201
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Predicting the location of the non-local contacts in α-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1201-1208. [DOI: 10.1016/j.bbapap.2018.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/17/2018] [Accepted: 09/25/2018] [Indexed: 11/18/2022]
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202
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Identifying the region responsible for Brucella abortus MucR higher-order oligomer formation and examining its role in gene regulation. Sci Rep 2018; 8:17238. [PMID: 30467359 PMCID: PMC6250670 DOI: 10.1038/s41598-018-35432-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/05/2018] [Indexed: 11/09/2022] Open
Abstract
MucR is a member of the Ros/MucR family of prokaryotic zinc-finger proteins found in the α-proteobacteria which regulate the expression of genes required for the successful pathogenic and symbiotic interactions of these bacteria with the eukaryotic hosts. The structure and function of their distinctive zinc-finger domain has been well-studied, but only recently the quaternary structure of the full length proteins was investigated demonstrating their ability to form higher-order oligomers. The aim of this study was to identify the region of MucR involved in higher-order oligomer formation by analysing deletion and point mutants of this protein by Light Scattering, and to determine the role that MucR oligomerization plays in the regulatory function of this protein. Here we demonstrate that a conserved hydrophobic region at the N-terminus of MucR is responsible for higher-order oligomer formation and that MucR oligomerization is essential for its regulatory function in Brucella. All these features of MucR are shared by the histone-like nucleoid structuring protein, (H-NS), leading us to propose that the prokaryotic zinc-finger proteins in the MucR/Ros family control gene expression employing a mechanism similar to that used by the H-NS proteins, rather than working as classical transcriptional regulators.
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203
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The 2.1 Å structure of protein F9 and its comparison to L1, two components of the conserved poxvirus entry-fusion complex. Sci Rep 2018; 8:16807. [PMID: 30429486 PMCID: PMC6235832 DOI: 10.1038/s41598-018-34244-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/12/2018] [Indexed: 11/18/2022] Open
Abstract
The poxvirus F9 protein is a component of the vaccinia virus entry fusion complex (EFC) which consists of 11 proteins. The EFC forms a unique apparatus among viral fusion proteins and complexes. We solved the atomic structure of the F9 ectodomain at 2.10 Å. A structural comparison to the ectodomain of the EFC protein L1 indicated a similar fold and organization, in which a bundle of five α-helices is packed against two pairs of β-strands. However, instead of the L1 myristoylation site and hydrophobic cavity, F9 possesses a protruding loop between α-helices α3 and α4 starting at Gly90. Gly90 is conserved in all poxviruses except Salmon gill poxvirus (SGPV) and Diachasmimorpha longicaudata entomopoxvirus. Phylogenetic sequence analysis of all Poxviridae F9 and L1 orthologs revealed the SGPV genome to contain the most distantly related F9 and L1 sequences compared to the vaccinia proteins studied here. The structural differences between F9 and L1 suggest functional adaptations during evolution from a common precursor that underlie the present requirement for each protein.
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204
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Evgrafova Z, Voigt B, Baumann M, Stephani M, Binder WH, Balbach J. Probing Polymer Chain Conformation and Fibril Formation of Peptide Conjugates. Chemphyschem 2018; 20:236-240. [PMID: 30221816 DOI: 10.1002/cphc.201800867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/29/2022]
Abstract
Covalent conjugates between a synthetic polymer and a peptide hormone were used to probe the molecular extension of these macromolecules and how the polymer modifies the fibril formation of the hormone. NMR spectroscopy of 15 N labeled parathyroid hormone (PTH) was employed to visualize the conformation of the conjugated synthetic polymer, triggered by small temperature changes via its lower critical solution temperature. A shroud-like polymer conformation dominated the molecular architecture of the conjugated chimeras. PTH readily forms amyloid fibrils, which is probably the physiological storage form of the hormone. The polyacrylate based polymers stimulated the nucleation processes of the peptide.
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Affiliation(s)
- Zhanna Evgrafova
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle (Saale), Germany
| | - Bruno Voigt
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120, Halle (Saale), Germany
| | - Monika Baumann
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120, Halle (Saale), Germany
| | - Madlen Stephani
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120, Halle (Saale), Germany
| | - Wolfgang H Binder
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle (Saale), Germany
| | - Jochen Balbach
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120, Halle (Saale), Germany
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205
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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206
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Hierarchical spidroin micellar nanoparticles as the fundamental precursors of spider silks. Proc Natl Acad Sci U S A 2018; 115:11507-11512. [PMID: 30348773 DOI: 10.1073/pnas.1810203115] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many natural silks produced by spiders and insects are unique materials in their exceptional toughness and tensile strength, while being lightweight and biodegradable-properties that are currently unparalleled in synthetic materials. Myriad approaches have been attempted to prepare artificial silks from recombinant spider silk spidroins but have each failed to achieve the advantageous properties of the natural material. This is because of an incomplete understanding of the in vivo spidroin-to-fiber spinning process and, particularly, because of a lack of knowledge of the true morphological nature of spidroin nanostructures in the precursor dope solution and the mechanisms by which these nanostructures transform into micrometer-scale silk fibers. Herein we determine the physical form of the natural spidroin precursor nanostructures stored within spider glands that seed the formation of their silks and reveal the fundamental structural transformations that occur during the initial stages of extrusion en route to fiber formation. Using a combination of solution phase diffusion NMR and cryogenic transmission electron microscopy (cryo-TEM), we reveal direct evidence that the concentrated spidroin proteins are stored in the silk glands of black widow spiders as complex, hierarchical nanoassemblies (∼300 nm diameter) that are composed of micellar subdomains, substructures that themselves are engaged in the initial nanoscale transformations that occur in response to shear. We find that the established micelle theory of silk fiber precursor storage is incomplete and that the first steps toward liquid crystalline organization during silk spinning involve the fibrillization of nanoscale hierarchical micelle subdomains.
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207
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Thakur AK, Meng W, Gierasch LM. Local and non-local topological information in the denatured state ensemble of a β-barrel protein. Protein Sci 2018; 27:2062-2072. [PMID: 30252171 DOI: 10.1002/pro.3516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 11/06/2022]
Abstract
The folding of predominantly β-sheet proteins is complicated by the presence of a large number of non-local interactions in their native states, which increase the ruggedness of their folding energy landscapes. However, forming non-local contacts early in folding or even in the unfolded state can smooth the energy landscape and facilitate productive folding. We report that several sequence regions of a β-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), populate native-like secondary structure to a significant extent in the denatured state in 8 M urea. In addition, we provide evidence for both local and non-local interactions in the denatured state of CRABP1. NMR chemical shift perturbations (CSPs) under denaturing conditions upon substitution of single residues by mutation support the presence of several non-local interactions in topologically key sites, arguing that the denatured state is conformationally restricted and contains topological information for the native fold. Among the most striking non-local interactions are those between the N- and C-terminal regions, which are involved in closure of the native β-barrel. In addition, CSPs support the presence of two features in the denatured state: a major hydrophobic cluster involving residues from various parts of the sequence and a native-like interaction similar to one identified in previous studies as forming early in folding (Budyak et al., Structure 21, 476 [2013]). Taken together, our data support a model in which transient structures involving nonlocal interactions prime early folding interactions in CRABP1, determine its barrel topology, and may protect this predominantly β-sheet protein against aggregation.
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Affiliation(s)
- Abhay K Thakur
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Wenli Meng
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
| | - Lila M Gierasch
- Departments of Biochemistry & Molecular Biology and Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, 01003
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208
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Al Bakri W, Donovan MD, Cueto M, Wu Y, Orekie C, Yang Z. Overview of intranasally delivered peptides: key considerations for pharmaceutical development. Expert Opin Drug Deliv 2018; 15:991-1005. [PMID: 30173579 DOI: 10.1080/17425247.2018.1517742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Intranasal (IN) delivery for peptides provides unique advantages compared to other invasive systemic delivery routes. However, there still lacks a clear understanding on how to evaluate the potential of the peptides for nasal delivery and key considerations for the nasal formulation development. AREAS COVERED A retrospective analysis of intranasally delivered peptides was conducted. The goals of this undertaking were 1) to build a database of the key physicochemical and pharmacokinetic properties of peptides delivered by the nasal route, 2) to evaluate formulation attributes applied to IN peptide delivery systems, and 3) to provide key considerations for IN delivery of peptides. EXPERT OPINION/COMMENTARY Extensive data mining showed that peptides with molecular weights up to 6000 Da have been delivered intranasally. The high solubility of some peptides highlighted the possibility of delivering sufficient amounts of peptide in the limited volume available for nasal sprays. Permeation enhancers and mucoadhesives have shown promise in improving the IN bioavailability of peptides. Other formulation considerations, such as the type of formulation, pH, osmolality, as well as drug deposition, are reviewed herein. Based on this retrospective analysis, key considerations for nasal peptides formulations were proposed to guide drug discovery and development for IN delivery of peptides.
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Affiliation(s)
- Wisam Al Bakri
- a Department of Pharmaceutical Sciences and Experimental Therapeutics , The University of Iowa, College of Pharmacy , Iowa City
| | - Maureen D Donovan
- a Department of Pharmaceutical Sciences and Experimental Therapeutics , The University of Iowa, College of Pharmacy , Iowa City
| | - Maria Cueto
- b Pharmaceutical Science , Exploratory Products & Technology, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Yunhui Wu
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Chinedu Orekie
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
| | - Zhen Yang
- c Pharmaceutical Science , Biopharmaceutics and Specialty Dosage Form, Merck & Co., Inc ., Kenilworth , NJ , USA
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209
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Sturlese M, Manta B, Bertarello A, Bonilla M, Lelli M, Zambelli B, Grunberg K, Mammi S, Comini MA, Bellanda M. The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region. Sci Rep 2018; 8:13716. [PMID: 30209332 PMCID: PMC6135854 DOI: 10.1038/s41598-018-31817-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Glutaredoxins (Grx) are small proteins conserved throughout all the kingdoms of life that are engaged in a wide variety of biological processes and share a common thioredoxin-fold. Among them, class II Grx are redox-inactive proteins involved in iron-sulfur (FeS) metabolism. They contain a single thiol group in their active site and use low molecular mass thiols such as glutathione as ligand for binding FeS-clusters. In this study, we investigated molecular aspects of 1CGrx1 from the pathogenic parasite Trypanosoma brucei brucei, a mitochondrial class II Grx that fulfills an indispensable role in vivo. Mitochondrial 1CGrx1 from trypanosomes differs from orthologues in several features including the presence of a parasite-specific N-terminal extension (NTE) whose role has yet to be elucidated. Previously we have solved the structure of a truncated form of 1CGrx1 containing only the conserved glutaredoxin domain but lacking the NTE. Our aim here is to investigate the effect of the NTE on the conformation of the protein. We therefore solved the NMR structure of the full-length protein, which reveals subtle but significant differences with the structure of the NTE-less form. By means of different experimental approaches, the NTE proved to be intrinsically disordered and not involved in the non-redox dependent protein dimerization, as previously suggested. Interestingly, the portion comprising residues 65–76 of the NTE modulates the conformational dynamics of the glutathione-binding pocket, which may play a role in iron-sulfur cluster assembly and delivery. Furthermore, we disclosed that the class II-strictly conserved loop that precedes the active site is critical for stabilizing the protein structure. So far, this represents the first communication of a Grx containing an intrinsically disordered region that defines a new protein subgroup within class II Grx.
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Affiliation(s)
- Mattia Sturlese
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.,Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy
| | - Bruno Manta
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Igua 4425, 11400, Montevideo, Uruguay.,New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA
| | - Andrea Bertarello
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Mariana Bonilla
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Moreno Lelli
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.,Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Barbara Zambelli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy
| | - Karin Grunberg
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Stefano Mammi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Marcelo A Comini
- Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
| | - Massimo Bellanda
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.
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210
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Yang YJ, Mai DJ, Dursch TJ, Olsen BD. Nucleopore-Inspired Polymer Hydrogels for Selective Biomolecular Transport. Biomacromolecules 2018; 19:3905-3916. [DOI: 10.1021/acs.biomac.8b00556] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Yun Jung Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Danielle J. Mai
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas J. Dursch
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bradley D. Olsen
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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211
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Zuk PJ, Cichocki B, Szymczak P. GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules. Biophys J 2018; 115:782-800. [PMID: 30144937 PMCID: PMC6127458 DOI: 10.1016/j.bpj.2018.07.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 10/28/2022] Open
Abstract
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
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Affiliation(s)
- Pawel J Zuk
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland; Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey
| | - Bogdan Cichocki
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Piotr Szymczak
- Institute of Theoretical Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.
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212
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Coty JB, Varenne F, Benmalek A, Garsaa O, Le Potier I, Taverna M, Smadja C, Vauthier C. Characterization of nanomedicines’ surface coverage using molecular probes and capillary electrophoresis. Eur J Pharm Biopharm 2018; 130:48-58. [DOI: 10.1016/j.ejpb.2018.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 11/17/2022]
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213
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Liu W, Liu X, Zhu G, Lu L, Yang D. A Method for Determining Structure Ensemble of Large Disordered Protein: Application to a Mechanosensing Protein. J Am Chem Soc 2018; 140:11276-11285. [PMID: 30124042 DOI: 10.1021/jacs.8b04792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structure characterization of intrinsically disordered proteins (IDPs) remains a key obstacle in understanding their functional mechanisms. Due to the highly dynamic feature of IDPs, structure ensembles instead of static unique structures are often derived from experimental data. Several state-of-the-art computational methods have been developed to select an optimal ensemble from a pregenerated structure pool, but they suffer from low efficiency for large IDPs. Here we present a matching pursuit genetic algorithm (MPGA) for structure ensemble determination, which takes advantages from both matching pursuit (MP) to reduce the search space and genetic algorithm (GA) to reduce the restriction on constraint types. The MPGA method is validated using a reference ensemble with predefined structures. In comparison with the conventional GA, MPGA takes much less computational time for large IDPs. The utility of the method is demonstrated by application to structure ensemble determination of a mechanosensing protein domain with 306 amino acids. The structure ensemble determined reveals that the N-terminal region 1-240 is more compact than the C-terminal region 240-306. The unique structural feature explains why only a small portion of YXXP tyrosine residues can be phosphorylated easily by kinases in the absence of extension force and why the phosphorylation is force-dependent.
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Affiliation(s)
- Wei Liu
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
| | - Xiao Liu
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
| | - Guanhua Zhu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore
| | - Lanyuan Lu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
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214
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A Luminal Loop of Wilson Disease Protein Binds Copper and Is Required for Protein Activity. Biophys J 2018; 115:1007-1018. [PMID: 30173886 PMCID: PMC6139820 DOI: 10.1016/j.bpj.2018.07.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 11/22/2022] Open
Abstract
The copper-transporting ATPase ATP7B is essential for loading of copper ions to copper-dependent enzymes in the secretory pathway; its inactivation results in Wilson disease. In contrast to copper-ion uptake by the cytoplasmic domains, ATP7B-mediated copper-ion release in the Golgi has not been explored yet. We demonstrate here that a luminal loop in ATP7B, rich in histidine/methionine residues, binds reduced copper (Cu(I)) ions, and identified copper-binding residues play an essential role in ATP7B-mediated metal ion release. NMR experiments on short-peptide models demonstrate that three methionine and two histidine residues are specifically involved in Cu(I) ion binding; with these residues replaced by alanines, no Cu(I) ion interaction is detected. Although more than one Cu(I) ion can interact with the wild-type peptide, removing either all histidine or all methionine residues reduces the stoichiometry to one Cu(I) ion binding per peptide. Using a yeast complementation assay, we show that for efficient copper transport by full-length ATP7B, the complete set of histidine and methionine residues in the lumen loop are required. The replacement of histidine/methionine residues by alanines does not perturb overall ATP7B structure, as the localization of ATP7B variants in yeast cells matches that of the wild-type protein. Thus, in similarity to ATP7A, ATP7B also appears to have a luminal “exit” copper ion site.
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215
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Cragnell C, Rieloff E, Skepö M. Utilizing Coarse-Grained Modeling and Monte Carlo Simulations to Evaluate the Conformational Ensemble of Intrinsically Disordered Proteins and Regions. J Mol Biol 2018; 430:2478-2492. [DOI: 10.1016/j.jmb.2018.03.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/03/2018] [Accepted: 03/12/2018] [Indexed: 11/16/2022]
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216
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Tedeschi G, Salladini E, Santambrogio C, Grandori R, Longhi S, Brocca S. Conformational response to charge clustering in synthetic intrinsically disordered proteins. Biochim Biophys Acta Gen Subj 2018; 1862:2204-2214. [PMID: 30025858 DOI: 10.1016/j.bbagen.2018.07.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Recent theoretical and computational studies have shown that the charge content and, most importantly, the linear distribution of opposite charges are major determinants of conformational properties of intrinsically disordered proteins (IDPs). Charge segregation in a sequence can be measured through κ, which represents a normalized measure of charge asymmetry. A strong inverse correlation between κ and radius of gyration has been previously demonstrated for two independent sets of permutated IDP sequences. METHODS We used two well-characterized IDPs, namely measles virus NTAIL and Hendra virus PNT4, sharing a very similar fraction of charged residues and net charge per residue, but differing in proline (Pro) content. For each protein, we have rationally designed a low- and a high-κ variant endowed with the highest and the lowest κ values compatible with their natural amino acid composition. Then, the conformational properties of wild-type and κ-variants have been assessed by biochemical and biophysical techniques. RESULTS We confirmed a direct correlation between κ and protein compaction. The analysis of our original data along with those available from the literature suggests that Pro content may affects the responsiveness to charge clustering. CONCLUSIONS Charge clustering promotes IDP compaction, but the extent of its effects depends on the sequence context. Proline residues seem to play a role contrasting compaction. GENERAL SIGNIFICANCE These results contribute to the identification of sequence determinants of IDP conformational properties. They may also serve as an asset for rational design of non-natural IDPs with tunable degree of compactness.
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Affiliation(s)
- Giulia Tedeschi
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Edoardo Salladini
- CNRS, Aix Marseille Univ, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille 13288, France
| | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Rita Grandori
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy
| | - Sonia Longhi
- CNRS, Aix Marseille Univ, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Marseille 13288, France.
| | - Stefania Brocca
- Department of Biotechnology and Biosciences, State University of Milano-Bicocca, Piazza della Scienza 2, Milano 20126, Italy.
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217
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Leone S, Fonderico J, Melchiorre C, Carpentieri A, Picone D. Structural effects of methylglyoxal glycation, a study on the model protein MNEI. Mol Cell Biochem 2018; 451:165-171. [PMID: 30014221 DOI: 10.1007/s11010-018-3403-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/12/2018] [Indexed: 12/23/2022]
Abstract
The reaction of free amino groups in proteins with reactive carbonyl species, known as glycation, leads to the formation of mixtures of products, collectively referred to as advanced glycation endproducts (AGEs). These compounds have been implicated in several important diseases, but their role in pathogenesis and clinical symptoms' development is still debated. Particularly, AGEs are often associated to the formation of amyloid deposits in conformational diseases, such as Alzheimer's and Parkinson's disease, and it has been suggested that they might influence the mechanisms and kinetics of protein aggregation. We here present the characterization of the products of glycation of the model protein MNEI with methylglyoxal and their effect on the protein structure. We demonstrate that, despite being an uncontrolled process, glycation occurs only at specific residues of the protein. Moreover, while not affecting the protein fold, it alters its shape and hydrodynamic properties and increases its tendency to fibrillar aggregation. Our study opens the way to in deep structural investigations to shed light on the complex link between protein post-translational modifications, structure, and stability.
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Affiliation(s)
- Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy.
| | - Jole Fonderico
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy.
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218
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Chakraborty D, Hori N, Thirumalai D. Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. J Chem Theory Comput 2018; 14:3763-3779. [PMID: 29870236 PMCID: PMC6423546 DOI: 10.1021/acs.jctc.8b00091] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduce the experimentally measured salt and sequence-dependence of the size of single-stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force, the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin and could be described by a standard polymer model. We also show that the persistence length of double-stranded DNA, formed from two complementary ssDNAs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. Our model predicts the melting temperatures of DNA hairpins with excellent accuracy, and we are able to recover the experimentally known sequence-specific trends. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Naoto Hori
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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219
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Contreras LM, Sevilla P, Cámara-Artigas A, Hernández-Cifre JG, Rizzuti B, Florencio FJ, Muro-Pastor MI, García de la Torre J, Neira JL. The Cyanobacterial Ribosomal-Associated Protein LrtA from Synechocystis sp. PCC 6803 Is an Oligomeric Protein in Solution with Chameleonic Sequence Properties. Int J Mol Sci 2018; 19:ijms19071857. [PMID: 29937518 PMCID: PMC6073757 DOI: 10.3390/ijms19071857] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/25/2022] Open
Abstract
The LrtA protein of Synechocystis sp. PCC 6803 intervenes in cyanobacterial post-stress survival and in stabilizing 70S ribosomal particles. It belongs to the hibernating promoting factor (HPF) family of proteins, involved in protein synthesis. In this work, we studied the conformational preferences and stability of isolated LrtA in solution. At physiological conditions, as shown by hydrodynamic techniques, LrtA was involved in a self-association equilibrium. As indicated by Nuclear Magnetic Resonance (NMR), circular dichroism (CD) and fluorescence, the protein acquired a folded, native-like conformation between pH 6.0 and 9.0. However, that conformation was not very stable, as suggested by thermal and chemical denaturations followed by CD and fluorescence. Theoretical studies of its highly-charged sequence suggest that LrtA had a Janus sequence, with a context-dependent fold. Our modelling and molecular dynamics (MD) simulations indicate that the protein adopted the same fold observed in other members of the HPF family (β-α-β-β-β-α) at its N-terminal region (residues 1–100), whereas the C terminus (residues 100–197) appeared disordered and collapsed, supporting the overall percentage of overall secondary structure obtained by CD deconvolution. Then, LrtA has a chameleonic sequence and it is the first member of the HPF family involved in a self-association equilibrium, when isolated in solution.
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Affiliation(s)
- Lellys M Contreras
- Center for Environmental Biology and Chemistry Research, Facultad Experimental de Ciencias y Tecnología, Universidad de Carabobo, 2001 Valencia, Venezuela.
| | - Paz Sevilla
- Facultad de Farmacia, Departamento de Química Física II, Universidad Complutense de Madrid, 28040 Madrid, Spain.
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, 04120 Almería, Spain.
| | | | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy.
| | - Francisco J Florencio
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | - María Isabel Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, 41092 Seville, Spain.
| | | | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202 Elche (Alicante), Spain.
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain.
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220
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Edwards JM, Derrick JP, van der Walle CF, Golovanov AP. 19F NMR as a Tool for Monitoring Individual Differentially Labeled Proteins in Complex Mixtures. Mol Pharm 2018; 15:2785-2796. [PMID: 29863878 DOI: 10.1021/acs.molpharmaceut.8b00282] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ability to monitor the behavior of individual proteins in complex mixtures has many potential uses, ranging from analysis of protein interactions in highly concentrated solutions, modeling biological fluids or the intracellular environment, to optimizing biopharmaceutical co-formulations. Differential labeling NMR approaches, which traditionally use 15N or 13C isotope incorporation during recombinant expression, are not always practical in cases when endogenous proteins are obtained from an organism, or where the expression system does not allow for efficient labeling, especially for larger proteins. This study proposes differential labeling of proteins by covalent attachment of 19F groups with distinct chemical shifts, giving each protein a unique spectral signature which can be monitored by 19F NMR without signal overlap, even in complex mixtures, and without any interfering signals from the buffer or other unlabeled components. Parameters, such as signal intensities, translational diffusion coefficients, and transverse relaxation rates, which report on the behavior of individual proteins in the mixture, can be recorded even for proteins as large as antibodies at a wide range of concentrations.
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Affiliation(s)
- John M Edwards
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering , University of Manchester , Manchester M1 7DN , U.K
| | - Jeremy P Derrick
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre , University of Manchester , Manchester M13 9PL , U.K
| | | | - Alexander P Golovanov
- Manchester Institute of Biotechnology, School of Chemistry, Faculty of Science and Engineering , University of Manchester , Manchester M1 7DN , U.K
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221
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Linke M, Köfinger J, Hummer G. Rotational Diffusion Depends on Box Size in Molecular Dynamics Simulations. J Phys Chem Lett 2018; 9:2874-2878. [PMID: 29749735 DOI: 10.1021/acs.jpclett.8b01090] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We show that the rotational dynamics of proteins and nucleic acids determined from molecular dynamics simulations under periodic boundary conditions suffer from significant finite-size effects. We remove the box-size dependence of the rotational diffusion coefficients by adding a hydrodynamic correction kB T/6 ηV with kB Boltzmann's constant, T the absolute temperature, η the solvent shear viscosity, and V the box volume. We show that this correction accounts for the finite-size dependence of the rotational diffusion coefficients of horse-heart myoglobin and a B-DNA dodecamer in aqueous solution. The resulting hydrodynamic radii are in excellent agreement with experiment.
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Affiliation(s)
- Max Linke
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue-Straße 3 , 60438 Frankfurt am Main , Germany
- Department of Physics , Goethe University Frankfurt , Max-von-Laue-Straße 1 , 60438 Frankfurt am Main , Germany
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222
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Welsch N, Brown AC, Barker TH, Lyon LA. Enhancing clot properties through fibrin-specific self-cross-linked PEG side-chain microgels. Colloids Surf B Biointerfaces 2018; 166:89-97. [PMID: 29549720 PMCID: PMC6050065 DOI: 10.1016/j.colsurfb.2018.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 01/14/2018] [Accepted: 03/01/2018] [Indexed: 02/06/2023]
Abstract
Excessive bleeding and resulting complications are a major cause of death in both trauma and surgical settings. Recently, there have been a number of investigations into the design of synthetic hemostatic agents with platelet-mimicking activity to effectively treat patients suffering from severe hemorrhage. We developed platelet-like particles from microgels composed of polymers carrying polyethylene glycol (PEG) side-chains and fibrin-targeting single domain variable fragment antibodies (PEG-PLPs). Comparable to natural platelets, PEG-PLPs were found to enhance the fibrin network formation in vitro through strong adhesion to the emerging fibrin clot and physical, non-covalent cross-linking of nascent fibrin fibers. Furthermore, the mechanical reinforcement of the fibrin mesh through the incorporation of particles into the network leads to a ∼three-fold decrease of the overall clot permeability as compared to control clots. However, transport of biomolecules through the fibrin clots, such as peptides and larger proteins is not hindered by the presence of PEG-PLPs and the altered microstructure. Compared to control clots with an elastic modulus of 460+/-260 Pa, PEG-PLP-reinforced fibrin clots exhibit higher degrees of stiffness as demonstrated by the significantly increased average Younǵs modulus of 1770 +/±720 Pa, as measured by AFM force spectroscopy. Furthermore, in vitro degradation studies with plasmin demonstrate that fibrin clots formed in presence of PEG-PLPs withstand hydrolysis for 24 h, indicating enhanced stabilization against exogenous fibrinolysis. The entire set of data suggests that the designed platelet-like particles have high potential for use as hemostatic agents in emergency medicine and surgical settings.
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Affiliation(s)
- Nicole Welsch
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ashley C Brown
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; Joint Department of Biomedical Engineering, North Carolina State University and The University of North Carolina, Chapel Hill, Raleigh, NC, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA
| | - Thomas H Barker
- The Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - L Andrew Lyon
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
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223
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Holehouse AS, Pappu RV. Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions. Annu Rev Biophys 2018; 47:19-39. [PMID: 29345991 PMCID: PMC10740066 DOI: 10.1146/annurev-biophys-070317-032838] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proteins can collapse into compact globules or form expanded, solvent-accessible, coil-like conformations. Additionally, they can fold into well-defined three-dimensional structures or remain partially or entirely disordered. Recent discoveries have shown that the tendency for proteins to collapse or remain expanded is not intrinsically coupled to their ability to fold. These observations suggest that proteins do not have to form compact globules in aqueous solutions. They can be intrinsically disordered, collapsed, or expanded, and even form well-folded, elongated structures. This ability to decouple collapse from folding is determined by the sequence details of proteins. In this review, we highlight insights gleaned from studies over the past decade. Using a polymer physics framework, we explain how the interplay among sidechains, backbone units, and solvent determines the driving forces for collapsed versus expanded states in aqueous solvents.
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Affiliation(s)
- Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130, USA; ,
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224
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Ragona L, Gasymov O, Guliyeva AJ, Aslanov RB, Zanzoni S, Botta C, Molinari H. Rhodamine binds to silk fibroin and inhibits its self-aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:661-667. [DOI: 10.1016/j.bbapap.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/16/2018] [Accepted: 03/22/2018] [Indexed: 01/19/2023]
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225
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Carroll B, Bocharova V, Carrillo JMY, Kisliuk A, Cheng S, Yamamoto U, Schweizer KS, Sumpter BG, Sokolov AP. Diffusion of Sticky Nanoparticles in a Polymer Melt: Crossover from Suppressed to Enhanced Transport. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02695] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | | | | | - Shiwang Cheng
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Umi Yamamoto
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Kenneth S. Schweizer
- Departments of Materials Science and Chemistry, Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, United States
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226
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Greenland KN, Carvajal MFCA, Preston JM, Ekblad S, Dean WL, Chiang JY, Koder RL, Wittebort RJ. Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein. J Phys Chem B 2018; 122:2725-2736. [PMID: 29461832 DOI: 10.1021/acs.jpcb.7b11596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial minielastin constructs have been designed that replicate the structure and function of natural elastins in a simpler context, allowing the NMR observation of structure and dynamics of elastin-like proteins with complete residue-specific resolution. We find that the alanine-rich cross-linking domains of elastin have a partially helical structure, but only when capped by proline-rich hydrophobic domains. We also find that the hydrophobic domains, composed of prominent 6-residue repeats VPGVGG and APGVGV found in natural elastins, appear random coil by both NMR chemical shift analysis and circular dichroism. However, these elastin hydrophobic domains exhibit structural bias for a dynamically disordered conformation that is neither helical nor β sheet with a degree of nonrandom structural bias which is dependent on residue type and position in the sequence. Another nonrandom-coil aspect of hydrophobic domain structure lies in the fact that, in contrast to other intrinsically disordered proteins, these hydrophobic domains retain a relatively condensed conformation whether attached to cross-linking domains or not. Importantly, these domains and the proteins containing them constrict with increasing temperature by up to 30% in volume without becoming more ordered. This property is often observed in nonbiological polymers and suggests that temperature-driven constriction is a new type of protein structural change that is linked to elastin's biological functions of coacervation-driven assembly and elastic recoil.
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Affiliation(s)
- Kelly N Greenland
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | | | - Jonathan M Preston
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Siri Ekblad
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - William L Dean
- Department of Biochemistry and Molecular Genetics and the James Brown Cancer Center , University of Louisville School of Medicine , Louisville , Kentucky 40292 , United States
| | - Jeff Y Chiang
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Ronald L Koder
- Department of Physics , The City College of New York , New York , New York 10031 , United States.,Graduate Programs of Physics, Chemistry and Biochemistry , The Graduate Center of CUNY , New York , New York 10016 , United States
| | - Richard J Wittebort
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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227
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Evans R, Dal Poggetto G, Nilsson M, Morris GA. Improving the Interpretation of Small Molecule Diffusion Coefficients. Anal Chem 2018; 90:3987-3994. [PMID: 29481057 DOI: 10.1021/acs.analchem.7b05032] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diffusion-ordered NMR spectroscopy (DOSY) is increasingly widely used for the analysis of mixtures by NMR spectroscopy, dispersing the signals of different species according to their diffusion coefficients. DOSY is used primarily to distinguish between the signals of different species, with the interpretation of the diffusion coefficients observed usually being purely qualitative, for example to deduce whether one species is bigger or smaller than another. In principle, the actual values of diffusion coefficient obtained carry important information about the sizes of different species and on interactions between species, but the relationship between diffusion coefficient and molecular mass is in general a very complex one. Here a recently proposed analytical relationship between diffusion coefficient and molecular mass for the restricted case of small organic molecules is tested against a wide range of data from the scientific literature and generalized to cover a range of solvents and temperatures.
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Affiliation(s)
- Robert Evans
- Aston Institute of Materials Research, School of Engineering and Applied Science , Aston University , Birmingham , B4 7ET , U.K
| | | | - Mathias Nilsson
- School of Chemistry , University of Manchester , Manchester M13 9PL , U.K
| | - Gareth A Morris
- School of Chemistry , University of Manchester , Manchester M13 9PL , U.K
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228
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Fleming PJ, Fleming KG. HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties. Biophys J 2018; 114:856-869. [PMID: 29490246 PMCID: PMC5984988 DOI: 10.1016/j.bpj.2018.01.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/28/2017] [Accepted: 01/02/2018] [Indexed: 11/16/2022] Open
Abstract
Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.
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Affiliation(s)
- Patrick J Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland
| | - Karen G Fleming
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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229
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Rose F, Karlsen K, Jensen PR, Jakobsen RU, Wood GK, Rand KD, Godiksen H, Andersen P, Follmann F, Foged C. Unusual Self-Assembly of the Recombinant Chlamydia trachomatis Major Outer Membrane Protein-Based Fusion Antigen CTH522 Into Protein Nanoparticles. J Pharm Sci 2018; 107:1690-1700. [PMID: 29452143 DOI: 10.1016/j.xphs.2018.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/21/2018] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
Abstract
Sexually transmitted Chlamydia trachomatis infects more than 100 million people annually, and untreated chlamydia infections can cause severe complications. Therefore, there is an urgent need for a chlamydia vaccine. The Ctrachomatis major outer membrane protein (MOMP) is highly immunogenic but is a challenging vaccine candidate by being an integral membrane protein, and the immunogenicity depends on a correctly folded structure. We investigated the biophysical properties of the recombinant MOMP-based fusion antigen CTH522, which is tested in early human clinical trials. It consists of a truncated and cysteine-free version of MOMP fused to 4 variable domains from serovars D-G. In the native state, CTH522 did not exist as a monomer but showed an unusual self-assembly into nanoparticles with a negative zeta potential. In contrast to the β-barrel structure of MOMP, native CTH522 contained no well-defined secondary structural elements, and no thermal transitions were measurable. Chemical unfolding resulted in monomers that upon removal of the denaturant self-assembled into higher order structures, comparable to the structure of the native protein. The conformation of CTH522 in nanoparticles is thus not entirely random and contains structural elements stabilized via denaturant-disruptable hydrophobic interactions. In conclusion, CTH522 has an unusual quaternary structure of supramolecular self-assemblies.
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Affiliation(s)
- Fabrice Rose
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Kasper Karlsen
- Department of Vaccine Development, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Pernille Rønde Jensen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark; Department of Vaccine Development, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Rasmus Uffe Jakobsen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Grith Krøyer Wood
- Department of Vaccine Development, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Kasper Dyrberg Rand
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark
| | - Helene Godiksen
- Department of Vaccine Development, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Peter Andersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Frank Follmann
- Department of Infectious Disease Immunology, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Camilla Foged
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark.
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230
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Zhang Y, Yates EV, Hong L, Saar KL, Meisl G, Dobson CM, Knowles TPJ. On-chip measurements of protein unfolding from direct observations of micron-scale diffusion. Chem Sci 2018; 9:3503-3507. [PMID: 29780480 PMCID: PMC5934698 DOI: 10.1039/c7sc04331g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 11/26/2022] Open
Abstract
The unfolding process of BSA in solution as a function of pH was studied by microfluidic diffusional sizing device.
Investigations of protein folding, unfolding and stability are critical for the understanding of the molecular basis of biological structure and function. We describe here a microfluidic approach to probe the unfolding of unlabelled protein molecules in microliter volumes. We achieve this objective through the use of a microfluidic platform, which allows the changes in molecular diffusivity upon folding and unfolding to be detected directly. We illustrate this approach by monitoring the unfolding of bovine serum albumin in solution as a function of pH. These results show the viability of probing protein stability on chip in small volumes.
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Affiliation(s)
- Yuewen Zhang
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Emma V Yates
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Liu Hong
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344.,Zhou Pei-Yuan Center for Applied Mathematics , Tsinghua University , Beijing , 10084 , P. R. China
| | - Kadi L Saar
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336344.,Cavendish Laboratory , University of Cambridge , J J Thomson Avenue , Cambridge , CB3 0HE , UK
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231
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Cascão J, Silva W, Ferreira ASD, Cabrita EJ. Ion pair and solvation dynamics of [Bmim][BF 4 ] + water system. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:127-139. [PMID: 29049867 DOI: 10.1002/mrc.4673] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
In this work, 1-butyl-3-methylimidazolium tetrafluoroborate/water mixtures were analysed over the whole water composition (xw ) in order to study the rotational and translational behaviour of the ions. We employed a multinuclear NMR approach to determine anion/cation/water diffusion coefficients and longitudinal relaxation rates at different water content. In neat ionic liquids (IL), the cation diffuses faster than the anion, and at low xw , anions and cations share almost the same diffusion coefficient, but above a critical water concentration, the anion begins to diffuse faster than the cation. We identified this composition as approximately 10% xw where the ions share the same diffusion coefficient. We found that the water at this composition seems to have a much more dramatic effect in the rotational diffusion of the anion that decreases substantially and approaches that of the anion in the diluted IL. Translational and rotational dynamics of the ions suggest that water is first incorporated in pockets in the nanostructure of the IL allowing the ions to maintain most of the cation/anion interactions present in neat IL but already disrupting some anion/cation interactions due to preferential interaction with the anion. HOESY and NOESY data show that water displays contacts both with the cation and the anion in a positive NOE regime in contrary to the negative regime found for the cation/anion and cation/cation cross-relaxation. This is in accordance with the high relative diffusion coefficient of water and suggests that water molecules can exchange between preferential location sites that allow water to maintain contacts both with the anion and cation.
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Affiliation(s)
- João Cascão
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. Da República, EAN, 2780-157, Oeiras, Portugal
| | - Wagner Silva
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
| | - Ana S D Ferreira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- Centro de Química Estrutural, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
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232
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Harris J, Shadrina M, Oliver C, Vogel J, Mittermaier A. Concerted millisecond timescale dynamics in the intrinsically disordered carboxyl terminus of γ-tubulin induced by mutation of a conserved tyrosine residue. Protein Sci 2018; 27:531-545. [PMID: 29127738 PMCID: PMC5775176 DOI: 10.1002/pro.3345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 12/30/2022]
Abstract
Tubulins are an ancient family of eukaryotic proteins characterized by an amino-terminal globular domain and disordered carboxyl terminus. These carboxyl termini play important roles in modulating the behavior of microtubules in living cells. However, the atomic-level basis of their function is not well understood. These regions contain multiple acidic residues and their overall charges are modulated in vivo by post-translational modifications, for example, phosphorylation. In this study, we describe an application of NMR and computer Monte Carlo simulations to investigate how the modification of local charge alters the conformational sampling of the γ-tubulin carboxyl terminus. We compared the dynamics of two 39-residue polypeptides corresponding to the carboxyl-terminus of yeast γ-tubulin. One polypeptide comprised the wild-type amino acid sequence while the second contained a Y > D mutation at Y11 in the polypeptide (Y445 in the full protein). This mutation introduces additional negative charge at a site that is phosphorylated in vivo and produces a phenotype with perturbed microtubule function. NMR relaxation measurements show that the Y11D mutation produces dramatic changes in the millisecond-timescale motions of the entire polypeptide. This observation is supported by Monte Carlo simulations that-similar to NMR-predict the WT γ-CT is largely unstructured and that the substitution of Tyr 11 with Asp causes the sampling of extended conformations that are unique to the Y11D polypeptide.
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Affiliation(s)
- Jason Harris
- Department of ChemistryMcGill University, 801 Sherbrooke St. WMontrealQuebecCanada
| | - Maria Shadrina
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
| | - Carlos Oliver
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
- The School of Computer ScienceMcGill University, 3480 University StMontrealQuebecCanada
| | - Jackie Vogel
- Department of BiologyMcGill University, 3649 Promenade Sir William OslerMontrealQuebecCanada
- The School of Computer ScienceMcGill University, 3480 University StMontrealQuebecCanada
| | - Anthony Mittermaier
- Department of ChemistryMcGill University, 801 Sherbrooke St. WMontrealQuebecCanada
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233
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Yuwen T, Brady JP, Kay LE. Probing Conformational Exchange in Weakly Interacting, Slowly Exchanging Protein Systems via Off-Resonance R1ρ Experiments: Application to Studies of Protein Phase Separation. J Am Chem Soc 2018; 140:2115-2126. [DOI: 10.1021/jacs.7b09576] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Tairan Yuwen
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Jacob P. Brady
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Lewis E. Kay
- Departments
of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
- Hospital for Sick Children, Program in Molecular Medicine, Toronto, Ontario, Canada M5G 1X8
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234
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Ryan VH, Dignon GL, Zerze GH, Chabata CV, Silva R, Conicella AE, Amaya J, Burke KA, Mittal J, Fawzi NL. Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation. Mol Cell 2018; 69:465-479.e7. [PMID: 29358076 DOI: 10.1016/j.molcel.2017.12.022] [Citation(s) in RCA: 261] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/10/2017] [Accepted: 12/22/2017] [Indexed: 01/21/2023]
Abstract
hnRNPA2, a component of RNA-processing membraneless organelles, forms inclusions when mutated in a syndrome characterized by the degeneration of neurons (bearing features of amyotrophic lateral sclerosis [ALS] and frontotemporal dementia), muscle, and bone. Here we provide a unified structural view of hnRNPA2 self-assembly, aggregation, and interaction and the distinct effects of small chemical changes-disease mutations and arginine methylation-on these assemblies. The hnRNPA2 low-complexity (LC) domain is compact and intrinsically disordered as a monomer, retaining predominant disorder in a liquid-liquid phase-separated form. Disease mutations D290V and P298L induce aggregation by enhancing and extending, respectively, the aggregation-prone region. Co-aggregating in disease inclusions, hnRNPA2 LC directly interacts with and induces phase separation of TDP-43. Conversely, arginine methylation reduces hnRNPA2 phase separation, disrupting arginine-mediated contacts. These results highlight the mechanistic role of specific LC domain interactions and modifications conserved across many hnRNP family members but altered by aggregation-causing pathological mutations.
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Affiliation(s)
- Veronica H Ryan
- Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA
| | - Gregory L Dignon
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Charlene V Chabata
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Rute Silva
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Alexander E Conicella
- Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Joshua Amaya
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Kathleen A Burke
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA.
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235
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Malyshka D, Schweitzer-Stenner R. Photoreduction of ferricytochrome c in the presence of potassium ferrocyanide. Photochem Photobiol Sci 2018; 17:1462-1468. [DOI: 10.1039/c8pp00286j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ferricytochrome c has been previously shown to photoreduce in the presence of ferrocyanide anions, but the process has been poorly understood.
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236
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Neira JL, Hornos F, Cozza C, Cámara-Artigas A, Abián O, Velázquez-Campoy A. The histidine phosphocarrier protein, HPr, binds to the highly thermostable regulator of sigma D protein, Rsd, and its isolated helical fragments. Arch Biochem Biophys 2017; 639:26-37. [PMID: 29288053 DOI: 10.1016/j.abb.2017.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 02/06/2023]
Abstract
The phosphotransferase system (PTS) controls the preferential use of sugars in bacteria and it is also involved in other processes, such as chemotaxis. It is formed by a protein cascade in which the first two proteins are general (namely, EI and HPr) and the others are sugar-specific permeases. The Rsd protein binds specifically to the RNA polymerase (RNAP) σ70 factor. We first characterized the conformational stability of Escherichia coli Rsd. And second, we delineated the binding regions of Streptomyces coelicolor, HPrsc, and E. coli Rsd, by using fragments derived from each protein. To that end, we used several biophysical probes, namely, fluorescence, CD, NMR, ITC and BLI. Rsd had a free energy of unfolding of 15 kcal mol-1 at 25 °C, and a thermal denaturation midpoint of 103 °C at pH 6.5. The affinity between Rsd and HPrsc was 2 μM. Interestingly enough, the isolated helical-peptides, comprising the third (RsdH3) and fourth (RsdH4) Rsd helices, also interacted with HPrsc in a specific manner, and with affinities similar to that of the whole Rsd. Moreover, the isolated peptide of HPrsc, HPr9-30, comprising the active site, His15, also was bound to intact Rsd with similar affinity. Therefore, binding between Rsd and HPrsc was modulated by the two helices H3 and H4 of Rsd, and the regions around the active site of HPrsc. This implies that specific fragments of Rsd and HPrsc can be used to interfere with other protein-protein interactions (PPIs) of each other protein.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain.
| | - Felipe Hornos
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Elche, Alicante, Spain
| | - Concetta Cozza
- Molecular Biophysics Laboratory, Department of Physics, University of Calabria, Rende, Italy
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, Research Centre CIAIMBITAL, University of Almería- ceiA3, Almería, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, Spain; Aragon Institute for Health Research (IIS Aragon), Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain; Fundación ARAID, Diputación General de Aragón, Zaragoza, Spain.
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237
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The energy cost of polypeptide knot formation and its folding consequences. Nat Commun 2017; 8:1581. [PMID: 29146980 PMCID: PMC5691195 DOI: 10.1038/s41467-017-01691-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 10/09/2017] [Indexed: 11/08/2022] Open
Abstract
Knots are natural topologies of chains. Yet, little is known about spontaneous knot formation in a polypeptide chain—an event that can potentially impair its folding—and about the effect of a knot on the stability and folding kinetics of a protein. Here we used optical tweezers to show that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 120 residues is 5.8 ± 1 kcal mol−1. Monte Carlo dynamics of random chains predict this value, indicating that the free energy cost of knot formation is of entropic origin. This cost is predicted to remain above 3 kcal mol−1 for denatured proteins as large as 900 residues. Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cost of knotting through contacts along their folding landscape. The effect of knots on protein stability and folding kinetics is not well understood. Here the authors combine optical tweezer experiments and calculations to experimentally determine the energy cost for knot formation, which indicates that knotted proteins evolved specific folding pathways because knot formation in unfolded chains is unfavorable.
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238
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Structural disorder and induced folding within two cereal, ABA stress and ripening (ASR) proteins. Sci Rep 2017; 7:15544. [PMID: 29138428 PMCID: PMC5686140 DOI: 10.1038/s41598-017-15299-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/04/2017] [Indexed: 11/13/2022] Open
Abstract
Abscisic acid (ABA), stress and ripening (ASR) proteins are plant-specific proteins involved in plant response to multiple abiotic stresses. We previously isolated the ASR genes and cDNAs from durum wheat (TtASR1) and barley (HvASR1). Here, we show that HvASR1 and TtASR1 are consistently predicted to be disordered and further confirm this experimentally. Addition of glycerol, which mimics dehydration, triggers a gain of structure in both proteins. Limited proteolysis showed that they are highly sensitive to protease degradation. Addition of 2,2,2-trifluoroethanol (TFE) however, results in a decreased susceptibility to proteolysis that is paralleled by a gain of structure. Mass spectrometry analyses (MS) led to the identification of a protein fragment resistant to proteolysis. Addition of zinc also induces a gain of structure and Hydrogen/Deuterium eXchange-Mass Spectrometry (HDX-MS) allowed identification of the region involved in the disorder-to-order transition. This study is the first reported experimental characterization of HvASR1 and TtASR1 proteins, and paves the way for future studies aimed at unveiling the functional impact of the structural transitions that these proteins undergo in the presence of zinc and at achieving atomic-resolution conformational ensemble description of these two plant intrinsically disordered proteins (IDPs).
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239
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Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res 2017; 45:5968-5979. [PMID: 28453854 PMCID: PMC5449598 DOI: 10.1093/nar/gkx294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/13/2017] [Indexed: 11/24/2022] Open
Abstract
Endonucleases that generate DNA double strand breaks often employ two independent subunits such that the active site from each subunit cuts either DNA strand. Restriction enzyme BcnI is a remarkable exception. It binds to the 5΄-CC/SGG-3΄ (where S = C or G, ‘/’ designates the cleavage position) target as a monomer forming an asymmetric complex, where a single catalytic center approaches the scissile phosphodiester bond in one of DNA strands. Bulk kinetic measurements have previously shown that the same BcnI molecule cuts both DNA strands at the target site without dissociation from the DNA. Here, we analyse the BcnI DNA binding and target recognition steps at the single molecule level. We find, using FRET, that BcnI adopts either ‘open’ or ‘closed’ conformation in solution. Next, we directly demonstrate that BcnI slides over long distances on DNA using 1D diffusion and show that sliding is accompanied by occasional jumping events, where the enzyme leaves the DNA and rebinds immediately at a distant site. Furthermore, we quantify the dynamics of the BcnI interactions with cognate and non-cognate DNA, and determine the preferred binding orientation of BcnI to the target site. These results provide new insights into the intricate dynamics of BcnI–DNA interactions.
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Affiliation(s)
- Georgij Kostiuk
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Jasmina Dikic
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Friedrich W Schwarz
- BCUBE, Technische Universitaet Dresden, Arnoldstrasse 18, 01307 Dresden, Germany
| | - Giedrius Sasnauskas
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
| | - Ralf Seidel
- Molecular Biophysics group, Institute for Experimental Physics I, Universität Leipzig, Linnéstr. 5, 04103 Leipzig, Germany
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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240
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Brady JP, Farber PJ, Sekhar A, Lin YH, Huang R, Bah A, Nott TJ, Chan HS, Baldwin AJ, Forman-Kay JD, Kay LE. Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation. Proc Natl Acad Sci U S A 2017; 114:E8194-E8203. [PMID: 28894006 PMCID: PMC5625912 DOI: 10.1073/pnas.1706197114] [Citation(s) in RCA: 313] [Impact Index Per Article: 44.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Membrane encapsulation is frequently used by the cell to sequester biomolecules and compartmentalize their function. Cells also concentrate molecules into phase-separated protein or protein/nucleic acid "membraneless organelles" that regulate a host of biochemical processes. Here, we use solution NMR spectroscopy to study phase-separated droplets formed from the intrinsically disordered N-terminal 236 residues of the germ-granule protein Ddx4. We show that the protein within the concentrated phase of phase-separated Ddx4, [Formula: see text], diffuses as a particle of 600-nm hydrodynamic radius dissolved in water. However, NMR spectra reveal sharp resonances with chemical shifts showing [Formula: see text] to be intrinsically disordered. Spin relaxation measurements indicate that the backbone amides of [Formula: see text] have significant mobility, explaining why high-resolution spectra are observed, but motion is reduced compared with an equivalently concentrated nonphase-separating control. Observation of a network of interchain interactions, as established by NOE spectroscopy, shows the importance of Phe and Arg interactions in driving the phase separation of Ddx4, while the salt dependence of both low- and high-concentration regions of phase diagrams establishes an important role for electrostatic interactions. The diffusion of a series of small probes and the compact but disordered 4E binding protein 2 (4E-BP2) protein in [Formula: see text] are explained by an excluded volume effect, similar to that found for globular protein solvents. No changes in structural propensities of 4E-BP2 dissolved in [Formula: see text] are observed, while changes to DNA and RNA molecules have been reported, highlighting the diverse roles that proteinaceous solvents play in dictating the properties of dissolved solutes.
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Affiliation(s)
- Jacob P Brady
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Patrick J Farber
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Ashok Sekhar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Yi-Hsuan Lin
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Rui Huang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Alaji Bah
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Timothy J Nott
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Hue Sun Chan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Julie D Forman-Kay
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8;
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8;
- Department of Chemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Division of Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada M5G 0A4
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241
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Kizilsavas G, Ledolter K, Kurzbach D. Hydrophobic Collapse of the Intrinsically Disordered Transcription Factor Myc Associated Factor X. Biochemistry 2017; 56:5365-5372. [DOI: 10.1021/acs.biochem.7b00679] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gönül Kizilsavas
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Département
de Chimie, Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Laboratoire des Biomolécules (LBM), 24 rue Lhomond, 75005 Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, CNRS, Laboratoire des Biomolécules (LBM), Paris, France
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242
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Astegno A, Bonza MC, Vallone R, La Verde V, D'Onofrio M, Luoni L, Molesini B, Dominici P. Arabidopsis calmodulin-like protein CML36 is a calcium (Ca 2+) sensor that interacts with the plasma membrane Ca 2+-ATPase isoform ACA8 and stimulates its activity. J Biol Chem 2017; 292:15049-15061. [PMID: 28726644 PMCID: PMC5592680 DOI: 10.1074/jbc.m117.787796] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/07/2017] [Indexed: 11/06/2022] Open
Abstract
Calmodulin-like (CML) proteins are major EF-hand-containing, calcium (Ca2+)-binding proteins with crucial roles in plant development and in coordinating plant stress tolerance. Given their abundance in plants, the properties of Ca2+ sensors and identification of novel target proteins of CMLs deserve special attention. To this end, we recombinantly produced and biochemically characterized CML36 from Arabidopsis thaliana We analyzed Ca2+ and Mg2+ binding to the individual EF-hands, observed metal-induced conformational changes, and identified a physiologically relevant target. CML36 possesses two high-affinity Ca2+/Mg2+ mixed binding sites and two low-affinity Ca2+-specific sites. Binding of Ca2+ induced an increase in the α-helical content and a conformational change that lead to the exposure of hydrophobic regions responsible for target protein recognition. Cation binding, either Ca2+ or Mg2+, stabilized the secondary and tertiary structures of CML36, guiding a large structural transition from a molten globule apo-state to a compact holoconformation. Importantly, through in vitro binding and activity assays, we showed that CML36 interacts directly with the regulative N terminus of the Arabidopsis plasma membrane Ca2+-ATPase isoform 8 (ACA8) and that this interaction stimulates ACA8 activity. Gene expression analysis revealed that CML36 and ACA8 are co-expressed mainly in inflorescences. Collectively, our results support a role for CML36 as a Ca2+ sensor that binds to and modulates ACA8, uncovering a possible involvement of the CML protein family in the modulation of plant-autoinhibited Ca2+ pumps.
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Affiliation(s)
- Alessandra Astegno
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
| | - Maria Cristina Bonza
- the Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Rosario Vallone
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
| | - Valentina La Verde
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
| | - Mariapina D'Onofrio
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
| | - Laura Luoni
- the Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Barbara Molesini
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
| | - Paola Dominici
- From the Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy and
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243
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Kjaergaard M, Kragelund BB. Functions of intrinsic disorder in transmembrane proteins. Cell Mol Life Sci 2017; 74:3205-3224. [PMID: 28601983 PMCID: PMC11107515 DOI: 10.1007/s00018-017-2562-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 12/19/2022]
Abstract
Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane proteins, and address why the flexibility afforded by disorder is mechanistically important. Intrinsically disordered regions are present in many common classes of membrane proteins including ion channels and transporters; G-protein coupled receptors (GPCRs), receptor tyrosine kinases and cytokine receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding protein disorder.
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Affiliation(s)
- Magnus Kjaergaard
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
- The Danish Research Institute of Translational Neuroscience (DANDRITE), Aarhus, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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244
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An Efficient Method for Estimating the Hydrodynamic Radius of Disordered Protein Conformations. Biophys J 2017; 113:550-557. [PMID: 28793210 DOI: 10.1016/j.bpj.2017.06.042] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered proteins play important roles throughout biology, yet our understanding of the relationship between their sequences, structural properties, and functions remains incomplete. The dynamic nature of these proteins, however, makes them difficult to characterize structurally. Many disordered proteins can attain both compact and expanded conformations, and the level of expansion may be regulated and important for function. Experimentally, the level of compaction and shape is often determined either by small-angle x-ray scattering experiments or pulsed-field-gradient NMR diffusion measurements, which provide ensemble-averaged estimates of the radius of gyration and hydrodynamic radius, respectively. Often, these experiments are interpreted using molecular simulations or are used to validate them. We here provide, to our knowledge, a new and efficient method to calculate the hydrodynamic radius of a disordered protein chain from a model of its structural ensemble. In particular, starting from basic concepts in polymer physics, we derive a relationship between the radius of gyration of a structure and its hydrodynamic ratio, which in turn can be used, for example, to compare a simulated ensemble of conformations to NMR diffusion measurements. The relationship may also be valuable when using NMR diffusion measurements to restrain molecular simulations.
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245
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Nardecchia I, Lechelon M, Gori M, Donato I, Preto J, Floriani E, Jaeger S, Mailfert S, Marguet D, Ferrier P, Pettini M. Detection of long-range electrostatic interactions between charged molecules by means of fluorescence correlation spectroscopy. Phys Rev E 2017; 96:022403. [PMID: 28950524 DOI: 10.1103/physreve.96.022403] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Indexed: 11/07/2022]
Abstract
In the present paper, an experimental feasibility study on the detection of long-range intermolecular interactions through three-dimensional molecular diffusion in solution is performed. This follows recent theoretical and numerical analyses reporting that long-range electrodynamic forces between biomolecules could be identified through deviations from Brownian diffusion. The suggested experimental technique was fluorescence correlation spectroscopy (FCS). By considering two oppositely charged molecular species in aqueous solution, namely, lysozymes and fluorescent dye molecules (Alexa488), the diffusion coefficient of the dyes has been measured for different values of the concentration of lysozyme, that is, for different average distances between the oppositely charged molecules. For our model, long-range interactions are of electrostatic origin, suggesting that their action radius can be varied by changing the ionic strength of the solution. The experimental outcomes clearly prove the detectability of long-range intermolecular interactions by means of the FCS technique. Molecular dynamics simulations provide a clear and unambiguous interpretation of the experimental results.
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Affiliation(s)
- Ilaria Nardecchia
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Mathias Lechelon
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | - Matteo Gori
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | - Irene Donato
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France
| | - Jordane Preto
- Department of Oncology, 3-336, Cross Cancer Institute, Edmonton, AB, T6G 1Z2, Canada
| | - Elena Floriani
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
| | | | | | - Didier Marguet
- Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Pierre Ferrier
- Aix Marseille Univ, CNRS, INSERM, CIML, 13288 Marseille, France
| | - Marco Pettini
- CNRS Centre de Physique Théorique UMR7332, 13288 Marseille, France.,Aix Marseille Univ, CNRS, CPT, 13288 Marseille, France
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246
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Rapid-Acting and Human Insulins: Hexamer Dissociation Kinetics upon Dilution of the Pharmaceutical Formulation. Pharm Res 2017; 34:2270-2286. [PMID: 28762200 PMCID: PMC5643355 DOI: 10.1007/s11095-017-2233-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/18/2017] [Indexed: 11/22/2022]
Abstract
Purpose Comparison of the dissociation kinetics of rapid-acting insulins lispro, aspart, glulisine and human insulin under physiologically relevant conditions. Methods Dissociation kinetics after dilution were monitored directly in terms of the average molecular mass using combined static and dynamic light scattering. Changes in tertiary structure were detected by near-UV circular dichroism. Results Glulisine forms compact hexamers in formulation even in the absence of Zn2+. Upon severe dilution, these rapidly dissociate into monomers in less than 10 s. In contrast, in formulations of lispro and aspart, the presence of Zn2+ and phenolic compounds is essential for formation of compact R6 hexamers. These slowly dissociate in times ranging from seconds to one hour depending on the concentration of phenolic additives. The disadvantage of the long dissociation times of lispro and aspart can be diminished by a rapid depletion of the concentration of phenolic additives independent of the insulin dilution. This is especially important in conditions similar to those after subcutaneous injection, where only minor dilution of the insulins occurs. Conclusion Knowledge of the diverging dissociation mechanisms of lispro and aspart compared to glulisine will be helpful for optimizing formulation conditions of rapid-acting insulins. Electronic supplementary material The online version of this article (doi:10.1007/s11095-017-2233-0) contains supplementary material, which is available to authorized users.
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247
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Vazquez L, e Lima LMTDR, Almeida MDS. Comprehensive structural analysis of designed incomplete polypeptide chains of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. PLoS One 2017; 12:e0182132. [PMID: 28750053 PMCID: PMC5531528 DOI: 10.1371/journal.pone.0182132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/12/2017] [Indexed: 11/18/2022] Open
Abstract
The cotranslational folding is recognized as a very cooperative process that occurs after the nearly completion of the polypeptide sequence of a domain. Here we investigated the challenges faced by polypeptide segments of a non-vectorial β-barrel fold. Besides the biological interest behind the SARS coronavirus non-structural protein 1 (nsp1, 117 amino acids), this study model has two structural features that motivated its use in this work: 1- its recombinant production is dependent on the temperature, with greater solubility when expressed at low temperatures. This is an indication of the cotranslational guidance to the native protein conformation. 2- Conversely, nsp1 has a six-stranded, mixed parallel/antiparallel β-barrel with intricate long-range interactions, indicating it will need the full-length protein to fold properly. We used non-denaturing purification conditions that allowed the characterization of polypeptide chains of different lengths, mimicking the landscape of the cotranslational fold of a β-barrel, and avoiding the major technical hindrances of working with the nascent polypeptide bound to the ribosome. Our results showed partially folded states formed as soon as the amino acids of the second β-strand were present (55 amino acids). These partially folded states are different based on the length of polypeptide chain. The native α-helix (amino acids 24-37) was identified as a transient structure (~20-30% propensity). We identified the presence of regular secondary structure after the fourth native β-strand is present (89 amino acids), in parallel to the collapse to a non-native 3D structure. Interestingly the polypeptide sequences of the native strands β2, β3 and β4 have characteristics of α-helices. Our comprehensive analyses support the idea that incomplete polypeptide chains, such as the ones of nascent proteins much earlier than the end of the translation, adopt an abundance of specific transient folds, instead of disordered conformations.
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Affiliation(s)
- Leonardo Vazquez
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Marcius da Silva Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Centro Nacional de Biologia Estrutural e Bioimagem (CENABIO), Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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248
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Challenges in Predicting Protein-Protein Interactions from Measurements of Molecular Diffusivity. Biophys J 2017; 111:1831-1842. [PMID: 27806265 DOI: 10.1016/j.bpj.2016.09.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 08/26/2016] [Accepted: 09/14/2016] [Indexed: 01/11/2023] Open
Abstract
Dynamic light scattering can be used to measure the diffusivity of a protein within a formulation. The dependence of molecular diffusivity on protein concentration (traditionally expressed in terms of the interaction parameter kD) is often used to infer whether protein-protein interactions are repulsive or attractive, resulting in solutions that are colloidally stable or unstable, respectively. However, a number of factors unrelated to intermolecular forces can also impact protein diffusion, complicating this interpretation. Here, we investigate the influence of multicomponent diffusion in a ternary protein-salt-water system on protein diffusion and kD in the context of Nernst-Planck theory. This analysis demonstrates that large changes in protein diffusivity with protein concentration can result even for hard-sphere systems in the absence of protein-protein interactions. In addition, we show that dynamic light scattering measurements of diffusivity made at low ionic strength cannot be reliably used to detect protein conformational changes. We recommend comparing experimentally determined kD values to theoretically predicted excluded-volume contributions, which will allow a more accurate assessment of protein-protein interactions.
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249
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Forcada-Nadal A, Palomino-Schätzlein M, Neira JL, Pineda-Lucena A, Rubio V. The PipX Protein, When Not Bound to Its Targets, Has Its Signaling C-Terminal Helix in a Flexed Conformation. Biochemistry 2017; 56:3211-3224. [PMID: 28581722 DOI: 10.1021/acs.biochem.7b00230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PipX, an 89-residue protein, acts as a coactivator of the global nitrogen regulator NtcA in cyanobacteria. NtcA-PipX interactions are regulated by 2-oxoglutarate (2-OG), an inverse indicator of the ammonia abundance, and by PII, a protein that binds to PipX at low 2-OG concentrations. The structure of PipX, when bound to NtcA or PII, consists of an N-terminal, five-stranded β-sheet (conforming a Tudor-like domain), and two long α-helices. These helices adopt either a flexed conformation, where they are in close contact and in an antiparallel mutual orientation, also packing against the β-sheet, or an open conformation (observed only in the PII-PipX complex) where the last α-helix moves apart from the rest of the protein. The aim of this work was to study the structure and dynamics of isolated PipX in solution by NMR. The backbone chemical shifts, the hydrogen-exchange, and the NOE patterns indicated that the isolated, monomeric PipX structure was formed by an N-terminal five-stranded β-sheet and two C-terminal α-helices. Furthermore, the observed NOEs between the two helices, and of α-helix2 with β-strand2 suggested that PipX adopted a flexed conformation. The β-strands 1 and 5 were highly flexible, as shown by the lack of interstrand backbone-backbone NOEs; in addition, the 15N-dynamics indicated that the C terminus of β-strand4 and the following β-turn (Phe42-Thr47), and the C-cap of α-helix1 (Arg70-Asn71) were particularly mobile. These two regions could act as hinges, allowing PipX to interact with its partners, including PlmA in the newly recognized PII-PipX-PlmA ternary complex.
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Affiliation(s)
| | | | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández , Elche (Alicante), Spain.,Instituto de Biocomputación y Física de Sistemas Complejos , Zaragoza, Spain
| | - Antonio Pineda-Lucena
- Centro de Investigación Príncipe Felipe , Valencia, Spain.,Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe , Valencia, Spain
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.,Group 739 of the CIBER de Enfermedades Raras (CIBERER-ISCIII) , Valencia, Spain
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250
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Very rapid amyloid fibril formation by a bacterial lipase in the absence of a detectable lag phase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:652-663. [DOI: 10.1016/j.bbapap.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/03/2017] [Accepted: 03/14/2017] [Indexed: 02/01/2023]
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