201
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Ramsey KM, Narang D, Komives EA. Prediction of the presence of a seventh ankyrin repeat in IκBε from homology modeling combined with hydrogen-deuterium exchange mass spectrometry (HDX-MS). Protein Sci 2019; 27:1624-1635. [PMID: 30133030 DOI: 10.1002/pro.3459] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/11/2018] [Accepted: 06/18/2018] [Indexed: 02/02/2023]
Abstract
The ankyrin repeat (AR) structure is a common protein-protein interaction motif and ankyrin repeat proteins comprise a vast family across a large array of different taxa. Natural AR proteins adopt a conserved fold comprised of several repeats with the N- and C-terminal repeats generally being of more divergent sequences. Obtaining experimental crystal structures for natural ankyrin repeat domains (ARD) can be difficult and often requires complexation with a binding partner. Homology modeling is an attractive method for creating a model of AR proteins due to the highly conserved fold; however, modeling the divergent N- and C-terminal "capping" repeats remains a challenge. We show here that amide hydrogen/deuterium exchange mass spectrometry (HDX-MS), which reports on the presence of secondary structural elements and "foldedness," can aid in the refinement and selection of AR protein homology models when multiple templates are identified with variations between them localizing to these terminal repeats. We report a homology model for the AR protein IκBε from three different templates and use HDX-MS to establish the presence of a seventh AR at the C-terminus identified by only one of the three templates used for modeling.
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Affiliation(s)
- Kristen M Ramsey
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92092-0378
| | - Dominic Narang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92092-0378
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92092-0378
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202
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Wada M, Hayashi Y, Arai M. Mutational analysis of a catalytically important loop containing active site and substrate-binding site in Escherichia coli phytase AppA. Biosci Biotechnol Biochem 2019; 83:860-868. [DOI: 10.1080/09168451.2019.1571897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
ABSTRACT
A phytase from Escherichia coli, AppA, has been the target of protein engineering to reduce the amount of undigested phosphates from livestock manure by making phosphorous from phytic acid available as a nutrient. To understand the contribution of each amino acid in the active site loop to the AppA activity, alanine and glycine scanning mutagenesis was undertaken. The results of phytase activity assay demonstrated loss of activity by mutations at charged residues within the conserved motif, supporting their importance in catalytic activity. In contrast, both conserved, non-polar residues and non-conserved residues tended to be tolerant to Ala and/or Gly mutations. Correlation analyses of chemical/structural characteristics of each mutation site against mutant activity revealed that the loop residues located closer to the substrate have greater contribution to the activity of AppA. These results may be useful in efficiently engineering AppA to improve its catalytic activity.
Abbreviations: AppA: pH 2.5 acid phosphatase; CSU: contacts of structural units; HAPs: histidine acid phosphatases; SASA: solvent accessible surface area; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SSM: site-saturation mutagenesis; WT: wild type
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Affiliation(s)
- Manami Wada
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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203
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Tuning the pH profile of β-glucuronidase by rational site-directed mutagenesis for efficient transformation of glycyrrhizin. Appl Microbiol Biotechnol 2019; 103:4813-4823. [PMID: 31055652 DOI: 10.1007/s00253-019-09790-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 02/05/2023]
Abstract
In this study, we aimed to shift the optimal pH of acidic β-glucuronidase from Aspergillus oryzae Li-3 (PGUS) to the neutral region by site-directed mutagenesis, thus allowing high efficient biotransformation of glycyrrhizin (GL) into glycyrrhetinic acid (GA) under higher pH where the solubility of GL could be greatly enhanced. Based on PGUS structure analysis, five critical aspartic acid and glutamic acid residues were replaced with arginine on the surface to generate a variant 5Rs with optimal pH shifting from 4.5 to 6.5. The catalytic efficiency (kcat /Km) value of 5Rs at pH 6.5 was 10.7-fold higher than that of PGUS wild-type at pH 6.5, even 1.4-fold higher than that of wild-type at pH 4.5. Molecular dynamics simulation was performed to explore the molecular mechanism for the shifted pH profile and enhanced pH stability of 5Rs.
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204
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Zhang Y, Zhang Y, McCready MJ, Maginn EJ. Prediction of membrane separation efficiency for hydrophobic and hydrophilic proteins. J Mol Model 2019; 25:132. [DOI: 10.1007/s00894-019-3985-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/13/2019] [Indexed: 11/25/2022]
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205
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Abstract
Refining predicted protein structures with all-atom molecular dynamics simulations is one route to producing, entirely by computational means, structural models of proteins that rival in quality those that are determined by X-ray diffraction experiments. Slow rearrangements within the compact folded state, however, make routine refinement of predicted structures by unrestrained simulations infeasible. In this work, we draw inspiration from the fields of metallurgy and blacksmithing, where practitioners have worked out practical means of controlling equilibration by mechanically deforming their samples. We describe a two-step refinement procedure that involves identifying collective variables for mechanical deformations using a coarse-grained model and then sampling along these deformation modes in all-atom simulations. Identifying those low-frequency collective modes that change the contact map the most proves to be an effective strategy for choosing which deformations to use for sampling. The method is tested on 20 refinement targets from the CASP12 competition and is found to induce large structural rearrangements that drive the structures closer to the experimentally determined structures during relatively short all-atom simulations of 50 ns. By examining the accuracy of side-chain rotamer states in subensembles of structures that have varying degrees of similarity to the experimental structure, we identified the reorientation of aromatic side chains as a step that remains slow even when encouraging global mechanical deformations in the all-atom simulations. Reducing the side-chain rotamer isomerization barriers in the all-atom force field is found to further speed up refinement.
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206
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Whittington AC, Mason AJ, Rokyta DR. A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin. Mol Biol Evol 2019; 35:887-898. [PMID: 29329419 DOI: 10.1093/molbev/msx334] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases. Type II venoms are highly neurotoxic and lack snake venom metalloproteinase expression and associated hemorrhagic activity. This dichotomy hinges on Mojave toxin (MTx), a phospholipase A2 (PLA2) based β-neurotoxin expressed in Type II venoms. MTx is comprised of a nontoxic acidic subunit that undergoes extensive proteolytic processing and allosterically regulates activity of a neurotoxic basic subunit. Evolution of the acidic subunit presents an evolutionary challenge because the need for high expression of a nontoxic venom component and the proteolytic machinery required for processing suggests genetic changes of seemingly little immediate benefit to fitness. We showed that MTx evolved through a cascading series of exaptations unlocked by a single nucleotide change. The evolution of one new cleavage site in the acidic subunit unmasked buried cleavage sites already present in ancestral PLA2s, enabling proteolytic processing. Snake venom serine proteases, already present in the venom to disrupt prey hemostasis, possess the requisite specificities for MTx acidic subunit proteolysis. The dimerization interface between MTx subunits evolved by exploiting a latent, but masked, hydrophobic interaction between ancestral PLA2s. The evolution of MTx through exaptation of existing functional and structural features suggests complex phenotypes that depend on evolutionary innovations can arise from minimal genetic change enabled by prior evolution.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Andrew J Mason
- Department of Biology, University of Central Florida, Orlando, FL
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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207
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Gudla R, Konduru GV, Nagarajaram HA, Siddavattam D. Organophosphate hydrolase interacts with Ton components and is targeted to the membrane only in the presence of the ExbB/ExbD complex. FEBS Lett 2019; 593:581-593. [DOI: 10.1002/1873-3468.13345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Ramurthy Gudla
- Department of Animal Biology School of Life Sciences University of Hyderabad India
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208
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Leser M, Chapman JR, Khine M, Pegan J, Law M, Makkaoui ME, Ueberheide BM, Brenowitz M. Chemical Generation of Hydroxyl Radical for Oxidative 'Footprinting'. Protein Pept Lett 2019; 26:61-69. [PMID: 30543161 DOI: 10.2174/0929866526666181212164812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of macromolecules. OBJECTIVE In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting. METHOD Pyrite Shrink-Wrap Laminate is fabricated by depositing pyrite (Fe-S2, aka 'fool's gold') nanocrystals onto thermolabile plastic (Shrinky Dink). The laminate can be thermoformed into a microtiter plate format into which samples are deposited for oxidation. RESULTS We demonstrate the utility of the Pyrite Shrink-Wrap Laminate for the chemical generation of hydroxyl radicals by mapping the surface of the T-cell co-stimulatory protein Programmed Death - 1 (PD-1) and the interface of the complex with its ligand PD-L1. CONCLUSION We have developed and validated an affordable and reliable benchtop method of hydroxyl radical generation that will broaden the application of protein oxidative footprinting. Due to the minimal equipment required to implement this method, it should be easily adaptable by many laboratories with access to mass spectrometry.
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Affiliation(s)
- Micheal Leser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jessica R Chapman
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States
| | - Michelle Khine
- Department of Biomedical Engineering, University of California, Irvine, CA, United States.,Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States
| | - Jonathan Pegan
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
| | - Matt Law
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Mohammed El Makkaoui
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Beatrix M Ueberheide
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
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209
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Kladova OA, Grin IR, Fedorova OS, Kuznetsov NA, Zharkov DO. Conformational Dynamics of Damage Processing by Human DNA Glycosylase NEIL1. J Mol Biol 2019; 431:1098-1112. [DOI: 10.1016/j.jmb.2019.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 10/27/2022]
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210
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Nambayan RJT, Sandin SI, Quint DA, Satyadi DM, de Alba E. The inflammasome adapter ASC assembles into filaments with integral participation of its two Death Domains, PYD and CARD. J Biol Chem 2019; 294:439-452. [PMID: 30459235 PMCID: PMC6333874 DOI: 10.1074/jbc.ra118.004407] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 11/17/2018] [Indexed: 11/06/2022] Open
Abstract
The inflammasome is a multiprotein complex necessary for the onset of inflammation. The adapter protein ASC assembles inflammasome components by acting as a molecular glue between danger-signal sensors and procaspase-1. The assembly is mediated by ASC self-association and protein interactions via its two Death Domains, PYD and CARD. Truncated versions of ASC have been shown to form filaments, but information on the filaments formed by full-length ASC is needed to construct a meaningful model of inflammasome assembly. To gain insights into this system, we used a combination of transmission EM, NMR, and computational analysis to investigate intact ASC structures. We show that ASC forms ∼6-7-nm-wide filaments that stack laterally to form bundles. The structural characteristics and dimensions of the bundles indicate that both PYD and CARD are integral parts of the filament. A truncated version of ASC with only the CARD domain (ASCCARD) forms different filaments (∼3-4-nm width), providing further evidence that both domains work in concert in filament assembly. Ring-shaped protein particles bound to pre-existing filaments match the size of ASC dimer structures generated by NMR-based protein docking, suggesting that the ASC dimer could be a basic building block for filament formation. Solution NMR binding studies identified the protein surfaces involved in the ASCCARD-ASCCARD interaction. These data provide new insights into the structural underpinnings of the inflammasome and should inform future efforts to interrogate this important biological system.
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Affiliation(s)
| | - Suzanne I Sandin
- From the Department of Bioengineering
- Chemistry and Chemical Biology Graduate Program
| | - David A Quint
- NSF-CREST Center for Cellular and Biomolecular Machines, and
- Department of Physics, University of California, Merced, California 95343
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211
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Žuvela P, Skoczylas M, Jay Liu J, Ba Czek T, Kaliszan R, Wong MW, Buszewski B, Héberger K. Column Characterization and Selection Systems in Reversed-Phase High-Performance Liquid Chromatography. Chem Rev 2019; 119:3674-3729. [PMID: 30604951 DOI: 10.1021/acs.chemrev.8b00246] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Reversed-phase high-performance liquid chromatography (RP-HPLC) is the most popular chromatographic mode, accounting for more than 90% of all separations. HPLC itself owes its immense popularity to it being relatively simple and inexpensive, with the equipment being reliable and easy to operate. Due to extensive automation, it can be run virtually unattended with multiple samples at various separation conditions, even by relatively low-skilled personnel. Currently, there are >600 RP-HPLC columns available to end users for purchase, some of which exhibit very large differences in selectivity and production quality. Often, two similar RP-HPLC columns are not equally suitable for the requisite separation, and to date, there is no universal RP-HPLC column covering a variety of analytes. This forces analytical laboratories to keep a multitude of diverse columns. Therefore, column selection is a crucial segment of RP-HPLC method development, especially since sample complexity is constantly increasing. Rationally choosing an appropriate column is complicated. In addition to the differences in the primary intermolecular interactions with analytes of the dispersive (London) type, individual columns can also exhibit a unique character owing to specific polar, hydrogen bond, and electron pair donor-acceptor interactions. They can also vary depending on the type of packing, amount and type of residual silanols, "end-capping", bonding density of ligands, and pore size, among others. Consequently, the chromatographic performance of RP-HPLC systems is often considerably altered depending on the selected column. Although a wide spectrum of knowledge is available on this important subject, there is still a lack of a comprehensive review for an objective comparison and/or selection of chromatographic columns. We aim for this review to be a comprehensive, authoritative, critical, and easily readable monograph of the most relevant publications regarding column selection and characterization in RP-HPLC covering the past four decades. Future perspectives, which involve the integration of state-of-the-art molecular simulations (molecular dynamics or Monte Carlo) with minimal experiments, aimed at nearly "experiment-free" column selection methodology, are proposed.
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Affiliation(s)
- Petar Žuvela
- Department of Chemistry , National University of Singapore , Singapore 117543 , Singapore
| | - Magdalena Skoczylas
- Department of Environmental Chemistry and Bioanalytics, Center for Modern Interdisciplinary Technologies , Nicolaus Copernicus University , Wileńska 4 , 87-100 Toruń , Poland
| | - J Jay Liu
- Department of Chemical Engineering , Pukyong National University , 365 Sinseon-ro , Nam-gu, 48-513 Busan , Korea
| | | | | | - Ming Wah Wong
- Department of Chemistry , National University of Singapore , Singapore 117543 , Singapore
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Center for Modern Interdisciplinary Technologies , Nicolaus Copernicus University , Wileńska 4 , 87-100 Toruń , Poland
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212
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Diaz-Parga P, de Alba E. Protein interactions of the inflammasome adapter ASC by solution NMR. Methods Enzymol 2019; 625:223-252. [PMID: 31455529 PMCID: PMC8455076 DOI: 10.1016/bs.mie.2019.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ASC (apoptosis-associated speck-like protein containing a CARD) is a modular protein that functions as an adapter of the inflammasome, a multi-protein complex that triggers the inflammatory response in the presence of infection or cell damage. ASC bridges the inflammasome components (PYD-containing sensors and procaspase 1) via homotypic interactions mediated by its two death domains, PYD and CARD. The self-assembly and oligomerization of multiple copies of these three proteins result in the activation of procaspase 1, in turn rendering different cytokines functional. An in-depth understanding of ASC binding capabilities is crucial to decipher the molecular mechanisms of its role in inflammasome formation. In this chapter, we discuss the use of solution NMR to identify specific interacting surfaces of the inflammasome adapter ASC, and describe detailed protocols to perform NMR titrations with Death Domains to obtain apparent dissociation constants of the resulting complexes. The incorporation of NMR restraints in molecular docking to obtain models of these protein assemblies is presented.
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Affiliation(s)
- Pedro Diaz-Parga
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Quantitative Systems Biology Graduate Program, University of California, Merced, CA, United States
| | - Eva de Alba
- Department of Bioengineering, School of Engineering, University of California, Merced, CA, United States,Corresponding author:
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213
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Devlin T, Hofman CR, Acevedo ZPV, Kohler KR, Tao L, Britt RD, Hoke KR, Hunsicker-Wang LM. DEPC modification of the Cu A protein from Thermus thermophilus. J Biol Inorg Chem 2018; 24:117-135. [PMID: 30523412 DOI: 10.1007/s00775-018-1632-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
Abstract
The CuA center is the initial electron acceptor in cytochrome c oxidase, and it consists of two copper ions bridged by two cysteines and ligated by two histidines, a methionine, and a carbonyl in the peptide backbone of a nearby glutamine. The two ligating histidines are of particular interest as they may influence the electronic and redox properties of the metal center. To test for the presence of reactive ligating histidines, a portion of cytochrome c oxidase from the bacteria Thermus thermophilus that contains the CuA site (the TtCuA protein) was treated with the chemical modifier diethyl pyrocarbonate (DEPC) and the reaction followed through UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopies at pH 5.0-9.0. A mutant protein (H40A/H117A) with the non-ligating histidines removed was similarly tested. Introduction of an electron-withdrawing DEPC-modification onto the ligating histidine 157 of TtCuA increased the reduction potential by over 70 mV, as assessed by cyclic voltammetry. Results from both proteins indicate that DEPC reacts with one of the two ligating histidines, modification of a ligating histidine raises the reduction potential of the CuA site, and formation of the DEPC adduct is reversible at room temperature. The existence of the reactive ligating histidine suggests that this residue may play a role in modulating the electronic and redox properties of TtCuA through kinetically-controlled proton exchange with the solvent. Lack of reactivity by the metalloproteins Sco and azurin, both of which contain a mononuclear copper center, indicate that reactivity toward DEPC is not a characteristic of all ligating histidines.
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Affiliation(s)
- Taylor Devlin
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Cristina R Hofman
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Zachary P V Acevedo
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Kelsey R Kohler
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, 30149, USA
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214
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Santibáñez-López CE, Kriebel R, Ballesteros JA, Rush N, Witter Z, Williams J, Janies DA, Sharma PP. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ 2018; 6:e5902. [PMID: 30479892 PMCID: PMC6240337 DOI: 10.7717/peerj.5902] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/09/2018] [Indexed: 12/25/2022] Open
Abstract
Scorpions have evolved a variety of toxins with a plethora of biological targets, but characterizing their evolution has been limited by the lack of a comprehensive phylogenetic hypothesis of scorpion relationships grounded in modern, genome-scale datasets. Disagreements over scorpion higher-level systematics have also incurred challenges to previous interpretations of venom families as ancestral or derived. To redress these gaps, we assessed the phylogenomic relationships of scorpions using the most comprehensive taxonomic sampling to date. We surveyed genomic resources for the incidence of calcins (a type of calcium channel toxin), which were previously known only from 16 scorpion species. Here, we show that calcins are diverse, but phylogenetically restricted only to parvorder Iurida, one of the two basal branches of scorpions. The other branch of scorpions, Buthida, bear the related LKTx toxins (absent in Iurida), but lack calcins entirely. Analysis of sequences and molecular models demonstrates remarkable phylogenetic inertia within both calcins and LKTx genes. These results provide the first synapomorphies (shared derived traits) for the recently redefined clades Buthida and Iurida, constituting the only known case of such traits defined from the morphology of molecules.
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Affiliation(s)
| | - Ricardo Kriebel
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Jesús A. Ballesteros
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nathaniel Rush
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Zachary Witter
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - John Williams
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Prashant P. Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, USA
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215
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Davila S, Liu P, Smith A, Marshall AG, Pedigo S. Spontaneous Calcium-Independent Dimerization of the Isolated First Domain of Neural Cadherin. Biochemistry 2018; 57:6404-6415. [PMID: 30387993 DOI: 10.1021/acs.biochem.8b00733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cadherins are calcium-dependent, transmembrane adhesion molecules that assemble through direct noncovalent association of their N-terminal extracellular modular domains. As the transmembrane component of adherens junctions, they indirectly link adherent cells' actin cytoskeletons. Here, we investigate the most distal extracellular domain of neural cadherin (N-cadherin), a protein required at excitatory synapses, the site of long-term potentiation. This domain is the site of the adhesive interface, and it forms a dimer spontaneously without binding calcium, a surprising finding given that calcium binding is required for proper physiological function. A critical tryptophan at position 2, W2, provides a spectroscopic probe for the "closed" monomer and strand-swapped dimer. Spectroscopic studies show that W2 remains docked in the two forms but has a different apparent interaction with the hydrophobic pocket. Size-exclusion chromatography was used to measure the levels of the monomer and dimer over time to study the kinetics and equilibria of the unexpected spontaneous dimer formation ( Kd = 130 μM; τ = 2 days at 4 °C). Our results support the idea that NCAD1 is missing critical contacts that facilitate the rapid exchange of the βA-strand. Furthermore, the monomer and dimer have equivalent and exceptionally high intrinsic stability for a 99-residue Ig-like domain with no internal disulfides ( Tm = 77 °C; Δ H = 85 kcal/mol). Ultimately, a complete analysis of synapse dynamics requires characterization of the kinetics and equilibria of N-cadherin. The studies reported here take a reductionist approach to understanding the essential biophysics of an atypical Ig-like domain that is the site of the adhesive interface of N-cadherin.
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Affiliation(s)
- Samantha Davila
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Peilu Liu
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Alexis Smith
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
| | - Alan G Marshall
- Department of Chemistry & Biochemistry , Florida State University , Tallahassee , Florida 32306 , United States.,Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory , Florida State University , Tallahassee , Florida 32310 , United States
| | - Susan Pedigo
- Department of Chemistry and Biochemistry , University of Mississippi , University , Mississippi 38677 , United States
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216
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Lermyte F, Valkenborg D, Loo JA, Sobott F. Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure. MASS SPECTROMETRY REVIEWS 2018; 37:750-771. [PMID: 29425406 PMCID: PMC6131092 DOI: 10.1002/mas.21560] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 01/19/2018] [Accepted: 01/19/2018] [Indexed: 05/11/2023]
Abstract
In recent years, electron capture (ECD) and electron transfer dissociation (ETD) have emerged as two of the most useful methods in mass spectrometry-based protein analysis, evidenced by a considerable and growing body of literature. In large part, the interest in these methods is due to their ability to induce backbone fragmentation with very little disruption of noncovalent interactions which allows inference of information regarding higher order structure from the observed fragmentation behavior. Here, we review the evolution of electron-based dissociation methods, and pay particular attention to their application in "native" mass spectrometry, their mechanism, determinants of fragmentation behavior, and recent developments in available instrumentation. Although we focus on the two most widely used methods-ECD and ETD-we also discuss the use of other ion/electron, ion/ion, and ion/neutral fragmentation methods, useful for interrogation of a range of classes of biomolecules in positive- and negative-ion mode, and speculate about how this exciting field might evolve in the coming years.
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Affiliation(s)
- Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - Dirk Valkenborg
- Centre for Proteomics, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Agoralaan, Diepenbeek, Belgium
- Applied Bio and Molecular Systems, Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, California
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry Group, Department of Chemistry, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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217
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Chen M, Lin X, Lu W, Schafer NP, Onuchic JN, Wolynes PG. Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields. J Chem Theory Comput 2018; 14:6102-6116. [PMID: 30240202 DOI: 10.1021/acs.jctc.8b00683] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
When good structural templates can be identified, template-based modeling is the most reliable way to predict the tertiary structure of proteins. In this study, we combine template-based modeling with a realistic coarse-grained force field, AWSEM, that has been optimized using the principles of energy landscape theory. The Associative memory, Water mediated, Structure and Energy Model (AWSEM) is a coarse-grained force field having both transferable tertiary interactions and knowledge-based local-in-sequence interaction terms. We incorporate template information into AWSEM by introducing soft collective biases to the template structures, resulting in a model that we call AWSEM-Template. Structure prediction tests on eight targets, four of which are in the low sequence identity "twilight zone" of homology modeling, show that AWSEM-Template can achieve high-resolution structure prediction. Our results also confirm that using a combination of AWSEM and a template-guided potential leads to more accurate prediction of protein structures than simply using a template-guided potential alone. Free energy profile analyses demonstrate that the soft collective biases to the template effectively increase funneling toward native-like structures while still allowing significant flexibility so as to allow for correction of discrepancies between the target structure and the template. A further stage of refinement using all-atom molecular dynamics augmented with soft collective biases to the structures predicted by AWSEM-Template leads to a further improvement of both backbone and side-chain accuracy by maintaining sufficient flexibility but at the same time discouraging unproductive unfolding events often seen in unrestrained all-atom refinement simulations. The all-atom refinement simulations also reduce patches of frustration of the initial predictions. Some of the backbones found among the structures produced during the initial coarse-grained prediction step already have CE-RMSD values of less than 3 Å with 90% or more of the residues aligned to the experimentally solved structure for all targets. All-atom structures generated during the following all-atom refinement simulations, which started from coarse-grained structures that were chosen without reference to any knowledge about the native structure, have CE-RMSD values of less than 2.5 Å with 90% or more of the residues aligned for 6 out of 8 targets. Clustering low energy structures generated during the initial coarse-grained annealing picks out reliably structures that are within 1 Å of the best sampled structures in 5 out of 8 cases. After the all-atom refinement, structures that are within 1 Å of the best sampled structures can be selected using a simple algorithm based on energetic features alone in 7 out of 8 cases.
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Affiliation(s)
- Mingchen Chen
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Bioengineering , Rice University , Houston , Texas 77005 , United States
| | - Xingcheng Lin
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Physics and Astronomy , Rice University , Houston , Texas 77005 , United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Physics and Astronomy , Rice University , Houston , Texas 77005 , United States
| | - Nicholas P Schafer
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Physics and Astronomy , Rice University , Houston , Texas 77005 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States.,Department of Biosciences , Rice University , Houston , Texas 77005 , United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University , Houston , Texas 77030 , United States.,Department of Chemistry , Rice University , Houston , Texas 77005 , United States.,Department of Biosciences , Rice University , Houston , Texas 77005 , United States
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218
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Lopez LC, Mukhitov N, Handley LD, Hamme CS, Hofman CR, Euers L, McKinney JR, Piers AD, Wadler E, Hunsicker-Wang LM. Characterization and effect of metal ions on the formation of the Thermus thermophilus Sco mixed disulfide intermediate. Protein Sci 2018; 27:1942-1954. [PMID: 30168216 DOI: 10.1002/pro.3502] [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: 06/30/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022]
Abstract
The Sco protein from Thermus thermophilus has previously been shown to perform a disulfide bond reduction in the CuA protein from T. thermophilus, which is a soluble protein engineered from subunit II of cytochrome ba 3 oxidase that lacks the transmembrane helix. The native cysteines on TtSco and TtCuA were mutated to serine residues to probe the reactivities of the individual cysteines. Conjugation of TNB to the remaining cysteine in TtCuA and subsequent release upon incubation with the complementary TtSco protein demonstrated the formation of the mixed disulfide intermediate. The cysteine of TtSco that attacks the disulfide bond in the target TtCuA protein was determined to be TtSco Cysteine 49. This cysteine is likely more reactive than Cysteine 53 due to a higher degree of solvent exposure. Removal of the metal binding histidine, His 139, does not change MDI formation. However, altering the arginine adjacent to the reactive cysteine in Sco (Arginine 48) does alter the formation of the MDI. Binding of Cu2+ or Cu+ to TtSco prior to reaction with TtCuA was found to preclude formation of the mixed disulfide intermediate. These results shed light on a mechanism of disulfide bond reduction by the TtSco protein and may point to a possible role of metal binding in regulating the activity. IMPORTANCE: The function of Sco is at the center of many studies. The disulfide bond reduction in CuA by Sco is investigated herein and the effect of metal ions on the ability to reduce and form a mixed disulfide intermediate are also probed.
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Affiliation(s)
- Liezelle C Lopez
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Baylor School of Medicine, One Baylor Plaza, Houston, Texas, 77030
| | - Nikita Mukhitov
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
| | - Lindsey D Handley
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,ThoughtSTEM, San Diego, California, 92108
| | - Cristina S Hamme
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Lone Star Family Health Center, Conroe, Texas, 77034
| | - Cristina R Hofman
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200
| | - Lindsay Euers
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Houston Methodist Hospital, Houston, Texas, 77303
| | - Jennifer R McKinney
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Department of Maternal Fetal Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, 77004
| | - Amani D Piers
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,Department of Psychology, Drexel University, Philadelphia, Pennsylvania, 19104
| | - Ellen Wadler
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200.,University of Texas Health Science Center Houston School of Public Health, Houston, Texas, 77030
| | - Laura M Hunsicker-Wang
- Department of Chemistry, Trinity University, One Trinity Place, San Antonio, Texas, 78212-7200
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219
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Lee CH, Jang EK, Yeon YJ, Pack SP. Stabilization of Bovine carbonic anhydrase II through rational site-specific immobilization. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.06.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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220
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Agajanian S, Odeyemi O, Bischoff N, Ratra S, Verkhivker GM. Machine Learning Classification and Structure–Functional Analysis of Cancer Mutations Reveal Unique Dynamic and Network Signatures of Driver Sites in Oncogenes and Tumor Suppressor Genes. J Chem Inf Model 2018; 58:2131-2150. [DOI: 10.1021/acs.jcim.8b00414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Steve Agajanian
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Oluyemi Odeyemi
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Nathaniel Bischoff
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Simrath Ratra
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
| | - Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Department of Computational Sciences, Schmid College of Science and Technology, Chapman University, One University
Drive, Orange, California 92866, United States
- Chapman University, School of Pharmacy, Irvine, California 92618, United States
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221
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Medina-Carmona E, Rizzuti B, Martín-Escolano R, Pacheco-García JL, Mesa-Torres N, Neira JL, Guzzi R, Pey AL. Phosphorylation compromises FAD binding and intracellular stability of wild-type and cancer-associated NQO1: Insights into flavo-proteome stability. Int J Biol Macromol 2018; 125:1275-1288. [PMID: 30243998 DOI: 10.1016/j.ijbiomac.2018.09.108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/30/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023]
Abstract
Over a quarter million of protein phosphorylation sites have been identified so far, although the effects of site-specific phosphorylation on protein function and stability, as well as their possible impact in the phenotypic manifestation in genetic diseases are vastly unknown. We investigated here the effects of phosphorylating S82 in human NADP(H):quinone oxidoreductase 1, a representative example of disease-associated flavoprotein in which protein stability is coupled to the intracellular flavin levels. Additionally, the cancer-associated P187S polymorphism causes inactivation and destabilization of the enzyme. By using extensive in vitro and in silico characterization of phosphomimetic S82D mutations, we showed that S82D locally affected the flavin binding site of the wild-type (WT) and P187S proteins thus altering flavin binding affinity, conformational stability and aggregation propensity. Consequently, the phosphomimetic S82D may destabilize the WT protein intracellularly by promoting the formation of the degradation-prone apo-protein. Noteworthy, WT and P187S proteins respond differently to the phosphomimetic mutation in terms of intracellular stability, further supporting differences in molecular recognition of these two variants by the proteasomal degradation pathway. We propose that phosphorylation could have critical consequences on stability and function of human flavoproteins, important for our understanding of genotype-phenotype relationships in their related genetic diseases.
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Affiliation(s)
| | - Bruno Rizzuti
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Rubén Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, 18071 Granada, Spain
| | | | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain
| | - José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, Avda. del Ferrocarril s/n, 03202 Elche, Alicante, Spain; Instituto de Biocomputación y Física de los Sistemas Complejos (BIFI), 50009 Zaragoza, Spain
| | - Rita Guzzi
- CNR-NANOTEC, Licryl-UOS Cosenza and CEMIF.Cal, Department of Physics, University of Calabria, 87036 Rende, Italy; Molecular Biophysics Laboratory, Department of Physics, University of Calabria, 87036 Rende, Italy
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain.
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222
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Medina-Carmona E, Betancor-Fernández I, Santos J, Mesa-Torres N, Grottelli S, Batlle C, Naganathan AN, Oppici E, Cellini B, Ventura S, Salido E, Pey AL. Insight into the specificity and severity of pathogenic mechanisms associated with missense mutations through experimental and structural perturbation analyses. Hum Mol Genet 2018; 28:1-15. [DOI: 10.1093/hmg/ddy323] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/09/2018] [Indexed: 12/21/2022] Open
Abstract
Abstract
Most pathogenic missense mutations cause specific molecular phenotypes through protein destabilization. However, how protein destabilization is manifested as a given molecular phenotype is not well understood. We develop here a structural and energetic approach to describe mutational effects on specific traits such as function, regulation, stability, subcellular targeting or aggregation propensity. This approach is tested using large-scale experimental and structural perturbation analyses in over thirty mutations in three different proteins (cancer-associated NQO1, transthyretin related with amyloidosis and AGT linked to primary hyperoxaluria type I) and comprising five very common pathogenic mechanisms (loss-of-function and gain-of-toxic function aggregation, enzyme inactivation, protein mistargeting and accelerated degradation). Our results revealed that the magnitude of destabilizing effects and, particularly, their propagation through the structure to promote disease-associated conformational states largely determine the severity and molecular mechanisms of disease-associated missense mutations. Modulation of the structural perturbation at a mutated site is also shown to cause switches between different molecular phenotypes. When very common disease-associated missense mutations were investigated, we also found that they were not among the most deleterious possible missense mutations at those sites, and required additional contributions from codon bias and effects of CpG sites to explain their high frequency in patients. Our work sheds light on the molecular basis of pathogenic mechanisms and genotype–phenotype relationships, with implications for discriminating between pathogenic and neutral changes within human genome variability from whole genome sequencing studies.
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Affiliation(s)
- Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, Granada, Spain
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Jaime Santos
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Silvia Grottelli
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Cristina Batlle
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai, India
| | - Elisa Oppici
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Strada Le Grazie, Verona, Italy
| | - Barbara Cellini
- Department of Experimental Medicine, University of Perugia, Piazzale Gambuli, Perugia
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases, Hospital Universitario de Canarias, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain
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223
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Rouhani M, Khodabakhsh F, Norouzian D, Cohan RA, Valizadeh V. Molecular dynamics simulation for rational protein engineering: Present and future prospectus. J Mol Graph Model 2018; 84:43-53. [DOI: 10.1016/j.jmgm.2018.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/19/2022]
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224
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Dergousova EA, Poluektov YM, Klimanova EA, Petrushanko IY, Mitkevich VA, Makarov AA, Lopina OD. Glutathionylation of Na,K-ATPase Alpha-Subunit Alters Enzyme Conformation and Sensitivity to Trypsinolysis. BIOCHEMISTRY. BIOKHIMIIA 2018; 83:969-981. [PMID: 30208833 DOI: 10.1134/s0006297918080084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 04/13/2018] [Indexed: 06/08/2023]
Abstract
We found earlier that Na,K-ATPase is purified from duck salt glands in partially glutathionylated state (up to 13 of the 23 cysteine residues of the Na,K-ATPase catalytic α-subunit can be S-glutathionylated). To determine the effect of glutathionylation on the enzyme conformation, we have analyzed the products of trypsinolysis of Na,K-ATPase α-subunit in different conformations with different extent of glutathionylation. Incubation of the protein in the E1 conformation with trypsin produced a large fragment with a molecular mass (MM) of 80 kDa with the following formation of smaller fragments with MM 40, 35.5, and 23 kDa. Tryptic digestion of Na,K-ATPase in the E2 conformation also resulted in the generation of the fragments with MM 40, 35.5, and 23 kDa. Deglutathionylation of Na,K-ATPase α-subunit increases the rate of proteolysis of the enzyme in both E1 and E2 conformations. The pattern of tryptic digestion of the α-subunit in E2 conformation additionally glutathionylated with oxidized glutathione is similar to that of partially deglutathionylated Na,K-ATPase. The pattern of tryptic digestion of the additionally glutathionylated α-subunit in E1 conformation is similar to that of the native enzyme. The highest rate of trypsinolysis was observed for the α-subunit in complex with ouabain (E2-OBN conformation). Additional glutathionylation increased the content of high-molecular-weight fragments among the digestion products, as compared to the native and deglutathionylated enzymes. The data obtained were confirmed using molecular modeling that revealed that number of sites accessible for trypsinolysis is higher in the E2P-OBN conformation than in the E1- and E2-conformations and that glutathionylation decreases the number of sites accessible for trypsin. Therefore, glutathionylation affects enzyme conformation and its sensitivity to trypsinolysis. The mechanisms responsible for the changes in the Na,K-ATPase sensitivity to trypsinolysis depending on the level of enzyme glutathionylation and increase in the enzyme sensitivity to proteolysis upon its binding to ouabain, as well as physiological role of these phenomena are discussed.
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Affiliation(s)
- E A Dergousova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - Y M Poluektov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - E A Klimanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - I Y Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - V A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - O D Lopina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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225
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Hari SB, Grant RA, Sauer RT. Structural and Functional Analysis of E. coli Cyclopropane Fatty Acid Synthase. Structure 2018; 26:1251-1258.e3. [PMID: 30057024 DOI: 10.1016/j.str.2018.06.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/18/2018] [Accepted: 06/20/2018] [Indexed: 01/17/2023]
Abstract
Cell membranes must adapt to different environments. In Gram-negative bacteria, the inner membrane can be remodeled directly by modification of lipids embedded in the bilayer. For example, when Escherichia coli enters stationary phase, cyclopropane fatty acid (CFA) synthase converts most double bonds in unsaturated inner-membrane lipids into cyclopropyl groups. Here we report the crystal structure of E. coli CFA synthase. The enzyme is a dimer in the crystal and in solution, with each subunit containing a smaller N-domain that associates tightly with a larger catalytic C-domain, even following cleavage of the inter-domain linker or co-expression of each individual domain. Efficient catalysis requires dimerization and proper linkage of the two domains. These findings support an avidity-based model in which one subunit of the dimer stabilizes membrane binding, while the other subunit carries out catalysis.
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Affiliation(s)
- Sanjay B Hari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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226
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Pey AL. Biophysical and functional perturbation analyses at cancer-associated P187 and K240 sites of the multifunctional NADP(H):quinone oxidoreductase 1. Int J Biol Macromol 2018; 118:1912-1923. [PMID: 30009918 DOI: 10.1016/j.ijbiomac.2018.07.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 12/14/2022]
Abstract
Once whole-genome sequencing has reached the clinical practice, a main challenge ahead is the high-throughput and accurate prediction of the pathogenicity of genetic variants. However, current prediction tools do not consider explicitly a well-known property of disease-causing mutations: their ability to affect multiple functional sites distant in the protein structure. Here we carried out an extensive biophysical characterization of fourteen mutant variants at two cancer-associated sites of the enzyme NQO1, a paradigm of multi-functional protein. We showed that the magnitude of destabilizing effects, their molecular origins (structural vs. dynamic) and their efficient propagation through the protein structure gradually led to functional perturbations at different sites. Modulation of these structural perturbations also led to switches between molecular phenotypes. Our work supports that experimental and computational perturbation analyses would improve our understanding of the molecular basis of many loss-of-function genetic diseases as well as our ability to accurately predict the pathogenicity of genetic variants in a high-throughput fashion.
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Affiliation(s)
- Angel L Pey
- Department of Physical Chemistry, University of Granada, Av. Fuentenueva S/N, 18071 Granada, Spain.
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227
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Kruziki MA, Sarma V, Hackel BJ. Constrained Combinatorial Libraries of Gp2 Proteins Enhance Discovery of PD-L1 Binders. ACS COMBINATORIAL SCIENCE 2018; 20:423-435. [PMID: 29799714 DOI: 10.1021/acscombsci.8b00010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Engineered protein ligands are used for molecular therapy, diagnostics, and industrial biotechnology. The Gp2 domain is a 45-amino acid scaffold that has been evolved for specific, high-affinity binding to multiple targets by diversification of two solvent-exposed loops. Inspired by sitewise enrichment of select amino acids, including cysteine pairs, in earlier Gp2 discovery campaigns, we hypothesized that the breadth and efficiency of de novo Gp2 discovery will be aided by sitewise amino acid constraint within combinatorial library design. We systematically constructed eight libraries and comparatively evaluated their efficacy for binder discovery via yeast display against a panel of targets. Conservation of a cysteine pair at the termini of the first diversified paratope loop increased binder discovery 16-fold ( p < 0.001). Yet two other libraries with conserved cysteine pairs, within the second loop or an interloop pair, did not aid discovery thereby indicating site-specific impact. Via a yeast display protease resistance assay, Gp2 variants from the loop one cysteine pair library were 3.3 ± 2.1-fold ( p = 0.005) more stable than nonconstrained variants. Sitewise constraint of noncysteine residues-guided by previously evolved binders, natural Gp2 homology, computed stability, and structural analysis-did not aid discovery. A panel of binders to programmed death ligand 1 (PD-L1), a key target in cancer immunotherapy, were discovered from the loop 1 cysteine constraint library. Affinity maturation via loop walking resulted in strong, specific cellular PD-L1 affinity ( Kd = 6-9 nM).
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Affiliation(s)
- Max A. Kruziki
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Vidur Sarma
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- University of Minnesota—Twin Cities, Department of Chemical Engineering and Materials Science, 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
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228
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Abstract
Based on molecular dynamics simulations of four globular proteins in dilute aqueous solution, with three different water models, we examine several, essentially geometrical, aspects of the protein-water interface that remain controversial or incompletely understood. First, we compare different hydration shell definitions, based on spatial or topological proximity criteria. We find that the best method for constructing monolayer shells with nearly complete coverage is to use a 5 Å water-carbon cutoff and a 4 Å water-water cutoff. Using this method, we determine a mean interfacial water area of 11.1 Å2 which appears to be a universal property of the protein-water interface. We then analyze the local coordination and packing density of water molecules in the hydration shells and in subsets of the first shell. The mean polar water coordination number in the first shell remains within 1% of the bulk-water value, and it is 5% lower in the nonpolar part of the first shell. The local packing density is obtained from additively weighted Voronoi tessellation, arguably the most physically realistic method for allocating space between protein and water. We find that water in all parts of the first hydration shell, including the nonpolar part, is more densely packed than in the bulk, with a shell-averaged density excess of 6% for all four proteins. We suggest reasons why this value differs from previous experimental and computational results, emphasizing the importance of a realistic placement of the protein-water dividing surface and the distinction between spatial correlation and packing density. The protein-induced perturbation of water coordination and packing density is found to be short-ranged, with an exponential decay "length" of 0.6 shells. We also compute the protein partial volume, analyze its decomposition, and argue against the relevance of electrostriction.
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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229
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Iuso A, Wiersma M, Schüller HJ, Pode-Shakked B, Marek-Yagel D, Grigat M, Schwarzmayr T, Berutti R, Alhaddad B, Kanon B, Grzeschik NA, Okun JG, Perles Z, Salem Y, Barel O, Vardi A, Rubinshtein M, Tirosh T, Dubnov-Raz G, Messias AC, Terrile C, Barshack I, Volkov A, Avivi C, Eyal E, Mastantuono E, Kumbar M, Abudi S, Braunisch M, Strom TM, Meitinger T, Hoffmann GF, Prokisch H, Haack TB, Brundel BJ, Haas D, Sibon OC, Anikster Y. Mutations in PPCS, Encoding Phosphopantothenoylcysteine Synthetase, Cause Autosomal-Recessive Dilated Cardiomyopathy. Am J Hum Genet 2018; 102:1018-1030. [PMID: 29754768 DOI: 10.1016/j.ajhg.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/22/2018] [Indexed: 01/25/2023] Open
Abstract
Coenzyme A (CoA) is an essential metabolic cofactor used by around 4% of cellular enzymes. Its role is to carry and transfer acetyl and acyl groups to other molecules. Cells can synthesize CoA de novo from vitamin B5 (pantothenate) through five consecutive enzymatic steps. Phosphopantothenoylcysteine synthetase (PPCS) catalyzes the second step of the pathway during which phosphopantothenate reacts with ATP and cysteine to form phosphopantothenoylcysteine. Inborn errors of CoA biosynthesis have been implicated in neurodegeneration with brain iron accumulation (NBIA), a group of rare neurological disorders characterized by accumulation of iron in the basal ganglia and progressive neurodegeneration. Exome sequencing in five individuals from two unrelated families presenting with dilated cardiomyopathy revealed biallelic mutations in PPCS, linking CoA synthesis with a cardiac phenotype. Studies in yeast and fruit flies confirmed the pathogenicity of identified mutations. Biochemical analysis revealed a decrease in CoA levels in fibroblasts of all affected individuals. CoA biosynthesis can occur with pantethine as a source independent from PPCS, suggesting pantethine as targeted treatment for the affected individuals still alive.
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230
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Affiliation(s)
- Filip Persson
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
| | - Bertil Halle
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, P.O. Box 124, SE-22100 Lund, Sweden
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231
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Pinarbasi ES, Cağatay T, Fung HYJ, Li YC, Chook YM, Thomas PJ. Active nuclear import and passive nuclear export are the primary determinants of TDP-43 localization. Sci Rep 2018; 8:7083. [PMID: 29728608 PMCID: PMC5935693 DOI: 10.1038/s41598-018-25008-4] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/13/2018] [Indexed: 12/12/2022] Open
Abstract
ALS (Amyotrophic Lateral Sclerosis) is a neurodegenerative disease characterized by the redistribution of the RNA binding protein TDP-43 in affected neurons: from predominantly nuclear to aggregated in the cytosol. However, the determinants of TDP-43 localization and the cellular insults that promote redistribution are incompletely understood. Here, we show that the putative Nuclear Export Signal (NES) is not required for nuclear egress of TDP-43. Moreover, when the TDP-43 domain which contains the putative NES is fused to a reporter protein, YFP, the presence of the NES is not sufficient to mediate nuclear exclusion of the fusion protein. We find that the previously studied "∆NES" mutant, in which conserved hydrophobic residues are mutated to alanines, disrupts both solubility and splicing function. We further show that nuclear export of TDP-43 is independent of the exportin XPO1. Finally, we provide evidence that nuclear egress of TDP-43 is size dependent; nuclear export of dTomato TDP-43 is significantly impaired compared to Flag TDP-43. Together, these results suggest nuclear export of TDP-43 is predominantly driven by passive diffusion.
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Affiliation(s)
- Emile S Pinarbasi
- Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
- Medical Scientist Training Program, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Tolga Cağatay
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Ho Yee Joyce Fung
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Ying C Li
- Medical Scientist Training Program, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
- Department of Neuroscience, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Yuh Min Chook
- Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
| | - Philip J Thomas
- Department of Physiology, UT Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA.
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232
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Mighell TL, Evans-Dutson S, O'Roak BJ. A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships. Am J Hum Genet 2018; 102:943-955. [PMID: 29706350 PMCID: PMC5986715 DOI: 10.1016/j.ajhg.2018.03.018] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
Phosphatase and tensin homolog (PTEN) is a tumor suppressor frequently mutated in diverse cancers. Germline PTEN mutations are also associated with a range of clinical outcomes, including PTEN hamartoma tumor syndrome (PHTS) and autism spectrum disorder (ASD). To empower new insights into PTEN function and clinically relevant genotype-phenotype relationships, we systematically evaluated the effect of PTEN mutations on lipid phosphatase activity in vivo. Using a massively parallel approach that leverages an artificial humanized yeast model, we derived high-confidence estimates of functional impact for 7,244 single amino acid PTEN variants (86% of possible). We identified 2,273 mutations with reduced cellular lipid phosphatase activity, which includes 1,789 missense mutations. These data recapitulated known functional findings but also uncovered new insights into PTEN protein structure, biochemistry, and mutation tolerance. Several residues in the catalytic pocket showed surprising mutational tolerance. We identified that the solvent exposure of wild-type residues is a critical determinant of mutational tolerance. Further, we created a comprehensive functional map by leveraging correlations between amino acid substitutions to impute functional scores for all variants, including those not present in the assay. Variant functional scores can reliably discriminate likely pathogenic from benign alleles. Further, 32% of ClinVar unclassified missense variants are phosphatase deficient in our assay, supporting their reclassification. ASD-associated mutations generally had less severe fitness scores relative to PHTS-associated mutations (p = 7.16 × 10-5) and a higher fraction of hypomorphic mutations, arguing for continued genotype-phenotype studies in larger clinical datasets that can further leverage these rich functional data.
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Affiliation(s)
- Taylor L Mighell
- Neuroscience Graduate Program, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Sara Evans-Dutson
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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233
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dos Santos RN, Khan S, Morcos F. Characterization of C-ring component assembly in flagellar motors from amino acid coevolution. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171854. [PMID: 29892378 PMCID: PMC5990795 DOI: 10.1098/rsos.171854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Bacterial flagellar motility, an important virulence factor, is energized by a rotary motor localized within the flagellar basal body. The rotor module consists of a large framework (the C-ring), composed of the FliG, FliM and FliN proteins. FliN and FliM contacts the FliG torque ring to control the direction of flagellar rotation. We report that structure-based models constrained only by residue coevolution can recover the binding interface of atomic X-ray dimer complexes with remarkable accuracy (approx. 1 Å RMSD). We propose a model for FliM-FliN heterodimerization, which agrees accurately with homologous interfaces as well as in situ cross-linking experiments, and hence supports a proposed architecture for the lower portion of the C-ring. Furthermore, this approach allowed the identification of two discrete and interchangeable homodimerization interfaces between FliM middle domains that agree with experimental measurements and might be associated with C-ring directional switching dynamics triggered upon binding of CheY signal protein. Our findings provide structural details of complex formation at the C-ring that have been difficult to obtain with previous methodologies and clarify the architectural principle that underpins the ultra-sensitive allostery exhibited by this ring assembly that controls the clockwise or counterclockwise rotation of flagella.
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Affiliation(s)
- Ricardo Nascimento dos Santos
- Institute of Chemistry and Center for Computational Engineering and Science, University of Campinas, Campinas, SP, Brazil
| | - Shahid Khan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX, USA
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234
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Agwa AJ, Peigneur S, Chow CY, Lawrence N, Craik DJ, Tytgat J, King GF, Henriques ST, Schroeder CI. Gating modifier toxins isolated from spider venom: Modulation of voltage-gated sodium channels and the role of lipid membranes. J Biol Chem 2018; 293:9041-9052. [PMID: 29703751 DOI: 10.1074/jbc.ra118.002553] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/25/2018] [Indexed: 11/06/2022] Open
Abstract
Gating modifier toxins (GMTs) are venom-derived peptides isolated from spiders and other venomous creatures and modulate activity of disease-relevant voltage-gated ion channels and are therefore being pursued as therapeutic leads. The amphipathic surface profile of GMTs has prompted the proposal that some GMTs simultaneously bind to the cell membrane and voltage-gated ion channels in a trimolecular complex. Here, we examined whether there is a relationship among spider GMT amphipathicity, membrane binding, and potency or selectivity for voltage-gated sodium (NaV) channels. We used NMR spectroscopy and in silico calculations to examine the structures and physicochemical properties of a panel of nine GMTs and deployed surface plasmon resonance to measure GMT affinity for lipids putatively found in proximity to NaV channels. Electrophysiology was used to quantify GMT activity on NaV1.7, an ion channel linked to chronic pain. Selectivity of the peptides was further examined against a panel of NaV channel subtypes. We show that GMTs adsorb to the outer leaflet of anionic lipid bilayers through electrostatic interactions. We did not observe a direct correlation between GMT amphipathicity and affinity for lipid bilayers. Furthermore, GMT-lipid bilayer interactions did not correlate with potency or selectivity for NaVs. We therefore propose that increased membrane binding is unlikely to improve subtype selectivity and that the conserved amphipathic GMT surface profile is an adaptation that facilitates simultaneous modulation of multiple NaVs.
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Affiliation(s)
- Akello J Agwa
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Chun Yuen Chow
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Nicole Lawrence
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - David J Craik
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Glenn F King
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Sónia Troeira Henriques
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Christina I Schroeder
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
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235
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Bodmer NK, Havranek JJ. Efficient minimization of multipole electrostatic potentials in torsion space. PLoS One 2018; 13:e0195578. [PMID: 29641557 PMCID: PMC5895050 DOI: 10.1371/journal.pone.0195578] [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: 09/18/2017] [Accepted: 03/26/2018] [Indexed: 11/24/2022] Open
Abstract
The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom.
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Affiliation(s)
- Nicholas K. Bodmer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - James J. Havranek
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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236
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Kearney C, Olenginski LT, Hirn TD, Fowler GD, Tariq D, Brewer SH, Phillips-Piro CM. Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine. RSC Adv 2018; 8:13503-13512. [PMID: 29780583 PMCID: PMC5944249 DOI: 10.1039/c8ra02000k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O2 ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.
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Affiliation(s)
- Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Lukasz T Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Trexler D Hirn
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Gwendolyn D Fowler
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Daniyal Tariq
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
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237
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Cardote TAF, Gadd MS, Ciulli A. Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Structure 2018; 25:901-911.e3. [PMID: 28591624 PMCID: PMC5462531 DOI: 10.1016/j.str.2017.04.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/07/2017] [Accepted: 04/28/2017] [Indexed: 01/07/2023]
Abstract
Cullin RING E3 ubiquitin ligases (CRLs) function in the ubiquitin proteasome system to catalyze the transfer of ubiquitin from E2 conjugating enzymes to specific substrate proteins. CRLs are large dynamic complexes and attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. The atomic details of whole CRL assembly and interactions that dictate subunit specificity remain elusive. Here we present the crystal structure of a pentameric CRL2VHL complex, composed of Cul2, Rbx1, Elongin B, Elongin C, and pVHL. The structure traps a closed state of full-length Cul2 and a new pose of Rbx1 in a trajectory from closed to open conformation. We characterize hotspots and binding thermodynamics at the interface between Cul2 and pVHL-EloBC and identify mutations that contribute toward a selectivity switch for Cul2 versus Cul5 recognition. Our findings provide structural and biophysical insights into the whole Cul2 complex that could aid future drug targeting.
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Affiliation(s)
- Teresa A F Cardote
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Morgan S Gadd
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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238
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Stenvang M, Schafer NP, Malmos KG, Pérez AMW, Niembro O, Sormanni P, Basaiawmoit RV, Christiansen G, Andreasen M, Otzen DE. Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain. J Mol Biol 2018. [PMID: 29524512 DOI: 10.1016/j.jmb.2018.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Numerous mutations in the corneal protein TGFBIp lead to opaque extracellular deposits and corneal dystrophies (CDs). Here we elucidate the molecular origins underlying TGFBIp's mutation-induced increase in aggregation propensity through comprehensive biophysical and bioinformatic analyses of mutations associated with every major subtype of TGFBIp-linked CDs including lattice corneal dystrophy (LCD) and three subtypes of granular corneal dystrophy (GCD 1-3). LCD mutations at buried positions in the C-terminal Fas1-4 domain lead to decreased stability. GCD variants show biophysical profiles distinct from those of LCD mutations. GCD 1 and 3 mutations reduce solubility rather than stability. Half of the 50 positions within Fas1-4 most sensitive to mutation are associated with at least one known disease-causing mutation, including 10 of the top 11 positions. Thus, TGFBIp aggregation is driven by mutations that despite their physico-chemical diversity target either the stability or solubility of Fas1-4 in predictable ways, suggesting straightforward general therapeutic strategies.
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Affiliation(s)
- Marcel Stenvang
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Kirsten Gade Malmos
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Adriana-Michelle Wolf Pérez
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Olatz Niembro
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom
| | - Rajiv Vaid Basaiawmoit
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Maria Andreasen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark; Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark.
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239
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Khoshnejad M, Greineder CF, Pulsipher KW, Villa CH, Altun B, Pan DC, Tsourkas A, Dmochowski IJ, Muzykantov VR. Ferritin Nanocages with Biologically Orthogonal Conjugation for Vascular Targeting and Imaging. Bioconjug Chem 2018; 29:1209-1218. [PMID: 29429330 DOI: 10.1021/acs.bioconjchem.8b00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Genetic incorporation of biologically orthogonal functional groups into macromolecules has the potential to yield efficient, controlled, reproducible, site-specific conjugation of affinity ligands, contrast agents, or therapeutic cargoes. Here, we applied this approach to ferritin, a ubiquitous iron-storage protein that self-assembles into multimeric nanocages with remarkable stability, size uniformity (12 nm), and endogenous capacity for loading and transport of a variety of inorganic and organic cargoes. The unnatural amino acid, 4-azidophenylalanine (4-AzF), was incorporated at different sites in the human ferritin light chain (hFTL) to allow site-specific conjugation of alkyne-containing small molecules or affinity ligands to the exterior surface of the nanocage. The optimal positioning of the 4-AzF residue was evaluated by screening a library of variants for the efficiency of copper-free click conjugation. One of the engineered ferritins, hFTL-5X, was found to accommodate ∼14 small-molecule fluorophores (AlexaFluor 488) and 3-4 IgG molecules per nanocage. Intravascular injection in mice of radiolabeled hFTL-5X carrying antibody to cell adhesion molecule ICAM-1, but not control IgG, enabled specific targeting to the lung due to high basal expression of ICAM-1 (43.3 ± 6.99 vs 3.48 ± 0.14%ID/g for Ab vs IgG). Treatment of mice with endotoxin known to stimulate inflammatory ICAM-1 overexpression resulted in 2-fold enhancement of pulmonary targeting (84.4 ± 12.89 vs 43.3 ± 6.99%ID/g). Likewise, injection of fluorescent, ICAM-targeted hFTL-5X nanocages revealed the effect of endotoxin by enhancement of near-infrared signal, indicating potential utility of this approach for both vascular targeting and imaging.
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240
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Lira AL, Ferreira RS, Torquato RJS, Zhao H, Oliva MLV, Hassan SA, Schuck P, Sousa AA. Binding kinetics of ultrasmall gold nanoparticles with proteins. NANOSCALE 2018; 10:3235-3244. [PMID: 29383361 PMCID: PMC5842697 DOI: 10.1039/c7nr06810g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Synthetic ultrasmall nanoparticles (NPs) can be designed to interact with biologically active proteins in a controlled manner. However, the rational design of NPs requires a clear understanding of their interactions with proteins and the precise molecular mechanisms that lead to association/dissociation in biological media. Although much effort has been devoted to the study of the kinetics mechanism of protein corona formation on large NPs, the nature of NP-protein interactions in the ultrasmall regime is radically different and poorly understood. Using a combination of experimental and computational approaches, we studied the interactions of a model protein, CrataBL, with ultrasmall gold NPs passivated with p-mercaptobenzoic acid (AuMBA) and glutathione (AuGSH). We have identified this system as an ideal in vitro platform to understand the dependence of binding affinity and kinetics on NP surface chemistry. We found that the structural and chemical complexity of the passivating NP layer leads to quite different association kinetics, from slow and reaction-limited (AuGSH) to fast and diffusion-limited (AuMBA). We also found that the otherwise weak and slow AuGSH-protein interactions measured in buffer solution are enhanced in macromolecular crowded solutions. These findings advance our mechanistic understanding of biomimetic NP-protein interactions in the ultrasmall regime and have implications for the design and use of NPs in the crowded conditions common to all biological media.
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Affiliation(s)
- André L Lira
- Department of Biochemistry, Federal University of São Paulo, São Paulo, SP, Brazil.
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241
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Danielson TA, Bowler BE. Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'. Biophys J 2018; 114:311-322. [PMID: 29401429 DOI: 10.1016/j.bpj.2017.11.3744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022] Open
Abstract
Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c' from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c'. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c'. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana.
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242
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Sussman D, Westendorf L, Meyer DW, Leiske CI, Anderson M, Okeley NM, Alley SC, Lyon R, Sanderson RJ, Carter PJ, Benjamin DR. Engineered cysteine antibodies: an improved antibody-drug conjugate platform with a novel mechanism of drug-linker stability. Protein Eng Des Sel 2018; 31:47-54. [DOI: 10.1093/protein/gzx067] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 01/08/2018] [Indexed: 12/16/2022] Open
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243
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Verrastro I, Tveen-Jensen K, Spickett CM, Pitt AR. The effect of HOCl-induced modifications on phosphatase and tensin homologue (PTEN) structure and function. Free Radic Res 2018; 52:232-247. [DOI: 10.1080/10715762.2018.1424333] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ivan Verrastro
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | | | | | - Andrew R. Pitt
- School of Life and Health Sciences, Aston University, Birmingham, UK
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244
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Martínez-Martínez M, Coscolín C, Santiago G, Chow J, Stogios PJ, Bargiela R, Gertler C, Navarro-Fernández J, Bollinger A, Thies S, Méndez-García C, Popovic A, Brown G, Chernikova TN, García-Moyano A, Bjerga GEK, Pérez-García P, Hai T, Del Pozo MV, Stokke R, Steen IH, Cui H, Xu X, Nocek BP, Alcaide M, Distaso M, Mesa V, Peláez AI, Sánchez J, Buchholz PCF, Pleiss J, Fernández-Guerra A, Glöckner FO, Golyshina OV, Yakimov MM, Savchenko A, Jaeger KE, Yakunin AF, Streit WR, Golyshin PN, Guallar V, Ferrer M, The INMARE Consortium. Determinants and Prediction of Esterase Substrate Promiscuity Patterns. ACS Chem Biol 2018; 13:225-234. [PMID: 29182315 DOI: 10.1021/acschembio.7b00996] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.
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Affiliation(s)
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Jennifer Chow
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter J. Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Christoph Gertler
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - José Navarro-Fernández
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Alexander Bollinger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Stephan Thies
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
| | - Celia Méndez-García
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | | | | | - Gro E. K. Bjerga
- Uni Research AS, Center for Applied Biotechnology, 5006 Bergen, Norway
| | - Pablo Pérez-García
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Tran Hai
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Mercedes V. Del Pozo
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Runar Stokke
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Ida H. Steen
- Department of Biology and KG Jebsen Centre for Deep Sea Research, University of Bergen, 5020 Bergen, Norway
| | - Hong Cui
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Xiaohui Xu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Boguslaw P. Nocek
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, 60439 Illinois, United States
| | - María Alcaide
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Marco Distaso
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Victoria Mesa
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Ana I. Peláez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Jesús Sánchez
- Department of Functional Biology-IUBA, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Antonio Fernández-Guerra
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- University of Oxford, Oxford e-Research Centre, Oxford, United Kingdom
| | - Frank O. Glöckner
- Jacobs University Bremen gGmbH, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Olga V. Golyshina
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, Consiglio Nazionale delle Ricerche, 98122 Messina, Italy
- Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, 52425 Jülich, Germany
- Institute for Bio- and Geosciences IBG-1: Biotechnology, Forschunsgzentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, M5S 3E5 Toronto, Ontario, Canada
| | - Wolfgang R. Streit
- Biozentrum Klein Flottbek, Mikrobiologie & Biotechnologie, Universität Hamburg, 22609 Hamburg, Germany
| | - Peter N. Golyshin
- School of Biological Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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245
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Zhang X, Wang JH, Tan D, Li Q, Li M, Gong Z, Tang C, Liu Z, Dong MQ, Lei X. Carboxylate-Selective Chemical Cross-Linkers for Mass Spectrometric Analysis of Protein Structures. Anal Chem 2018; 90:1195-1201. [DOI: 10.1021/acs.analchem.7b03789] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Xiaoyun Zhang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Dan Tan
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Qiang Li
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
| | - Maodong Li
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhou Gong
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Chun Tang
- CAS
Key Laboratory of Magnetic Resonance in Biological Systems, State
Key Laboratory of Magnetic Resonance and Atomic Molecular Physics,
National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Zhirong Liu
- Center
for Quantitative Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Meng-Qiu Dong
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
Synthetic and Functional Biomolecules Center, and Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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246
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Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP. A framework for exhaustively mapping functional missense variants. Mol Syst Biol 2017; 13:957. [PMID: 29269382 PMCID: PMC5740498 DOI: 10.15252/msb.20177908] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin‐like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.
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Affiliation(s)
- Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Song Sun
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Atina G Cote
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jennifer Knapp
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Marta Verby
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joseph C Mellor
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,SeqWell Inc, Boston, MA, USA
| | - Yingzhou Wu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Fan Yang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Murat Tasan
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Shan Yang
- Invitae Corp., San Francisco, CA, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada .,The Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
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247
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Mitra A, Muralidharan M, Srivastava D, Das R, Bhat V, Mandal AK. Assessment of Cysteine Reactivity of Human Hemoglobin at Its Residue Level: A Mass Spectrometry-Based Approach. Hemoglobin 2017; 41:300-305. [PMID: 29210301 DOI: 10.1080/03630269.2017.1399905] [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] [Indexed: 01/09/2023]
Abstract
In general, the reactivity of cysteine residues of proteins is measured by 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) kinetics using spectrophotometry. Proteins with several cysteine residues may exhibit varying DTNB kinetics but residue level information can only be obtained with the prior knowledge of their three-dimensional structure. However, this method is limited in its application to the proteins containing chromophores having overlapping absorption profile with 2-nitro-5-thiobenzoic acid, such as hemoglobin (Hb). Additionally, this method is incapable of assigning cysteine reactivity at the residue levels of proteins with unknown crystal structures. However, a mass spectrometry (MS)-based platform might provide a solution to these problems. In the present study, alkylation kinetics of cysteine residues of adult human Hb (Hb A; α2β2) and sickle cell Hb (Hb S; HBB: c.20A>T) were investigated using matrix-assisted laser desorption/ionization (MALDI) MS. Differential site-specific reactivities of cysteine residues of Hb were investigated using alkylation kinetics with iodoacetamide (IAM). The observed reactivities corroborated well with the differential surface accessibilities of cysteine residues in the crystal structures of human Hb. The proposed method might be used to investigate cysteine reactivities of all the genetic and post-translational variants of Hb discovered to date. In addition, this method can be extended to explore cysteine reactivities of proteins, irrespective of the presence of chromophores and availability of crystal structures.
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Affiliation(s)
- Amrita Mitra
- a Clinical Proteomics Unit, Division of Molecular Medicine , St. John's Research Institute, St. John's National Academy of Health Sciences , Koramangala, Bangalore , India
| | - Monita Muralidharan
- a Clinical Proteomics Unit, Division of Molecular Medicine , St. John's Research Institute, St. John's National Academy of Health Sciences , Koramangala, Bangalore , India
| | - Deepsikha Srivastava
- a Clinical Proteomics Unit, Division of Molecular Medicine , St. John's Research Institute, St. John's National Academy of Health Sciences , Koramangala, Bangalore , India
| | - Rajdeep Das
- a Clinical Proteomics Unit, Division of Molecular Medicine , St. John's Research Institute, St. John's National Academy of Health Sciences , Koramangala, Bangalore , India
| | - Vijay Bhat
- b Department of Biochemistry , Manipal Hospital Diagnostic Services, Manipal Hospital , Bangalore , India
| | - Amit K Mandal
- a Clinical Proteomics Unit, Division of Molecular Medicine , St. John's Research Institute, St. John's National Academy of Health Sciences , Koramangala, Bangalore , India
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248
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Karmakar S, Guenther DC, Gibbons BC, Hrdlicka PJ. Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2'-triphenylene- and coronene-functionalized RNA monomers. Org Biomol Chem 2017; 15:9362-9371. [PMID: 29090304 PMCID: PMC5700769 DOI: 10.1039/c7ob01920c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that nucleic acid duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2'-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA. In the present work, we follow up on our previous structure-activity relationship studies and explore if the dsDNA-recognition efficiency of these so-called Invader probes can be improved by using larger intercalators than pyrene. Oligodeoxyribonucleotides modified with 2'-O-(triphenylen-2-yl)methyl-uridine monomer X and 2'-O-(coronen-1-yl)methyl-uridine monomer Z form extraordinarily stabilized duplexes with complementary DNA (ΔTm's per modification of up to 13 °C and 20 °C, respectively). Invader probes based on X- and Z-monomers are shown to recognize model dsDNA targets with exceptional binding specificity, but are less efficient than reference probes modified with 2'-O-(pyren-1-yl)methyl-uridine monomer Y. The insight from this study will inform further optimization of Invader probes.
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Affiliation(s)
- Saswata Karmakar
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA.
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249
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Lee TS, Potts SJ, McGinniss MJ, Strom CM. Multiple Property Tolerance Analysis for the Evaluation of Missense Mutations. Evol Bioinform Online 2017. [DOI: 10.1177/117693430600200019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Computational prediction of the impact of a mutation on protein function is still not accurate enough for clinical diagnostics without additional human expert analysis. Sequence alignment-based methods have been extensively used but their results highly depend on the quality of the input alignments and the choice of sequences. Incorporating the structural information with alignments improves prediction accuracy. Here, we present a conservation of amino acid properties method for mutation prediction, Multiple Properties Tolerance Analysis (MuTA), and a new strategy, MuTA/S, to incorporate the solvent accessible surface (SAS) property into MuTA. Instead of combining multiple features by machine learning or mathematical methods, an intuitive strategy is used to divide the residues of a protein into different groups, and in each group the properties used is adjusted. The results for LacI, lysozyme, and HIV protease show that MuTA performs as well as the widely used SIFT algorithm while MuTA/S outperforms SIFT and MuTA by 2%–25% in terms of prediction accuracy. By incorporating the SAS term alone, the alignment dependency of overall prediction accuracy is significantly reduced. MuTA/S also defines a new way to incorporate any structural features and knowledge and may lead to more accurate predictions.
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Affiliation(s)
- Tai-Sung Lee
- Consortium for Bioinformatics and Computational Biology, and Department of Chemistry, University of Minnesota, P.O. Box 14800, Minneapolis, MN 55414
| | - Steven J. Potts
- Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA 92690
| | - Matthew J. McGinniss
- Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA 92690
| | - Charles M. Strom
- Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA 92690
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250
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Protein separations using enhanced-fluidity liquid chromatography. J Chromatogr A 2017; 1523:257-264. [DOI: 10.1016/j.chroma.2017.07.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 11/21/2022]
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