandem CXW-C-H-H) that is shared with GLI, Glis and some fungal ZF proteins. Furthermore, we found that knockdown of Karyopherin α1/α6 impaired ZIC3 nuclear localization, and physical interactions between the NLS and the nuclear import adapter proteins were disturbed by mutations in the NLS but not by W255G. These results indicate that ZIC3 is imported into the cell nucleus by the Karyopherin (Importin) system and that the impaired nuclear localization by the ZF1 mutation is not due to a direct influence on the NLS.
Collapse
Affiliation(s)
- Minoru Hatayama
- Laboratory for Behavioral and Developmental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Brayer KJ, Kulshreshtha S, Segal DJ. The protein-binding potential of C2H2 zinc finger domains. Cell Biochem Biophys 2008; 51:9-19. [PMID: 18286240 DOI: 10.1007/s12013-008-9007-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 12/28/2007] [Indexed: 12/22/2022]
Abstract
There are over 10,000 C2H2-type zinc finger (ZF) domains distributed among more than 1,000 ZF proteins in the human genome. These domains are frequently observed to be involved in sequence-specific DNA binding, and uncharacterized domains are typically assumed to facilitate DNA interactions. However, some ZFs also facilitate binding to proteins or RNA. Over 100 Cys2-His2 (C2H2) ZF-protein interactions have been described. We initially attempted a bioinformatics analysis to identify sequence features that would predict a DNA- or protein-binding function. These efforts were complicated by several issues, including uncertainties about the full functional capabilities of the ZFs. We therefore applied an unbiased approach to directly examine the potential for ZFs to facilitate DNA or protein interactions. The human OLF-1/EBF associated zinc finger (OAZ) protein was used as a model. The human O/E-1-associated zinc finger protein (hOAZ) contains 30 ZFs in 6 clusters, some of which have been previously indicated in DNA or protein interactions. DNA binding was assessed using a target site selection (CAST) assay, and protein binding was assessed using a yeast two-hybrid assay. We observed that clusters known to bind DNA could facilitate specific protein interactions, but clusters known to bind protein did not facilitate specific DNA interactions. Our primary conclusion is that DNA binding is a more restricted function of ZFs, and that their potential for mediating protein interactions is likely greater. These results suggest that the role of C2H2 ZF domains in protein interactions has probably been underestimated. The implication of these findings for the prediction of ZF function is discussed.
Collapse
Affiliation(s)
- Kathryn J Brayer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | | | | |
Collapse
|
47
|
Sakai-Kato K, Ishiguro A, Mikoshiba K, Aruga J, Utsunomiya-Tate N. CD spectra show the relational style between Zic-, Gli-, Glis-zinc finger protein and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1011-9. [PMID: 18298960 DOI: 10.1016/j.bbapap.2008.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 01/16/2008] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
Abstract
Zic family proteins have five C2H2-type zinc finger motifs. The Zic-zinc finger domains show high homology to the corresponding domains of the Gli and Glis families, which also contain five C2H2-type zinc finger motifs. The zinc finger motifs of the proteins of these three protein families form an alpha-helix conformation in solution. The addition of oligo DNA that included a Gli-binding sequence increased the alpha-helix content estimated by using circular dichroism spectroscopy. Comparison of the Zic-, Gli-, and Glis-zinc fingers indicated that the alpha-helix content after the addition of oligo DNA correlated well with the affinity of each zinc finger for the oligo DNA (correlation coefficient, 0.85). The importance of the zinc ion for protein folding was reflected in a reduction in the alpha-helix content upon removal of the zinc ion. Owing to the compact globular structure, the alpha-helix structure of the proteins of these three protein families is extremely thermally stable. These results suggest that the alpha-helix structure is important for DNA binding and profoundly related to functional and structural diversity among the three families.
Collapse
Affiliation(s)
- Kumiko Sakai-Kato
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585, Japan
| | | | | | | | | |
Collapse
|
48
|
Brayer KJ, Segal DJ. Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains. Cell Biochem Biophys 2008; 50:111-31. [PMID: 18253864 DOI: 10.1007/s12013-008-9008-5] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 12/28/2007] [Indexed: 11/28/2022]
Abstract
Cys2-His2 (C2H2) zinc finger domains (ZFs) were originally identified as DNA-binding domains, and uncharacterized domains are typically assumed to function in DNA binding. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. There are even examples of zinc fingers that support both DNA and protein interactions, which can be found in well-known DNA-binding proteins such as Sp1, Zif268, and Ying Yang 1 (YY1). C2H2 protein-protein interactions (PPIs) are proving to be more abundant than previously appreciated, more plastic than their DNA-binding counterparts, and more variable and complex in their interactions surfaces. Here we review the current knowledge of over 100 C2H2 zinc finger-mediated PPIs, focusing on what is known about the binding surface, contributions of individual fingers to the interaction, and function. An accurate understanding of zinc finger biology will likely require greater insights into the potential protein interaction capabilities of C2H2 ZFs.
Collapse
Affiliation(s)
- Kathryn J Brayer
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | | |
Collapse
|
49
|
Hood L. A personal journey of discovery: developing technology and changing biology. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:1-43. [PMID: 20636073 DOI: 10.1146/annurev.anchem.1.031207.113113] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This autobiographical article describes my experiences in developing chemically based, biological technologies for deciphering biological information: DNA, RNA, proteins, interactions, and networks. The instruments developed include protein and DNA sequencers and synthesizers, as well as ink-jet technology for synthesizing DNA chips. Diverse new strategies for doing biology also arose from novel applications of these instruments. The functioning of these instruments can be integrated to generate powerful new approaches to cloning and characterizing genes from a small amount of protein sequence or to using gene sequences to synthesize peptide fragments so as to characterize various properties of the proteins. I also discuss the five paradigm changes in which I have participated: the development and integration of biological instrumentation; the human genome project; cross-disciplinary biology; systems biology; and predictive, personalized, preventive, and participatory (P4) medicine. Finally, I discuss the origins, the philosophy, some accomplishments, and the future trajectories of the Institute for Systems Biology.
Collapse
Affiliation(s)
- Lee Hood
- Institute for Systems Biology, Seattle, Washington 98103, USA.
| |
Collapse
|
50
|
Li W, Zhang J, Wang J, Wang W. Metal-coupled folding of Cys2His2 zinc-finger. J Am Chem Soc 2007; 130:892-900. [PMID: 18163620 DOI: 10.1021/ja075302g] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Zinc-fingers, which widely exist in eukaryotic cell and play crucial roles in life processes, depend on the binding of zinc ion for their proper folding. To computationally study the zinc-coupled folding of the zinc-fingers, charge transfer and metal induced protonation/deprotonation effects have to be considered. Here, by attempting to implicitly account for such effects in classical molecular dynamics and performing intensive simulations with explicit solvent for the peptides with and without zinc binding, we investigate the folding of the Cys2His2-type zinc-finger motif and the coupling between the peptide folding and zinc binding. We find that zinc ion not only stabilizes the native structure but also participates in the whole folding process. It binds to the peptide at an early stage of folding and directs or modulates the folding and stabilizations of the component beta-hairpin and alpha-helix. Such a crucial role of zinc binding is mediated by the packing of the conserved hydrophobic residues. We also find that the packing of the hydrophobic residues and the coordination of the native ligands are coupled. Meanwhile, the processes of zinc binding, mis-ligation, ligand exchange, and zinc induced secondary structure conversion as well as the water behavior due to the involvement of zinc ion are characterized. Our results are in good agreement with related experimental observations and provide significant insight into the general mechanisms of the metal cofactor dependent protein folding and other metal-induced conformational changes of biological importance.
Collapse
Affiliation(s)
- Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China
| | | | | | | |
Collapse
|