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Zavrtanik U, Medved T, Purič S, Vranken W, Lah J, Hadži S. Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins. J Mol Biol 2024; 436:168444. [PMID: 38218366 DOI: 10.1016/j.jmb.2024.168444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Medved
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Samo Purič
- Graduate Study Program, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wim Vranken
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB Structural Biology Research Centre, Brussels 1050, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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2
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Hughes RG, Zhao S, Oas TG, Schmidler SC. Efficient enumeration and visualization of helix-coil ensembles. Biophys J 2024; 123:317-333. [PMID: 38158653 PMCID: PMC10870177 DOI: 10.1016/j.bpj.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/26/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
Helix-coil models are routinely used to interpret circular dichroism data of helical peptides or predict the helicity of naturally-occurring and designed polypeptides. However, a helix-coil model contains significantly more information than mean helicity alone, as it defines the entire ensemble-the equilibrium population of every possible helix-coil configuration-for a given sequence. Many desirable quantities of this ensemble are either not obtained as ensemble averages or are not available using standard helicity-averaging calculations. Enumeration of the entire ensemble can allow calculation of a wider set of ensemble properties, but the exponential size of the configuration space typically renders this intractable. We present an algorithm that efficiently approximates the helix-coil ensemble to arbitrary accuracy by sequentially generating a list of the M highest populated configurations in descending order of population. Truncating this list of (configuration, population) pairs at a desired accuracy provides an approximating sub-ensemble. We demonstrate several uses of this approach for providing insight into helix-coil ensembles and folding mechanisms, including landscape visualization.
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Affiliation(s)
- Roy G Hughes
- Department of Biochemistry, Duke University, Durham, North Carolina
| | - Shiwen Zhao
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina
| | - Terrence G Oas
- Department of Biochemistry, Duke University, Durham, North Carolina
| | - Scott C Schmidler
- Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina; Department of Statistical Science, Duke University, Durham, North Carolina.
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3
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Martinez-Yamout MA, Nasir I, Shnitkind S, Ellis JP, Berlow RB, Kroon G, Deniz AA, Dyson HJ, Wright PE. Glutamine-rich regions of the disordered CREB transactivation domain mediate dynamic intra- and intermolecular interactions. Proc Natl Acad Sci U S A 2023; 120:e2313835120. [PMID: 37971402 PMCID: PMC10666024 DOI: 10.1073/pnas.2313835120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023] Open
Abstract
The cyclic AMP response element (CRE) binding protein (CREB) is a transcription factor that contains a 280-residue N-terminal transactivation domain and a basic leucine zipper that mediates interaction with DNA. The transactivation domain comprises three subdomains, the glutamine-rich domains Q1 and Q2 and the kinase inducible activation domain (KID). NMR chemical shifts show that the isolated subdomains are intrinsically disordered but have a propensity to populate local elements of secondary structure. The Q1 and Q2 domains exhibit a propensity for formation of short β-hairpin motifs that function as binding sites for glutamine-rich sequences. These motifs mediate intramolecular interactions between the CREB Q1 and Q2 domains as well as intermolecular interactions with the glutamine-rich Q1 domain of the TATA-box binding protein associated factor 4 (TAF4) subunit of transcription factor IID (TFIID). Using small-angle X-ray scattering, NMR, and single-molecule Förster resonance energy transfer, we show that the Q1, Q2, and KID regions remain dynamically disordered in a full-length CREB transactivation domain (CREBTAD) construct. The CREBTAD polypeptide chain is largely extended although some compaction is evident in the KID and Q2 domains. Paramagnetic relaxation enhancement reveals transient long-range contacts both within and between the Q1 and Q2 domains while the intervening KID domain is largely devoid of intramolecular interactions. Phosphorylation results in expansion of the KID domain, presumably making it more accessible for binding the CBP/p300 transcriptional coactivators. Our study reveals the complex nature of the interactions within the intrinsically disordered transactivation domain of CREB and provides molecular-level insights into dynamic and transient interactions mediated by the glutamine-rich domains.
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Affiliation(s)
- Maria A. Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Irem Nasir
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Sergey Shnitkind
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jamie P. Ellis
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Rebecca B. Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard Kroon
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ashok A. Deniz
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
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4
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Bhambid M, Dey V, Walunj S, Patankar S. Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition. Protein J 2023:10.1007/s10930-023-10128-2. [PMID: 37284905 DOI: 10.1007/s10930-023-10128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Importin α is a nuclear transporter that binds to nuclear localization signals (NLSs), consisting of 7-20 positively charged amino acids found within cargo proteins. In addition to cargo binding, intramolecular interactions also occur within the importin α protein due to binding between the importin β-binding (IBB) domain and the NLS-binding sites, a phenomenon called auto-inhibition. The interactions causing auto-inhibition are driven by a stretch of basic residues, similar to an NLS, in the IBB domain. Consistent with this, importin α proteins that do not have some of these basic residues lack auto-inhibition; a naturally occurring example of such a protein is found in the apicomplexan parasite Plasmodium falciparum. In this report, we show that importin α from another apicomplexan parasite, Toxoplasma gondii, harbors basic residues (KKR) in the IBB domain and exhibits auto-inhibition. This protein has a long, unstructured hinge motif (between the IBB domain and the NLS-binding sites) that does not contribute to auto-inhibition. However, the IBB domain may have a higher propensity to form an α-helical structure, positioning the wild-type KKR motif in an orientation that results in weaker interactions with the NLS-binding site than a KRR mutant. We conclude that the importin α protein from T. gondii shows auto-inhibition, exhibiting a different phenotype from that of P. falciparum importin α. However, our data indicate that T. gondii importin α may have a low strength of auto-inhibition. We hypothesize that low levels of auto-inhibition may confer an advantage to these important human pathogens.
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Affiliation(s)
- Manasi Bhambid
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Vishakha Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Indiana University School of Medicine, Indianapolis, USA
| | - Sujata Walunj
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- IITB-Monash Research Academy, IIT Bombay, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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5
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Sato N, Suetaka S, Hayashi Y, Arai M. Rational peptide design for inhibition of the KIX-MLL interaction. Sci Rep 2023; 13:6330. [PMID: 37072438 PMCID: PMC10113271 DOI: 10.1038/s41598-023-32848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023] Open
Abstract
The kinase-inducible domain interacting (KIX) domain is an integral part of the general transcriptional coactivator CREB-binding protein, and has been associated with leukemia, cancer, and various viral diseases. Hence, the KIX domain has attracted considerable attention in drug discovery and development. Here, we rationally designed a KIX inhibitor using a peptide fragment corresponding to the transactivation domain (TAD) of the transcriptional activator, mixed-lineage leukemia protein (MLL). We performed theoretical saturation mutagenesis using the Rosetta software to search for mutants expected to bind KIX more tightly than the wild-type MLL TAD. Mutant peptides with higher helical propensities were selected for experimental characterization. We found that the T2857W mutant of the MLL TAD peptide had the highest binding affinity for KIX compared to the other 12 peptides designed in this study. Moreover, the peptide had a high inhibitory effect on the KIX-MLL interaction with a half-maximal inhibitory concentration close to the dissociation constant for this interaction. To our knowledge, this peptide has the highest affinity for KIX among all previously reported inhibitors that target the MLL site of KIX. Thus, our approach may be useful for rationally developing helical peptides that inhibit protein-protein interactions implicated in the progression of various diseases.
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Affiliation(s)
- Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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6
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Tsirigoni AM, Goktas M, Atris Z, Valleriani A, Vila Verde A, Blank KG. Chain Sliding versus β-Sheet Formation upon Shearing Single α-Helical Coiled Coils. Macromol Biosci 2023; 23:e2200563. [PMID: 36861255 DOI: 10.1002/mabi.202200563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/20/2023] [Indexed: 03/03/2023]
Abstract
Coiled coils (CCs) are key building blocks of biogenic materials and determine their mechanical response to large deformations. Of particular interest is the observation that CC-based materials display a force-induced transition from α-helices to mechanically stronger β-sheets (αβT). Steered molecular dynamics simulations predict that this αβT requires a minimum, pulling speed-dependent CC length. Here, de novo designed CCs with a length between four to seven heptads are utilized to probe if the transition found in natural CCs can be mimicked with synthetic sequences. Using single-molecule force spectroscopy and molecular dynamics simulations, these CCs are mechanically loaded in shear geometry and their rupture forces and structural responses to the applied load are determined. Simulations at the highest pulling speed (0.01 nm ns-1 ) show the appearance of β-sheet structures for the five- and six-heptad CCs and a concomitant increase in mechanical strength. The αβT is less probable at a lower pulling speed of 0.001 nm ns-1 and is not observed in force spectroscopy experiments. For CCs loaded in shear geometry, the formation of β-sheets competes with interchain sliding. β-sheet formation is only possible in higher-order CC assemblies or in tensile-loading geometries where chain sliding and dissociation are prohibited.
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Affiliation(s)
- Anna-Maria Tsirigoni
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Melis Goktas
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Zeynep Atris
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057, Duisburg, Germany
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Am Mühlenberg 1, 14476, Potsdam, Germany.,Johannes Kepler University Linz, Institute of Experimental Physics, Department of Biomolecular & Selforganizing Matter, Altenberger Strasse 69, Linz, 4040, Austria
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7
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NMR Analysis of the Interactions and Conformational Plasticity of Dynein Intermediate Chain. Methods Mol Biol 2023; 2623:241-256. [PMID: 36602690 DOI: 10.1007/978-1-0716-2958-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cytoplasmic dynein complexes play crucial roles in intracellular transport of cellular organelles. While the motor domain of dynein is well characterized by techniques such as X-ray crystallography and cryo-electron microscopy (Cryo-EM), structural representations of dynein usually include only the more packed and easily resolved regions and omit the long flexible and poorly structured regions. One such flexible region is the N-terminal half of the intermediate chain (IC), which contains almost 300 amino acids that are predicted to be disordered. This level of disorder makes IC impossible to study by X-ray crystallography and Cryo-EM, but amenable to study by solution nuclear magnetic resonance (NMR), a powerful technique that can elucidate residue-specific information in a dynamic ensemble of structures, and transient binding interactions of associated proteins. Here, we describe the methods we use to characterize flexible and disordered proteins including protein expression, purification, sample preparation, and NMR data acquisition and analysis.
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8
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Marzella DF, Crocioni G, Parizi FM, Xue LC. The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling. Methods Mol Biol 2023; 2673:251-271. [PMID: 37258920 DOI: 10.1007/978-1-0716-3239-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Major histocompatibility complexes (MHC) play a key role in the immune surveillance system in all jawed vertebrates. MHC class I molecules randomly sample cytosolic peptides from inside the cell, while MHC class II sample exogenous peptides. Both types of peptide:MHC complex are then presented on the cell surface for recognition by αβ T cells (CD8+ and CD4+, respectively). The three-dimensional structure of such complexes can give crucial insights in the presentation and recognition mechanisms. For this reason, softwares like PANDORA have been developed to rapidly and accurately generate peptide:MHC (pMHC) 3D structures. In this chapter, we describe the protocol of PANDORA. PANDORA exploits the structural knowledge on anchor pockets that MHC molecules use to dock peptides. PANDORA provides anchor positions as restraints to guide the modeling process. This allows PANDORA to generate twenty 3D models in just about 5 min. PANDORA is highly customizable, easy to install, supports parallel processing, and is suitable to provide large datasets for deep learning algorithms.
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Affiliation(s)
- Dario F Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | | | - Farzaneh M Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Li C Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.
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9
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Jara KA, Loening NM, Reardon PN, Yu Z, Woonnimani P, Brooks C, Vesely CH, Barbar EJ. Multivalency, autoinhibition, and protein disorder in the regulation of interactions of dynein intermediate chain with dynactin and the nuclear distribution protein. eLife 2022; 11:e80217. [PMID: 36416224 PMCID: PMC9771362 DOI: 10.7554/elife.80217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
As the only major retrograde transporter along microtubules, cytoplasmic dynein plays crucial roles in the intracellular transport of organelles and other cargoes. Central to the function of this motor protein complex is dynein intermediate chain (IC), which binds the three dimeric dynein light chains at multivalent sites, and dynactin p150Glued and nuclear distribution protein (NudE) at overlapping sites of its intrinsically disordered N-terminal domain. The disorder in IC has hindered cryo-electron microscopy and X-ray crystallography studies of its structure and interactions. Here we use a suite of biophysical methods to reveal how multivalent binding of the three light chains regulates IC interactions with p150Glued and NudE. Using IC from Chaetomium thermophilum, a tractable species to interrogate IC interactions, we identify a significant reduction in binding affinity of IC to p150Glued and a loss of binding to NudE for constructs containing the entire N-terminal domain as well as for full-length constructs when compared to the tight binding observed with short IC constructs. We attribute this difference to autoinhibition caused by long-range intramolecular interactions between the N-terminal single α-helix of IC, the common site for p150Glued, and NudE binding, and residues closer to the end of the N-terminal domain. Reconstitution of IC subcomplexes demonstrates that autoinhibition is differentially regulated by light chains binding, underscoring their importance both in assembly and organization of IC, and in selection between multiple binding partners at the same site.
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Affiliation(s)
- Kayla A Jara
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | | | - Patrick N Reardon
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
- Oregon State University NMR FacilityCorvallisUnited States
| | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Prajna Woonnimani
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Coban Brooks
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Cat H Vesely
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State UniversityCorvallisUnited States
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10
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Lopes JLS, Araujo CCF, Neves RC, Bürck J, Couto SG. Structural analysis of the peptides temporin-Ra and temporin-Rb and interactions with model membranes. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:493-502. [PMID: 35978176 DOI: 10.1007/s00249-022-01615-y] [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: 04/08/2022] [Revised: 07/27/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The skin of amphibians is widely exploited as rich sources of membrane active peptides that differ in chain size, polypeptide net charge, secondary structure, target selectivity and toxicity. In this study, two small antimicrobial peptides, temporin-Ra and temporin-Rb, originally isolated from the skin of the European marsh frog (Rana ridibunda), described as active against pathogen bacteria and presenting low toxicity to eukaryotic cells were synthesized and had their physicochemical properties and mechanism of action investigated. The temporin peptides were examined in aqueous solution and in the presence of membrane models (lipid monolayers, micelles, lipid bilayers and vesicles). A combined approach of bioinformatics analyses, biological activity assays, surface pressure measurements, synchrotron radiation circular dichroism spectroscopy, and oriented circular dichroism spectroscopy were employed. Both peptides were able to adsorb at a lipid-air interface with a negative surface charge density, and efficiently disturb the lipid surface packing. A disorder-to-helix transition was observed on the secondary structure of both peptides when either in a non-polar environment or interacting with model membranes containing a negative net charge density. The binding of both temporin-Ra and temporin-Rb to membrane models is modulated by the presence of negatively charged lipids in the membrane. The amphipathic helix induced in temporin-Ra is oriented parallel to the membrane surface in negatively charged or in zwitterionic lipid bilayers, with no tendency for realignment after binding. Temporin-Rb, instead, assumes a β-sheet conformation when deposited into oriented stacked lipid bilayers. Due to their short size and simple composition, both peptides are quite attractive for the development of new classes of peptide-based anti-infective drugs.
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Affiliation(s)
- José L S Lopes
- Instituto de Física, Universidade de São Paulo, São Paulo, SP, 05080-900, Brazil
| | - Caio C F Araujo
- Faculdade de Medicina, Universidade Federal de Goiás, Goiânia, GO, 74690-900, Brazil
| | - Rogério C Neves
- Instituto de Patologia Tropical E Saúde Pública, Universidade Federal de Goiás, Goiânia, GO, 74605050, Brazil
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Sheila G Couto
- Instituto de Física, Universidade Federal de Goiás, Av. Esperança, s/n - Campus Samambaia, Goiânia, GO, 74690-900, Brazil.
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11
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Marzella DF, Parizi FM, van Tilborg D, Renaud N, Sybrandi D, Buzatu R, Rademaker DT, 't Hoen PAC, Xue LC. PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes. Front Immunol 2022; 13:878762. [PMID: 35619705 PMCID: PMC9127323 DOI: 10.3389/fimmu.2022.878762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
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Affiliation(s)
- Dario F Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Farzaneh M Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Derek van Tilborg
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands.,Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nicolas Renaud
- Natural Sciences and Engineering section, Netherlands eScience Center, Amsterdam, Netherlands
| | - Daan Sybrandi
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, Netherlands
| | - Rafaella Buzatu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Daniel T Rademaker
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Peter A C 't Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Li C Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
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12
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Disordered regions flanking the binding interface modulate affinity between CBP and NCOA. J Mol Biol 2022; 434:167643. [DOI: 10.1016/j.jmb.2022.167643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 01/01/2023]
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13
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Houston DR, Hanna JG, Lathe JC, Hillier SG, Lathe R. Evidence that nuclear receptors are related to terpene synthases. J Mol Endocrinol 2022; 68:153-166. [PMID: 35112668 PMCID: PMC8942334 DOI: 10.1530/jme-21-0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/03/2022] [Indexed: 11/08/2022]
Abstract
Ligand-activated nuclear receptors (NRs) orchestrate development, growth, and reproduction across all animal lifeforms - the Metazoa - but how NRs evolved remains mysterious. Given the NR ligands including steroids and retinoids are predominantly terpenoids, we asked whether NRs might have evolved from enzymes that catalyze terpene synthesis and metabolism. We provide evidence suggesting that NRs may be related to the terpene synthase (TS) enzyme superfamily. Based on over 10,000 3D structural comparisons, we report that the NR ligand-binding domain and TS enzymes share a conserved core of seven α-helical segments. In addition, the 3D locations of the major ligand-contacting residues are also conserved between the two protein classes. Primary sequence comparisons reveal suggestive similarities specifically between NRs and the subfamily of cis-isoprene transferases, notably with dehydrodolichyl pyrophosphate synthase and its obligate partner, NUS1/NOGOB receptor. Pharmacological overlaps between NRs and TS enzymes add weight to the contention that they share a distant evolutionary origin, and the combined data raise the possibility that a ligand-gated receptor may have arisen from an enzyme antecedent. However, our findings do not formally exclude other interpretations such as convergent evolution, and further analysis will be necessary to confirm the inferred relationship between the two protein classes.
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Affiliation(s)
- Douglas R Houston
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jane G Hanna
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Stephen G Hillier
- Medical Research Council Centre for Reproductive Health, University of Edinburgh, Edinburgh, UK
- Correspondence should be addressed to S G Hillier or R Lathe: or
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Edinburgh, UK
- Correspondence should be addressed to S G Hillier or R Lathe: or
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14
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Belčič Mikič T, Vratanar B, Pajič T, Anžej Doma S, Debeljak N, Preložnik Zupan I, Sever M, Zver S. Is It Possible to Predict Clonal Thrombocytosis in Triple-Negative Patients with Isolated Thrombocytosis Based Only on Clinical or Blood Findings? J Clin Med 2021; 10:jcm10245803. [PMID: 34945099 PMCID: PMC8706709 DOI: 10.3390/jcm10245803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/29/2022] Open
Abstract
JAK2, MPL, and CALR mutations define clonal thrombocytosis in about 90% of patients with sustained isolated thrombocytosis. In the remainder of patients (triple-negative patients) diagnosing clonal thrombocytosis is especially difficult due to the different underlying conditions and possible inconclusive bone marrow biopsy results. The ability to predict patients with sustained isolated thrombocytosis with a potential clonal origin has a prognostic value and warrants further examination. The aim of our study was to define a non-invasive clinical or blood parameter that could help predict clonal thrombocytosis in triple-negative patients. We studied 237 JAK2 V617-negative patients who were diagnosed with isolated thrombocytosis and referred to the haematology service. Sixteen routine clinical and blood parameters were included in the logistic regression model which was used to predict the type of thrombocytosis (reactive/clonal). Platelet count and lactate dehydrogenase (LDH) were the only statistically significant predictors of clonal thrombocytosis. The platelet count threshold for the most accurate prediction of clonal or reactive thrombocytosis was 449 × 109/L. Other tested clinical and blood parameters were not statistically significant predictors of clonal thrombocytosis. The level of LDH was significantly higher in CALR-positive patients compared to CALR-negative patients. We did not identify any new clinical or blood parameters that could distinguish clonal from reactive thrombocytosis. When diagnosing clonal thrombocytosis triple-negative patients are most likely to be misdiagnosed. Treatment in patients with suspected triple negative clonal thrombocytosis should not be delayed if cardiovascular risk factors or pregnancy coexist, even in the absence of firm diagnostic criteria. In those cases the approach “better treat more than less” should be followed.
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Affiliation(s)
- Tanja Belčič Mikič
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
| | - Bor Vratanar
- Institute of Biomedical Statistics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Tadej Pajič
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Clinical Institute for Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Clinical Biochemistry, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - Saša Anžej Doma
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nataša Debeljak
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia;
| | - Irena Preložnik Zupan
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Matjaž Sever
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Samo Zver
- Department of Haematology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia; (T.P.); (S.A.D.); (I.P.Z.); (M.S.); (S.Z.)
- Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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15
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Zhao VY, Rodrigues JV, Lozovsky ER, Hartl DL, Shakhnovich EI. Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity. Biophys J 2021; 120:4738-4750. [PMID: 34571014 PMCID: PMC8595743 DOI: 10.1016/j.bpj.2021.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 11/23/2022] Open
Abstract
To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study subdomain modularity by creating 20 chimeras of an enzyme, Escherichia coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. Reversion to phenylalanine at key position 31 was found to partially restore catalytic activity, which could be explained by evolutionary coupling values. We performed molecular dynamics simulations using replica exchange with solute tempering. Chimeras with low catalytic activity exhibit nonhelical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate-binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.
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Affiliation(s)
- Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Elena R Lozovsky
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts.
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16
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Murvai N, Kalmar L, Szabo B, Schad E, Micsonai A, Kardos J, Buday L, Han KH, Tompa P, Tantos A. Cellular Chaperone Function of Intrinsically Disordered Dehydrin ERD14. Int J Mol Sci 2021; 22:6190. [PMID: 34201246 PMCID: PMC8230022 DOI: 10.3390/ijms22126190] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/04/2022] Open
Abstract
Disordered plant chaperones play key roles in helping plants survive in harsh conditions, and they are indispensable for seeds to remain viable. Aside from well-known and thoroughly characterized globular chaperone proteins, there are a number of intrinsically disordered proteins (IDPs) that can also serve as highly effective protecting agents in the cells. One of the largest groups of disordered chaperones is the group of dehydrins, proteins that are expressed at high levels under different abiotic stress conditions, such as drought, high temperature, or osmotic stress. Dehydrins are characterized by the presence of different conserved sequence motifs that also serve as the basis for their categorization. Despite their accepted importance, the exact role and relevance of the conserved regions have not yet been formally addressed. Here, we explored the involvement of each conserved segment in the protective function of the intrinsically disordered stress protein (IDSP) A. thaliana's Early Response to Dehydration (ERD14). We show that segments that are directly involved in partner binding, and others that are not, are equally necessary for proper function and that cellular protection emerges from the balanced interplay of different regions of ERD14.
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Grants
- G.0029.12 Research Foundation Flanders
- 2010-88343 Korea Research Council of Fundamental Science and Technology
- NTM2231712 National Research Council of Science and Technology
- K124670 National Research, Development and Innovation Office, Hungary
- K131702 National Research, Development and Innovation Office, Hungary
- K125340 National Research, Development and Innovation Office, Hungary
- K120391 National Research, Development and Innovation Office, Hungary
- KH125597 National Research, Development and Innovation Office, Hungary
- PD135510 National Research, Development and Innovation Office, Hungary
- Bolyai János Scholarship Hungarian Academy of Sciences
- 20171582 SOLEIL Synchrotron, France
- 20180805 SOLEIL Synchrotron, France
- 20181890 SOLEIL Synchrotron, France
- Lendület Grant Hungarian Academy of Sciences
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Affiliation(s)
- Nikoletta Murvai
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Lajos Kalmar
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Beata Szabo
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Eva Schad
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - András Micsonai
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary; (A.M.); (J.K.)
| | - László Buday
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
| | - Kyou-Hoon Han
- Biomedical Translational Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Gene Editing Research Center, Division of Convergent Biomedical Research, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Peter Tompa
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
- VIB-VUB Center for Structural Biology (CSB), Vlaams Instituut voor Biotechnologie (VIB), 1050 Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium
| | - Agnes Tantos
- Research Centre for Natural Sciences, Institute of Enzymology, 1117 Budapest, Hungary; (N.M.); (L.K.); (B.S.); (E.S.); (L.B.); (P.T.)
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17
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Robustelli J, Baumgart T. Membrane partitioning and lipid selectivity of the N-terminal amphipathic H0 helices of endophilin isoforms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183660. [PMID: 34090873 DOI: 10.1016/j.bbamem.2021.183660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/23/2021] [Accepted: 05/26/2021] [Indexed: 11/26/2022]
Abstract
Endophilin is an N-BAR protein, which is characterized by a crescent-shaped BAR domain and an amphipathic helix that contributes to the membrane binding of these proteins. The exact function of that H0 helix has been a topic of debate. In mammals, there are five different endophilin isoforms, grouped into A (three members) and B (two members) subclasses, which have been described to differ in their subcellular localization and function. We asked to what extent molecular properties of the H0 helices of these members affect their membrane targeting behavior. We found that all H0 helices of the endophilin isoforms display a two-state equilibrium between disordered and α-helical states in which the helical secondary structure can be stabilized through trifluoroethanol. The helicities in high TFE were strikingly different among the H0 peptides. We investigated H0-membrane partitioning by the monitoring of secondary structure changes via CD spectroscopy. We found that the presence of anionic phospholipids is critical for all H0 helices partitioning into membranes. Membrane partitioning is found to be sensitive to variations in membrane complexity. Overall, the H0 B subfamily displays stronger membrane partitioning than the H0 A subfamily. The H0 A peptide-membrane binding occurs predominantly through electrostatic interactions. Variation among the H0 A subfamily may be attributed to slight alterations in the amino acid sequence. Meanwhile, the H0 B subfamily displays greater specificity for certain membrane compositions, and this may link H0 B peptide binding to endophilin B's cellular function.
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Affiliation(s)
- Jaclyn Robustelli
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States.
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18
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Glaser M, Bruce NJ, Han SB, Wade RC. Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics. J Phys Chem B 2021; 125:4654-4666. [PMID: 33944558 DOI: 10.1021/acs.jpcb.1c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The S100A1ct peptide, consisting of the C-terminal 20 residues of the S100A1 protein fused to an N-terminal 6-residue hydrophilic tag, has been found to exert a positive inotropic effect, resulting in improved contractile performance of failing cardiac and skeletal muscle without arrhythmic side-effects. The S100A1ct peptide thus has high potential for the treatment of acute heart failure. As a step toward understanding its molecular mechanism of action, and to provide a basis for peptidomimetic design to optimize its properties, we here describe de novo structure predictions and molecular dynamics simulations to characterize the conformational landscape of S100A1ct in aqueous environment. In S100A1, the C-terminal 20 residues form an α-helix, but de novo peptide structure predictions indicate that other conformations are also possible. Conventional molecular dynamics simulations in implicit and explicit solvent corroborated this finding. To ensure adequate sampling, we performed simulations of a tagged 10-residue segment of S100A1ct, and we carried out Gaussian accelerated molecular dynamics simulations of the peptides. These simulations showed that although the helical conformation of S100A1ct was the most energetically stable, the peptide can adopt a range of kinked conformations, suggesting that its activity may be related to its ability to act as a conformational switch.
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Affiliation(s)
- Manuel Glaser
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany
| | - Neil J Bruce
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany
| | - Sungho Bosco Han
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Rebecca C Wade
- Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany.,Informatics for Life, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), 69120 Heidelberg, Germany
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19
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Bersch B, Tarbouriech N, Burmeister WP, Iseni F. Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor. J Mol Biol 2021; 433:167009. [PMID: 33901538 DOI: 10.1016/j.jmb.2021.167009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/26/2022]
Abstract
Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304-426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20304-426-E9 complex, which is in excellent accordance with previous experimental data.
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Affiliation(s)
- Beate Bersch
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Wim P Burmeister
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP73, F-91223 Brétigny-sur-Orge Cedex, France
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20
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A unique C2 domain at the C terminus of Munc13 promotes synaptic vesicle priming. Proc Natl Acad Sci U S A 2021; 118:2016276118. [PMID: 33836576 DOI: 10.1073/pnas.2016276118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Neurotransmitter release during synaptic transmission comprises a tightly orchestrated sequence of molecular events, and Munc13-1 is a cornerstone of the fusion machinery. A forward genetic screen for defects in neurotransmitter release in Caenorhabditis elegans identified a mutation in the Munc13-1 ortholog UNC-13 that eliminated its unique and deeply conserved C-terminal module (referred to as HC2M) containing a Ca2+-insensitive C2 domain flanked by membrane-binding helices. The HC2M module could be functionally replaced in vivo by protein domains that localize to synaptic vesicles but not to the plasma membrane. HC2M is broadly conserved in other Unc13 family members and is required for efficient synaptic vesicle priming. We propose that the HC2M domain evolved as a vesicle/endosome adaptor and acquired synaptic vesicle specificity in the Unc13ABC protein family.
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21
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Sjøgaard-Frich LM, Prestel A, Pedersen ES, Severin M, Kristensen KK, Olsen JG, Kragelund BB, Pedersen SF. Dynamic Na +/H + exchanger 1 (NHE1) - calmodulin complexes of varying stoichiometry and structure regulate Ca 2+-dependent NHE1 activation. eLife 2021; 10:60889. [PMID: 33655882 PMCID: PMC8009664 DOI: 10.7554/elife.60889] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 03/01/2021] [Indexed: 11/25/2022] Open
Abstract
Calmodulin (CaM) engages in Ca2+-dependent interactions with numerous proteins, including a still incompletely understood physical and functional interaction with the human Na+/H+-exchanger NHE1. Using nuclear magnetic resonance (NMR) spectroscopy, isothermal titration calorimetry, and fibroblasts stably expressing wildtype and mutant NHE1, we discovered multiple accessible states of this functionally important complex existing in different NHE1:CaM stoichiometries and structures. We determined the NMR solution structure of a ternary complex in which CaM links two NHE1 cytosolic tails. In vitro, stoichiometries and affinities could be tuned by variations in NHE1:CaM ratio and calcium ([Ca2+]) and by phosphorylation of S648 in the first CaM-binding α-helix. In cells, Ca2+-CaM-induced NHE1 activity was reduced by mimicking S648 phosphorylation and by mutation of the first CaM-binding α-helix, whereas it was unaffected by inhibition of Akt, one of several kinases phosphorylating S648. Our results demonstrate a diversity of NHE1:CaM interaction modes and suggest that CaM may contribute to NHE1 dimerization and thereby augment NHE1 regulation. We propose that a similar structural diversity is of relevance to many other CaM complexes.
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Affiliation(s)
- Lise M Sjøgaard-Frich
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Emilie S Pedersen
- Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Marc Severin
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kølby Kristensen
- Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Stine Falsig Pedersen
- Section for Cell Biology and Physiology, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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22
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El Jahrani N, Cretin G, de Brevern AG. CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia. Platelets 2021; 33:157-167. [PMID: 33444113 DOI: 10.1080/09537104.2020.1869712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Essential thrombocythemia (ET) is a blood cancer defined by a strong increase of platelet numbers. A quarter of patients suffering from ET show mutations in the last exon of calreticulin (CALR) gene. Two variants named type 1 and type 2 represent 85% of these patients. However, a large number of other variants have been determined. In this study, we have compiled variants taken from COSMIC database and literature leading to 155 different variants. This large number of variants allowed redefining 5 new classes extending the classification of type 1-like and type 2-like to a finer description. These analyses showed that last class, named E, corresponding to more than 10% of CALR variants seemed not attached to ET. Structural properties analyzed showed that CALR variants associated to ET have common features. All the compiled and refined information had been included into a freely dedicated database CALR-ETdb (https://www.dsimb.inserm.fr/CALR-ET).
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Affiliation(s)
- Nora El Jahrani
- Université de Paris, UMR_S 1134, Université De La Réunion, Université Des Antilles, Paris, France.,INSERM, U 1134, DSIMB, Paris, France.,Institut National De La Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Gabriel Cretin
- Université de Paris, UMR_S 1134, Université De La Réunion, Université Des Antilles, Paris, France.,INSERM, U 1134, DSIMB, Paris, France.,Institut National De La Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | - Alexandre G de Brevern
- Université de Paris, UMR_S 1134, Université De La Réunion, Université Des Antilles, Paris, France.,INSERM, U 1134, DSIMB, Paris, France.,Institut National De La Transfusion Sanguine (INTS), Paris, France.,Laboratoire d'Excellence GR-Ex, Paris, France
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23
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Hendus-Altenburger R, Vogensen J, Pedersen ES, Luchini A, Araya-Secchi R, Bendsoe AH, Prasad NS, Prestel A, Cardenas M, Pedraz-Cuesta E, Arleth L, Pedersen SF, Kragelund BB. The intracellular lipid-binding domain of human Na +/H + exchanger 1 forms a lipid-protein co-structure essential for activity. Commun Biol 2020; 3:731. [PMID: 33273619 PMCID: PMC7713384 DOI: 10.1038/s42003-020-01455-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 11/03/2020] [Indexed: 12/03/2022] Open
Abstract
Dynamic interactions of proteins with lipid membranes are essential regulatory events in biology, but remain rudimentarily understood and particularly overlooked in membrane proteins. The ubiquitously expressed membrane protein Na+/H+-exchanger 1 (NHE1) regulates intracellular pH (pHi) with dysregulation linked to e.g. cancer and cardiovascular diseases. NHE1 has a long, regulatory cytosolic domain carrying a membrane-proximal region described as a lipid-interacting domain (LID), yet, the LID structure and underlying molecular mechanisms are unknown. Here we decompose these, combining structural and biophysical methods, molecular dynamics simulations, cellular biotinylation- and immunofluorescence analysis and exchanger activity assays. We find that the NHE1-LID is intrinsically disordered and, in presence of membrane mimetics, forms a helical αα-hairpin co-structure with the membrane, anchoring the regulatory domain vis-a-vis the transport domain. This co-structure is fundamental for NHE1 activity, as its disintegration reduced steady-state pHi and the rate of pHi recovery after acid loading. We propose that regulatory lipid-protein co-structures may play equally important roles in other membrane proteins.
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Affiliation(s)
- Ruth Hendus-Altenburger
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Jens Vogensen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Emilie Skotte Pedersen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Alessandra Luchini
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Raul Araya-Secchi
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Anne H Bendsoe
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Nanditha Shyam Prasad
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Marité Cardenas
- Biofilms Research Center for Biointerfaces, Malmö University, Per Albin Hanssons Väg 35, 214 32, Malmö, Sweden
| | - Elena Pedraz-Cuesta
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark
| | - Lise Arleth
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark.
| | - Stine F Pedersen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Universitetsparken 13, DK-2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.
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24
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Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
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25
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Djajamuliadi J, Ohgo K, Kumashiro KK. A Two-State Model Describes the Temperature-Dependent Conformational Equilibrium in the Alanine-Rich Domains in Elastin. J Phys Chem B 2020; 124:9017-9028. [PMID: 32936634 DOI: 10.1021/acs.jpcb.0c06811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Elastin is the insoluble elastomeric protein that provides extensibility and resilience to vertebrate tissues. Limited high-resolution structural data for elastin are notably complex. To access this information, this protein is considered in the simplified context of its two general domain types, that is, hydrophobic (HP) and crosslinking (CL). The question of elastin's structure-function has directed the focus of nearly all previous studies in the literature to the unique repeating sequences characteristic of this protein, found primarily in the HP domains. The CL domains were assumed to play a very limited role in biological elasticity due in part to the significant α-helical character that was (incorrectly) predicted for these regions. In this study, the conformational heterogeneity of alanines in native elastin's CL domains is examined in the context of helix-coil transition theory (HCTT) using solid-state nuclear magnetic resonance (SSNMR) spectroscopy in tandem with strategic isotopic labeling. Helix and coil populations are observed at all temperatures, but the former increases significantly at lower temperatures. Below the glass transition temperature (Tg), two major populations of alanines in the CL regions are resolved by two-dimensional SSNMR; one-dimensional methods are used for characterization in nativelike conditions. The spectra of 13CO-Ala in the CL regions are simulated using an HCTT-based statistical mechanical representation. Below Tg, longer segments with significant helical probabilities are consistent with the experimental data. At higher temperatures, the SSNMR lineshapes are best fit with a distribution of shorter (Ala)n segments, most in random coil. These results are used to refine a structure-function model for elastin in the context of HCTT, redirecting attention to the CL domains and their role in elasticity.
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Affiliation(s)
- Jhonsen Djajamuliadi
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kosuke Ohgo
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
| | - Kristin K Kumashiro
- Department of Chemistry, University of Hawaii, 2545 McCarthy Mall, Honolulu, Hawaii 96822, United States
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26
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Disorder in a two-domain neuronal Ca 2+-binding protein regulates domain stability and dynamics using ligand mimicry. Cell Mol Life Sci 2020; 78:2263-2278. [PMID: 32936312 PMCID: PMC7966663 DOI: 10.1007/s00018-020-03639-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/08/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]
Abstract
Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order-disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.
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27
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Loening NM, Saravanan S, Jespersen NE, Jara K, Barbar E. Interplay of Disorder and Sequence Specificity in the Formation of Stable Dynein-Dynactin Complexes. Biophys J 2020; 119:950-965. [PMID: 32814057 DOI: 10.1016/j.bpj.2020.07.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 01/22/2023] Open
Abstract
Cytoplasmic dynein is a eukaryotic motor protein complex that, along with its regulatory protein dynactin, is essential to the transport of organelles within cells. The interaction of dynein with dynactin is regulated by binding between the intermediate chain (IC) subunit of dynein and the p150Glued subunit of dynactin. Even though in the rat versions of these proteins this interaction primarily involves the single α-helix region at the N-terminus of the IC, in Drosophila and yeast ICs the removal of a nascent helix (H2) downstream of the single α-helix considerably diminishes IC-p150Glued complex stability. We find that for ICs from various species, there is a correlation between disorder in H2 and its contribution to binding affinity, and that sequence variations in H2 that do not change the level of disorder show similar binding behavior. Analysis of the structure and interactions of the IC from Chaetomium thermophilum demonstrates that the H2 region of C. thermophilum IC has a low helical propensity and establishes that H2 binds directly to the coiled-coil 1B (CC1B) domain of p150Glued, thus explaining why H2 is necessary for tight binding. Isothermal titration calorimetry, circular dichroism, and NMR studies of smaller CC1B constructs localize the region of CC1B most essential for a tight interaction with IC. These results suggest that it is the level of disorder in H2 of IC along with its charge, rather than sequence specificity, that underlie its importance in initiating tight IC-p150Glued complex formation. We speculate that the nascent H2 helix may provide conformational flexibility to initiate binding, whereas those species that have a fully folded H2 have co-opted an alternative mechanism for promoting p150Glued binding.
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Affiliation(s)
| | - Sanjana Saravanan
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Nathan E Jespersen
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Kayla Jara
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon.
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28
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Ramakrishnan R, Houben B, Rousseau F, Schymkowitz J. Differential proteostatic regulation of insoluble and abundant proteins. Bioinformatics 2020; 35:4098-4107. [PMID: 30903148 PMCID: PMC6792106 DOI: 10.1093/bioinformatics/btz214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 12/19/2022] Open
Abstract
Motivation Despite intense effort, it has been difficult to explain chaperone dependencies of proteins from sequence or structural properties. Results We constructed a database collecting all publicly available data of experimental chaperone interaction and dependency data for the Escherichia coli proteome, and enriched it with an extensive set of protein-specific as well as cell-context-dependent proteostatic parameters. Employing this new resource, we performed a comprehensive meta-analysis of the key determinants of chaperone interaction. Our study confirms that GroEL client proteins are biased toward insoluble proteins of low abundance, but for client proteins of the Trigger Factor/DnaK axis, we instead find that cellular parameters such as high protein abundance, translational efficiency and mRNA turnover are key determinants. We experimentally confirmed the finding that chaperone dependence is a function of translation rate and not protein-intrinsic parameters by tuning chaperone dependence of Green Fluorescent Protein (GFP) in E.coli by synonymous mutations only. The juxtaposition of both protein-intrinsic and cell-contextual chaperone triage mechanisms explains how the E.coli proteome achieves combining reliable production of abundant and conserved proteins, while also enabling the evolution of diverging metabolic functions. Availability and implementation The database will be made available via http://phdb.switchlab.org. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Reshmi Ramakrishnan
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Bert Houben
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Frederic Rousseau
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
| | - Joost Schymkowitz
- Switch Laboratory, Center for Brain and Disease Research, VIB.,Department of Cellular and Molecular Medicine, KULeuven, Leuven Belgium
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29
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Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma. Oncogenesis 2020; 9:59. [PMID: 32522977 PMCID: PMC7286916 DOI: 10.1038/s41389-020-0238-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Peroxisome proliferator-activated receptor-gamma (PPARγ) is a transcription factor drugable by agonists approved for treatment of type 2 diabetes, but also inhibits carcinogenesis and cell proliferation in vivo. Activating mutations in the Kirsten rat sarcoma viral oncogene homologue (KRAS) gene mitigate these beneficial effects by promoting a negative feedback-loop comprising extracellular signal-regulated kinase 1/2 (ERK1/2) and mitogen-activated kinase kinase 1/2 (MEK1/2)-dependent inactivation of PPARγ. To overcome this inhibitory mechanism, we searched for novel post-translational regulators of PPARγ. Phosphoinositide phosphatase Myotubularin-Related-Protein-7 (MTMR7) was identified as cytosolic interaction partner of PPARγ. Synthetic peptides were designed resembling the regulatory coiled-coil (CC) domain of MTMR7, and their activities studied in human cancer cell lines and C57BL6/J mice. MTMR7 formed a complex with PPARγ and increased its transcriptional activity by inhibiting ERK1/2-dependent phosphorylation of PPARγ. MTMR7-CC peptides mimicked PPARγ-activation in vitro and in vivo due to LXXLL motifs in the CC domain. Molecular dynamics simulations and docking predicted that peptides interact with the steroid receptor coactivator 1 (SRC1)-binding site of PPARγ. Thus, MTMR7 is a positive regulator of PPARγ, and its mimicry by synthetic peptides overcomes inhibitory mechanisms active in cancer cells possibly contributing to the failure of clinical studies targeting PPARγ.
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30
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Belcic Mikic T, Pajic T, Sever M. CALR mutations in a cohort of JAK2 V617F negative patients with suspected myeloproliferative neoplasms. Sci Rep 2019; 9:19838. [PMID: 31882869 PMCID: PMC6934448 DOI: 10.1038/s41598-019-56236-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Suspicion of myeloproliferative neoplasms (MPNs) and especially essential thrombocythemia (ET) in primary care is often based solely on blood counts, with patients referred to a haematologist without a thorough evaluation. We retrospectively assessed the role of calreticulin gene (CALR) mutations in the diagnosis of MPN in this population. We studied CALR mutations in 524 JAK2 V617F-negative patients with suspected MPN. Uncommon CALR mutations were confirmed by Sanger sequencing and searched for in the COSMIC or HGMD database. Mutations were defined as frameshift or non-frameshift mutations. CALR mutations were detected in 23 patients (23/524 = 4.4%). Four mutations detected in our study were newly identified mutations. Non-frameshift mutations were detected in two patients. Most patients (380/524 = 72.5%) were diagnosed with secondary conditions leading to blood count abnormalities such as iron deficiency, inflammatory and infectious diseases, malignancy and hyposplenism. Nine patients (9/23 = 39%) were retrospectively diagnosed with ET based on CALR mutation confirmation. Two patients with non-frameshift CALR mutations were diagnosed with reactive thrombocytosis and MPN unclassifiable, respectively. Our study showed that CALR mutations are important, non-invasive diagnostic indicators of ET and can aid in its diagnosis. Moreover, the type of CALR mutation must be accurately defined, as non-frameshift mutations may not be associated with ET. Finally, CALR mutation detection should be reserved for patients with high suspicion of clonal haematological disease.
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Affiliation(s)
- Tanja Belcic Mikic
- Department of Haematology, University Medical Centre Ljubljana, Zaloska 7, 1000, Ljubljana, Slovenia. .,Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Tadej Pajic
- Department of Haematology, University Medical Centre Ljubljana, Zaloska 7, 1000, Ljubljana, Slovenia.,Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000, Maribor, Slovenia
| | - Matjaz Sever
- Department of Haematology, University Medical Centre Ljubljana, Zaloska 7, 1000, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
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31
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Kumar A, Parveen S, Sharma I, Pathak H, Deshmukh MV, Sharp JA, Kumar S. Structural and mechanistic insights into EchAMP: A antimicrobial protein from the Echidna milk. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1260-1274. [PMID: 30951703 DOI: 10.1016/j.bbamem.2019.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Antibiotic resistance is a problem that necessitates the identification of new antimicrobial molecules. Milk is known to have molecules with antimicrobial properties (AMPs). Echidna Antimicrobial Protein (EchAMP) is one such lactation specific AMP exclusively found in the milk of Echidna, an egg-laying mammal geographically restricted to Australia and New Guinea. Previous studies established that EchAMP exhibits substantial bacteriostatic activity against multiple bacterial genera. However, the subsequent structural and functional studies were hindered due to the unavailability of pure protein. RESULTS In this study, we expressed EchAMP protein using a heterologous expression system and successfully purified it to >95% homogeneity. The purified recombinant protein exhibits bacteriolytic activity against both Gram-positive and Gram-negative bacteria as confirmed by live-dead staining and scanning electron microscopy. Structurally, this AMP belongs to the family of intrinsically disordered proteins (IDPs) as deciphered by the circular-dichroism, tryptophan fluorescence, and NMR spectroscopy. Nonetheless, EchAMP has the propensity to acquire structure with amphipathic molecules, or membrane mimics like SDS, lipopolysaccharides, and liposomes as again observed through multiple spectroscopic techniques. CONCLUSIONS Recombinant EchAMP exhibits broad-spectrum bacteriolytic activity by compromising the bacterial cell membrane integrity. Hence, we propose that this intrinsically disordered antimicrobial protein interact with the bacterial cell membrane and undergoes conformational changes to form channels in the membrane resulting in cell lysis. GENERAL SIGNIFICANCE EchAMP, the evolutionarily conserved, lactation specific AMP from an oviparous mammal may find application as a broad-spectrum antimicrobial against pathogens that affect mammary gland or otherwise cause routine infections in humans and livestock.
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Affiliation(s)
- Alok Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Sadiya Parveen
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Isha Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Himani Pathak
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Julie A Sharp
- Instit for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia
| | - Satish Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India.
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32
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Rodrigues JV, Ogbunugafor CB, Hartl DL, Shakhnovich EI. Chimeric dihydrofolate reductases display properties of modularity and biophysical diversity. Protein Sci 2019; 28:1359-1367. [PMID: 31095809 DOI: 10.1002/pro.3646] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/13/2019] [Indexed: 01/12/2023]
Abstract
While reverse genetics and functional genomics have long affirmed the role of individual mutations in determining protein function, there have been fewer studies addressing how large-scale changes in protein sequences, such as in entire modular segments, influence protein function and evolution. Given how recombination can reassort protein sequences, these types of changes may play an underappreciated role in how novel protein functions evolve in nature. Such studies could aid our understanding of whether certain organismal phenotypes related to protein function-such as growth in the presence or absence of an antibiotic-are robust with respect to the identity of certain modular segments. In this study, we combine molecular genetics with biochemical and biophysical methods to gain a better understanding of protein modularity in dihydrofolate reductase (DHFR), an enzyme target of antibiotics also widely used as a model for protein evolution. We replace an integral α-helical segment of Escherichia coli DHFR with segments from a number of different organisms (many nonmicrobial) and examine how these chimeric enzymes affect organismal phenotypes (e.g., resistance to an antibiotic) as well as biophysical properties of the enzyme (e.g., thermostability). We find that organismal phenotypes and enzyme properties are highly sensitive to the identity of DHFR modules, and that this chimeric approach can create enzymes with diverse biophysical characteristics.
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Affiliation(s)
- João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
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33
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Mariño L, Casasnovas R, Ramis R, Vilanova B, Ortega-Castro J, Frau J, Adrover M. Does glycation really distort the peptide α-helicity? Int J Biol Macromol 2019; 129:254-266. [DOI: 10.1016/j.ijbiomac.2019.01.213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/23/2018] [Accepted: 01/31/2019] [Indexed: 01/19/2023]
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34
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Frappier V, Jenson JM, Zhou J, Grigoryan G, Keating AE. Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1. Structure 2019; 27:606-617.e5. [PMID: 30773399 PMCID: PMC6447450 DOI: 10.1016/j.str.2019.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/20/2018] [Accepted: 01/18/2019] [Indexed: 12/25/2022]
Abstract
Understanding the relationship between protein sequence and structure well enough to design new proteins with desired functions is a longstanding goal in protein science. Here, we show that recurring tertiary structural motifs (TERMs) in the PDB provide rich information for protein-peptide interaction prediction and design. TERM statistics can be used to predict peptide binding energies for Bcl-2 family proteins as accurately as widely used structure-based tools. Furthermore, design using TERM energies (dTERMen) rapidly and reliably generates high-affinity peptide binders of anti-apoptotic proteins Bfl-1 and Mcl-1 with just 15%-38% sequence identity to any known native Bcl-2 family protein ligand. High-resolution structures of four designed peptides bound to their targets provide opportunities to analyze the strengths and limitations of the computational design method. Our results support dTERMen as a powerful approach that can complement existing tools for protein engineering.
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Affiliation(s)
- Vincent Frappier
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin M Jenson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA; Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover, NH 03755, USA; Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Center for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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35
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Conserved Glycines Control Disorder and Function in the Cold-Regulated Protein, COR15A. Biomolecules 2019; 9:biom9030084. [PMID: 30832369 PMCID: PMC6468432 DOI: 10.3390/biom9030084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/15/2019] [Accepted: 02/25/2019] [Indexed: 01/12/2023] Open
Abstract
Cold-regulated (COR) 15A is an intrinsically disordered protein (IDP) from Arabidopsis thaliana important for freezing tolerance. During freezing-induced cellular dehydration, COR15A transitions from a disordered to mostly α-helical structure. We tested whether mutations that increase the helicity of COR15A also increase its protective function. Conserved glycine residues were identified and mutated to alanine. Nuclear magnetic resonance (NMR) spectroscopy was used to identify residue-specific changes in helicity for wildtype (WT) COR15A and the mutants. Circular dichroism (CD) spectroscopy was used to monitor the coil–helix transition in response to increasing concentrations of trifluoroethanol (TFE) and ethylene glycol. The impact of the COR15A mutants on the stability of model membranes during a freeze–thaw cycle was investigated by fluorescence spectroscopy. The results of these experiments showed the mutants had a higher content of α-helical structure and the increased α-helicity improved membrane stabilization during freezing. Comparison of the TFE- and ethylene glycol-induced coil–helix transitions support our conclusion that increasing the transient helicity of COR15A in aqueous solution increases its ability to stabilize membranes during freezing. Altogether, our results suggest the conserved glycine residues are important for maintaining the disordered structure of COR15A but are also compatible with the formation of α-helical structure during freezing induced dehydration.
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36
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Teresinski HJ, Gidda SK, Nguyen TND, Howard NJM, Porter BK, Grimberg N, Smith MD, Andrews DW, Dyer JM, Mullen RT. An RK/ST C-Terminal Motif is Required for Targeting of OEP7.2 and a Subset of Other Arabidopsis Tail-Anchored Proteins to the Plastid Outer Envelope Membrane. PLANT & CELL PHYSIOLOGY 2019; 60:516-537. [PMID: 30521026 DOI: 10.1093/pcp/pcy234] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/03/2018] [Indexed: 06/09/2023]
Abstract
Tail-anchored (TA) proteins are a unique class of integral membrane proteins that possess a single C-terminal transmembrane domain and target post-translationally to the specific organelles at which they function. While significant advances have been made in recent years in elucidating the mechanisms and molecular targeting signals involved in the proper sorting of TA proteins, particularly to the endoplasmic reticulum and mitochondria, relatively little is known about the targeting of TA proteins to the plastid outer envelope. Here we show that several known or predicted plastid TA outer envelope proteins (OEPs) in Arabidopsis possess a C-terminal RK/ST sequence motif that serves as a conserved element of their plastid targeting signal. Evidence for this conclusion comes primarily from experiments with OEP7.2, which is a member of the Arabidopsis 7 kDa OEP family. We confirmed that OEP7.2 is localized to the plastid outer envelope and possesses a TA topology, and its C-terminal sequence (CTS), which includes the RK/ST motif, is essential for proper targeting to plastids. The CTS of OEP7.2 is functionally interchangeable with the CTSs of other TA OEPs that possess similar RK/ST motifs, but not with those that lack the motif. Further, a bioinformatics search based on a consensus sequence led to the identification of several new OEP TA proteins. Collectively, this study provides new insight into the mechanisms of TA protein sorting in plant cells, defines a new targeting signal element for a subset of TA OEPs and expands the number and repertoire of TA proteins at the plastid outer envelope.
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Affiliation(s)
- Howard J Teresinski
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Satinder K Gidda
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Thuy N D Nguyen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Naomi J Marty Howard
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Brittany K Porter
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Nicholas Grimberg
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - David W Andrews
- Sunnybrook Research Institute and Departments of Biochemistry and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - John M Dyer
- United States Department of Agriculture, Agricultural Research Service, US Arid-Land Agricultural Research Center, Maricopa, USA
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Degrossi JJ, Merino C, Isasmendi AM, Ibarra LM, Collins C, Bo NE, Papalia M, Fernandez JS, Hernandez CM, Papp-Wallace KM, Bonomo RA, Vazquez MS, Power P, Ramirez MS. Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases. Curr Microbiol 2019; 76:485-494. [PMID: 30783798 DOI: 10.1007/s00284-019-01653-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22-44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, blaPenO gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.
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Affiliation(s)
- José J Degrossi
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cindy Merino
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Adela M Isasmendi
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Lorena M Ibarra
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Chelsea Collins
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Nicolás E Bo
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Papalia
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jennifer S Fernandez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Claudia M Hernandez
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Departments of Microbiology and Molecular Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miryam S Vazquez
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Pablo Power
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María S Ramirez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA.
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Acharyya A, Ge Y, Wu H, DeGrado WF, Voelz VA, Gai F. Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study. J Phys Chem B 2019; 123:1797-1807. [PMID: 30694671 DOI: 10.1021/acs.jpcb.8b12220] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
One of the fundamental events in protein folding is α-helix formation, which involves sequential development of a series of helical hydrogen bonds between the backbone C═O group of residues i and the -NH group of residues i + 4. While we now know a great deal about α-helix folding dynamics, a key question that remains to be answered is where the productive helical nucleation event occurs. Statistically, a helical nucleus (or the first helical hydrogen-bond) can form anywhere within the peptide sequence in question; however, the one that leads to productive folding may only form at a preferred location. This consideration is based on the fact that the α-helical structure is inherently asymmetric, due to the specific alignment of the helical hydrogen bonds. While this hypothesis is plausible, validating it is challenging because there is not an experimental observable that can be used to directly pinpoint the location of the productive nucleation process. Therefore, in this study we combine several techniques, including peptide cross-linking, laser-induced temperature-jump infrared spectroscopy, and molecular dynamics simulations, to tackle this challenge. Taken together, our experimental and simulation results support an α-helix folding mechanism wherein the productive nucleus is formed at the N-terminus, which propagates toward the C-terminal end of the peptide to yield the folded structure. In addition, our results show that incorporation of a cross-linker can lead to formation of differently folded conformations, underscoring the need for all-atom simulations to quantitatively assess the proposed cross-linking design.
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Affiliation(s)
- Arusha Acharyya
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Yunhui Ge
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Haifan Wu
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry , University of California , San Francisco , California 94158 , United States
| | - Vincent A Voelz
- Department of Chemistry , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Feng Gai
- Department of Chemistry , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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βαβ Super-Secondary Motifs: Sequence, Structural Overview, and Pursuit of Potential Autonomously Folding βαβ Sequences from (β/α) 8/TIM Barrels. Methods Mol Biol 2019; 1958:221-236. [PMID: 30945221 DOI: 10.1007/978-1-4939-9161-7_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
βαβ super-secondary structures constitute the basic building blocks of (β/α)8 class of proteins. Despite the success in designing super-secondary structures, till date, there is not a single example of a natural βαβ sequence known to fold in isolation. In this chapter, to address the finding the "needles" in the haystack scenario, we have combined the sequence preferences and structural features of independent βαβ motifs, dictated by natural selection, with rationally derived parameters from a designed βαβ motif adopting stable fold in solution. Guided by this approach, a set of potential βαβ sequences from (β/α)8/TIM barrels are proposed as likely candidates for autonomously folding based on the assessment of their foldability.
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Anderson SA, Singhal R, Fernandez DE. Membrane-Specific Targeting of Tail-Anchored Proteins SECE1 and SECE2 Within Chloroplasts. FRONTIERS IN PLANT SCIENCE 2019; 10:1401. [PMID: 31781139 PMCID: PMC6857650 DOI: 10.3389/fpls.2019.01401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/10/2019] [Indexed: 05/20/2023]
Abstract
Membrane proteins that are imported into chloroplasts must be accurately targeted in order to maintain the identity and function of the highly differentiated internal membranes. Relatively little is known about the targeting information or pathways that direct proteins with transmembrane domains to either the inner envelope or thylakoids. In this study, we focused on a structurally simple class of membrane proteins, the tail-anchored proteins, which have stroma-exposed amino-terminal domains and a single transmembrane domain within 30 amino acids of the carboxy-terminus. SECE1 and SECE2 are essential tail-anchored proteins that function as components of the dual SEC translocases in chloroplasts. SECE1 localizes to the thylakoids, while SECE2 localizes to the inner envelope. We have used transient expression in Arabidopsis leaf protoplasts and confocal microscopy in combination with a domain-swapping strategy to identify regions that contain important targeting determinants. We show that membrane-specific targeting depends on features of the transmembrane domains and the short C-terminal tails. We probed the contributions of these regions to targeting processes further through site-directed mutagenesis. We show that thylakoid targeting still occurs when changes are made to the tail of SECE1, but changing residues in the tail of SECE2 abolishes inner envelope targeting. Finally, we discuss possible parallels between sorting of tail-anchored proteins in the stroma and in the cytosol.
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Promiscuous and Selective: How Intrinsically Disordered BH3 Proteins Interact with Their Pro-survival Partner MCL-1. J Mol Biol 2018; 430:2468-2477. [DOI: 10.1016/j.jmb.2018.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
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Wall JS, Williams A, Richey T, Stuckey A, Wooliver C, Christopher Scott J, Donnell R, Martin EB, Kennel SJ. Specific Amyloid Binding of Polybasic Peptides In Vivo Is Retained by β-Sheet Conformers but Lost in the Disrupted Coil and All D-Amino Acid Variants. Mol Imaging Biol 2018; 19:714-722. [PMID: 28229334 DOI: 10.1007/s11307-017-1063-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
PURPOSE The heparin-reactive, helical peptide p5 is an effective amyloid imaging agent in mice with systemic amyloidosis. Analogs of p5 with modified secondary structure characteristics exhibited altered binding to heparin, synthetic amyloid fibrils, and amyloid extracts in vitro. Herein, we further study the effects of peptide helicity and chirality on specific amyloid binding using a mouse model of systemic inflammation-associated (AA) amyloidosis. PROCEDURES Peptides with disrupted helical structure [p5(coil) and p5(Pro3)], with an extended sheet conformation [p5(sheet)] or an all-D enantiomer [p5(D)], were chemically synthesized, radioiodinated, and their biodistribution studied in WT mice as well as transgenic animals with severe systemic AA amyloidosis. Peptide binding was assessed qualitatively by using small animal single-photon emission computed tomography/x-ray computed tomography imaging and microautoradiography and quantitatively using tissue counting. RESULTS Peptides with reduced helical propensity, p5(coil) and p5(Pro3), exhibited significantly reduced binding to AA amyloid-laden organs. In contrast, peptide p5(D) was retained by non-amyloid-related ligands in the liver and kidneys of both WT and AA mice, but it also bound AA amyloid in the spleen. The p5(sheet) peptide specifically bound AA amyloid in vivo and was not retained by healthy tissues in WT animals. CONCLUSIONS Modification of amyloid-targeting peptides using D-amino acids should be performed cautiously due to the introduction of unexpected secondary pharmacologic effects. Peptides that adopt a helical structure, to align charged amino acid side chains along one face, exhibit specific reactivity with amyloid; however, polybasic peptides with a propensity for β-sheet conformation are also amyloid-reactive and may yield a novel class of amyloid-targeting agents for imaging and therapy.
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Affiliation(s)
- Jonathan S Wall
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA. .,Departments of Radiology, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA.
| | - Angela Williams
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Tina Richey
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Alan Stuckey
- Departments of Radiology, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Craig Wooliver
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - J Christopher Scott
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Robert Donnell
- Department of Pathobiology, University of Tennessee College of Veterinary Medicine, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Emily B Martin
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
| | - Stephen J Kennel
- Departments of Medicine, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA.,Departments of Radiology, Graduate School of Medicine, University of Tennessee, 1924 Alcoa Hwy, Knoxville, TN, 37920, USA
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Dahal L, Shammas SL, Clarke J. Phosphorylation of the IDP KID Modulates Affinity for KIX by Increasing the Lifetime of the Complex. Biophys J 2018; 113:2706-2712. [PMID: 29262363 PMCID: PMC5770967 DOI: 10.1016/j.bpj.2017.10.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 11/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are known to undergo a range of posttranslational modifications, but by what mechanism do such modifications affect the binding of an IDP to its partner protein? We investigate this question using one such IDP, the kinase inducible domain (KID) of the transcription factor CREB, which interacts with the KIX domain of CREB-binding protein upon phosphorylation. As with many other IDPs, KID undergoes coupled folding and binding to form α-helical structure upon interacting with KIX. This single site phosphorylation plays an important role in the control of transcriptional activation in vivo. Here we show that, contrary to expectation, phosphorylation has no effect on association rates—unphosphorylated KID binds just as rapidly as pKID, the phosphorylated form—but rather, acts by increasing the lifetime of the complex. We propose that by controlling the lifetime of the bound complex of pKID:KIX via altering the dissociation rate, phosphorylation can facilitate effective control of transcription regulation.
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Affiliation(s)
- Liza Dahal
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Sarah L Shammas
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
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Cohen-Khait R, Dym O, Hamer-Rogotner S, Schreiber G. Promiscuous Protein Binding as a Function of Protein Stability. Structure 2017; 25:1867-1874.e3. [DOI: 10.1016/j.str.2017.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 11/03/2017] [Indexed: 11/28/2022]
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Genetic Separation of Sae2 Nuclease Activity from Mre11 Nuclease Functions in Budding Yeast. Mol Cell Biol 2017; 37:MCB.00156-17. [PMID: 28970327 DOI: 10.1128/mcb.00156-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
Sae2 promotes the repair of DNA double-strand breaks in Saccharomyces cerevisiae The role of Sae2 is linked to the Mre11/Rad50/Xrs2 (MRX) complex, which is important for the processing of DNA ends into single-stranded substrates for homologous recombination. Sae2 has intrinsic endonuclease activity, but the role of this activity has not been assessed independently from its functions in promoting Mre11 nuclease activity. Here we identify and characterize separation-of-function mutants that lack intrinsic nuclease activity or the ability to promote Mre11 endonucleolytic activity. We find that the ability of Sae2 to promote MRX nuclease functions is important for DNA damage survival, particularly in the absence of Dna2 nuclease activity. In contrast, Sae2 nuclease activity is essential for DNA repair when the Mre11 nuclease is compromised. Resection of DNA breaks is impaired when either Sae2 activity is blocked, suggesting roles for both Mre11 and Sae2 nuclease activities in promoting the processing of DNA ends in vivo Finally, both activities of Sae2 are important for sporulation, indicating that the processing of meiotic breaks requires both Mre11 and Sae2 nuclease activities.
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Leprince J, Bagnol D, Bureau R, Fukusumi S, Granata R, Hinuma S, Larhammar D, Primeaux S, Sopkova-de Oliveiras Santos J, Tsutsui K, Ukena K, Vaudry H. The Arg-Phe-amide peptide 26RFa/glutamine RF-amide peptide and its receptor: IUPHAR Review 24. Br J Pharmacol 2017; 174:3573-3607. [PMID: 28613414 DOI: 10.1111/bph.13907] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 05/30/2017] [Accepted: 06/05/2017] [Indexed: 12/21/2022] Open
Abstract
The RFamide neuropeptide 26RFa was first isolated from the brain of the European green frog on the basis of cross-reactivity with antibodies raised against bovine neuropeptide FF (NPFF). 26RFa and its N-terminally extended form glutamine RF-amide peptide (QRFP) have been identified as cognate ligands of the former orphan receptor GPR103, now renamed glutamine RF-amide peptide receptor (QRFP receptor). The 26RFa/QRFP precursor has been characterized in various mammalian and non-mammalian species. In the brain of mammals, including humans, 26RFa/QRFP mRNA is almost exclusively expressed in hypothalamic nuclei. The 26RFa/QRFP transcript is also present in various organs especially in endocrine glands. While humans express only one QRFP receptor, two isoforms are present in rodents. The QRFP receptor genes are widely expressed in the CNS and in peripheral tissues, notably in bone, heart, kidney, pancreas and testis. Structure-activity relationship studies have led to the identification of low MW peptidergic agonists and antagonists of QRFP receptor. Concurrently, several selective non-peptidic antagonists have been designed from high-throughput screening hit optimization. Consistent with the widespread distribution of QRFP receptor mRNA and 26RFa binding sites, 26RFa/QRFP exerts a large range of biological activities, notably in the control of energy homeostasis, bone formation and nociception that are mediated by QRFP receptor or NPFF2. The present report reviews the current knowledge concerning the 26RFa/QRFP-QRFP receptor system and discusses the potential use of selective QRFP receptor ligands for therapeutic applications.
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Affiliation(s)
- Jérôme Leprince
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, Normandy University, Rouen, France
| | - Didier Bagnol
- CNS Drug Discovery, Arena Pharmaceuticals Inc., San Diego, CA, USA
| | - Ronan Bureau
- Normandy Centre for Studies and Research on Medicines (CERMN), Normandy University, Caen, France
| | - Shoji Fukusumi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Riccarda Granata
- Laboratory of Molecular and Cellular Endocrinology, Division of Endocrinology, Diabetes and Metabolism, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Shuji Hinuma
- Department of Food and Nutrition, Faculty of Human Life Science, Senri Kinran University, Suita-City, Osaka, Japan
| | - Dan Larhammar
- Department of Neuroscience, Unit of Pharmacology, Uppsala University, Uppsala, Sweden
| | - Stefany Primeaux
- Department of Physiology, Joint Diabetes, Endocrinology & Metabolism Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | | | - Kazuyoshi Tsutsui
- Laboratory of Integrative Brain Sciences, Department of Biology, Waseda University, Center for Medical Life Science, Tokyo, Japan
| | - Kazuyoshi Ukena
- Section of Behavioral Sciences, Graduate School of Integrated Arts and Sciences, Hiroshima University, Higashi-Hiroshima, Japan
| | - Hubert Vaudry
- INSERM U1239, Laboratory of Neuronal and Neuroendocrine Differentiation and Communication, Normandy University, Rouen, France
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Affinity of IDPs to their targets is modulated by ion-specific changes in kinetics and residual structure. Proc Natl Acad Sci U S A 2017; 114:9882-9887. [PMID: 28847960 DOI: 10.1073/pnas.1705105114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure. Instead, they populate ensembles of rapidly interconverting conformations with marginal structural stabilities. Changes in solution conditions such as temperature and crowding agents consequently affect IDPs more than their folded counterparts. Here we reveal that the residual structure content of IDPs is modulated both by ionic strength and by the type of ions present in solution. We show that these ion-specific structural changes result in binding affinity shifts of up to sixfold, which happen through alteration of both association and dissociation rates. These effects follow the Hofmeister series, but unlike the well-established effects on the stability of folded proteins, they already occur at low, hypotonic concentrations of salt. We attribute this sensitivity to the marginal stability of IDPs, which could have physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of different cellular compartments, and the role of ions in biology.
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Burra G, Thakur AK. Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease. Biopolymers 2017; 108. [DOI: 10.1002/bip.23021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 04/03/2017] [Accepted: 04/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Gunasekhar Burra
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
| | - Ashwani Kumar Thakur
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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Wragg RT, Parisotto DA, Li Z, Terakawa MS, Snead D, Basu I, Weinstein H, Eliezer D, Dittman JS. Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins. Front Mol Neurosci 2017; 10:146. [PMID: 28603484 PMCID: PMC5445133 DOI: 10.3389/fnmol.2017.00146] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/30/2017] [Indexed: 12/19/2022] Open
Abstract
Complexin is a critical presynaptic protein that regulates both spontaneous and calcium-triggered neurotransmitter release in all synapses. Although the SNARE-binding central helix of complexin is highly conserved and required for all known complexin functions, the remainder of the protein has profoundly diverged across the animal kingdom. Striking disparities in complexin inhibitory activity are observed between vertebrate and invertebrate complexins but little is known about the source of these differences or their relevance to the underlying mechanism of complexin regulation. We found that mouse complexin 1 (mCpx1) failed to inhibit neurotransmitter secretion in Caenorhabditis elegans neuromuscular junctions lacking the worm complexin 1 (CPX-1). This lack of inhibition stemmed from differences in the C-terminal domain (CTD) of mCpx1. Previous studies revealed that the CTD selectively binds to highly curved membranes and directs complexin to synaptic vesicles. Although mouse and worm complexin have similar lipid binding affinity, their last few amino acids differ in both hydrophobicity and in lipid binding conformation, and these differences strongly impacted CPX-1 inhibitory function. Moreover, function was not maintained if a critical amphipathic helix in the worm CPX-1 CTD was replaced with the corresponding mCpx1 amphipathic helix. Invertebrate complexins generally shared more C-terminal similarity with vertebrate complexin 3 and 4 isoforms, and the amphipathic region of mouse complexin 3 significantly restored inhibitory function to worm CPX-1. We hypothesize that the CTD of complexin is essential in conferring an inhibitory function to complexin, and that this inhibitory activity has been attenuated in the vertebrate complexin 1 and 2 isoforms. Thus, evolutionary changes in the complexin CTD differentially shape its synaptic role across phylogeny.
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Affiliation(s)
- Rachel T Wragg
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - Daniel A Parisotto
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - Zhenlong Li
- Department of Physiology and Biophysics, Weill Cornell Medical College, New YorkNY, United States
| | - Mayu S Terakawa
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - David Snead
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - Ishani Basu
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medical College, New YorkNY, United States.,Institute for Computational Biomedicine, Weill Cornell Medical College, New YorkNY, United States
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, New YorkNY, United States
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Lin CW, Gai F. Microscopic nucleation and propagation rates of an alanine-based α-helix. Phys Chem Chem Phys 2017; 19:5028-5036. [PMID: 28165082 PMCID: PMC5359971 DOI: 10.1039/c6cp08924k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared temperature-jump (T-jump) study by Huang et al. (Proc. Natl. Acad. Sci. U. S. A., 2002, 99, 2788-2793) showed that the conformational relaxation kinetics of an alanine-based α-helical peptide depend not only on the final temperature (Tf) but also on the initial temperature (Ti) when Tf is fixed. Their finding indicates that the folding free energy landscape of this peptide is non-two-state like, allowing for the population of conformational ensembles with different helical lengths and relaxation times in the temperature range of the experiment. Because α-helix folding involves two fundamental events, nucleation and propagation, the results of Huang et al. thus present a unique opportunity to determine their rate constants - a long-sought goal in the study of the helix-coil transition dynamics. Herein, we capitalize on this notion and develop a coarse-grained kinetic model to globally fit the thermal unfolding curve and T-jump kinetic traces of this peptide. Using this strategy, we are able to explicitly determine the microscopic rate constants of the kinetic steps encountered in the nucleation and propagation processes. Our results reveal that the time taken to form one α-helical turn (i.e., an α-helical segment with one helical hydrogen bond) is about 315 ns, whereas the time taken to elongate this nucleus by one residue (or backbone unit) is 5.9 ns, depending on the position of the residue.
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Affiliation(s)
- Chun-Wei Lin
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, USA.
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