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  1. Article ; Online: Three-Dimensional Soft Tissue Simulation in Orthognathic Surgery.

    Thomas, Paul M

    Atlas of the oral and maxillofacial surgery clinics of North America

    2020  Volume 28, Issue 2, Page(s) 73–82

    MeSH term(s) Facial Bones ; Humans ; Imaging, Three-Dimensional ; Orthognathic Surgery ; Orthognathic Surgical Procedures ; Patient Care Planning ; Surgery, Computer-Assisted ; User-Computer Interface
    Language English
    Publishing date 2020-07-08
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1169550-x
    ISSN 1558-4275 ; 1061-3315
    ISSN (online) 1558-4275
    ISSN 1061-3315
    DOI 10.1016/j.cxom.2020.05.003
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  2. Article: In vitro-Constructed Ribosomes Enable Multi-site Incorporation of Noncanonical Amino Acids into Proteins

    Liu, Yi / Davis, Roderick G / Thomas, Paul M / Kelleher, Neil L / Jewett, Michael C

    Biochemistry. 2021 Jan. 11, v. 60, no. 3

    2021  

    Abstract: Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, ... ...

    Abstract Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, assembly, and translation (iSAT) system was established to construct functional ribosomes in cell-free systems. However, the iSAT system has not been shown to be compatible with genetic code expansion. Here, to address this gap, we develop an iSAT platform capable of manufacturing pure proteins with site-specifically incorporated ncAAs. We first establish an iSAT platform based on extracts from genomically recoded Escherichia coli lacking release factor 1 (RF-1). This permits complete reassignment of the amber codon translation function. Next, we optimize orthogonal translation system components to demonstrate the benefits of genomic RF-1 deletion on incorporation of ncAAs into proteins. Using our optimized platform, we demonstrate high-level, multi-site incorporation of p-acetyl-phenylalanine (pAcF) and p-azido-phenylalanine into superfolder green fluorescent protein (sfGFP). Mass spectrometry analysis confirms the high accuracy of incorporation for pAcF at one, two, and five amber sites in sfGFP. The iSAT system updated for ncAA incorporation sets the stage for investigating ribosomal mutations to better understand the fundamental basis of protein synthesis, manufacturing proteins with new properties, and engineering ribosomes for novel polymerization chemistries.
    Keywords Escherichia coli ; accuracy ; amber ; amino acids ; engineering ; enzymes ; extracts ; genetic code ; genomics ; green fluorescent protein ; manufacturing ; mass spectrometry ; materials ; mutation ; peptides ; polymerization ; protein synthesis ; ribosomes ; stop codon ; synthesis ; therapeutics
    Language English
    Dates of publication 2021-0111
    Size p. 161-169.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-light
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00829
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  3. Article ; Online: In vitro

    Liu, Yi / Davis, Roderick G / Thomas, Paul M / Kelleher, Neil L / Jewett, Michael C

    Biochemistry

    2021  Volume 60, Issue 3, Page(s) 161–169

    Abstract: Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, ... ...

    Abstract Efforts to expand the scope of ribosome-mediated polymerization to incorporate noncanonical amino acids (ncAAs) into peptides and proteins hold promise for creating new classes of enzymes, therapeutics, and materials. Recently, the integrated synthesis, assembly, and translation (iSAT) system was established to construct functional ribosomes in cell-free systems. However, the iSAT system has not been shown to be compatible with genetic code expansion. Here, to address this gap, we develop an iSAT platform capable of manufacturing pure proteins with site-specifically incorporated ncAAs. We first establish an iSAT platform based on extracts from genomically recoded
    MeSH term(s) Amino Acids ; Amino Acyl-tRNA Synthetases/chemistry ; Cell-Free System/chemistry ; Codon, Terminator ; Escherichia coli/chemistry ; Green Fluorescent Proteins/biosynthesis ; Protein Biosynthesis ; Ribosomes/chemistry
    Chemical Substances Amino Acids ; Codon, Terminator ; Green Fluorescent Proteins (147336-22-9) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-)
    Language English
    Publishing date 2021-01-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00829
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  4. Article ; Online: Characterization of a Copper-Chelating Natural Product from the Methanotroph

    Park, Yun Ji / Roberts, Gerri M / Montaser, Rana / Kenney, Grace E / Thomas, Paul M / Kelleher, Neil L / Rosenzweig, Amy C

    Biochemistry

    2021  Volume 60, Issue 38, Page(s) 2845–2850

    Abstract: Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptidic natural products that bind copper with high affinity. Methanotrophic bacteria use Mbns to acquire copper needed for enzymatic methane oxidation. Despite the presence ... ...

    Abstract Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptidic natural products that bind copper with high affinity. Methanotrophic bacteria use Mbns to acquire copper needed for enzymatic methane oxidation. Despite the presence of Mbn operons in a range of methanotroph and other bacterial genomes, few Mbns have been isolated and structurally characterized. Here we report the isolation of a novel Mbn from the methanotroph
    MeSH term(s) Amino Acid Sequence/genetics ; Bacterial Proteins/metabolism ; Biological Products/metabolism ; Chelating Agents/chemistry ; Copper/chemistry ; Copper/metabolism ; Gene Expression/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genome, Bacterial/genetics ; Imidazoles/metabolism ; Methane/metabolism ; Methylosinus/enzymology ; Methylosinus/genetics ; Methylosinus/metabolism ; Methylosinus trichosporium/enzymology ; Methylosinus trichosporium/genetics ; Methylosinus trichosporium/metabolism ; Oligopeptides/metabolism ; Operon/genetics ; Oxidation-Reduction ; Peptides/metabolism
    Chemical Substances Bacterial Proteins ; Biological Products ; Chelating Agents ; Imidazoles ; Oligopeptides ; Peptides ; methanobactin ; Copper (789U1901C5) ; Methane (OP0UW79H66)
    Language English
    Publishing date 2021-09-12
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.1c00443
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  5. Article ; Online: The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms.

    Hollas, Michael A R / Robey, Matthew T / Fellers, Ryan T / LeDuc, Richard D / Thomas, Paul M / Kelleher, Neil L

    Nucleic acids research

    2021  Volume 50, Issue D1, Page(s) D526–D533

    Abstract: The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms on-line at http://human-proteoform-atlas.org and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas. ... ...

    Abstract The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms on-line at http://human-proteoform-atlas.org and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas. Proteoforms are the specific forms of protein molecules expressed by our cells and include the unique combination of post-translational modifications (PTMs), alternative splicing and other sources of variation deriving from a specific gene. The HPfA uses a FAIR system to assign persistent identifiers to proteoforms which allows for redundancy calling and tracking from prior and future studies in the growing community of proteoform biology and measurement. The HPfA is organized around open ontologies and enables flexible classification of proteoforms. To achieve this, a public registry of experimentally verified proteoforms was also created. Submission of new proteoforms can be processed through email vianrtdphelp@northwestern.edu, and future iterations of these proteoform atlases will help to organize and assign function to proteoforms, their PTMs and their complexes in the years ahead.
    MeSH term(s) Alternative Splicing ; Amino Acid Sequence ; Atlases as Topic ; Databases, Protein ; Gene Ontology ; Humans ; Models, Molecular ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Protein Conformation ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Protein Processing, Post-Translational ; Proteome/chemistry ; Proteome/classification ; Proteome/genetics ; Proteome/metabolism ; Proto-Oncogene Proteins p21(ras)/chemistry ; Proto-Oncogene Proteins p21(ras)/genetics ; Proto-Oncogene Proteins p21(ras)/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; User-Computer Interface
    Chemical Substances KRAS protein, human ; Protein Isoforms ; Proteome ; RNA, Messenger ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2)
    Language English
    Publishing date 2021-12-17
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab1086
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    Zs.A 1067: Show issues Location:
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  6. Article ; Online: A Highly Productive, One-Pot Cell-Free Protein Synthesis Platform Based on Genomically Recoded Escherichia coli.

    Des Soye, Benjamin J / Gerbasi, Vincent R / Thomas, Paul M / Kelleher, Neil L / Jewett, Michael C

    Cell chemical biology

    2019  Volume 26, Issue 12, Page(s) 1743–1754.e9

    Abstract: The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 ( ...

    Abstract The site-specific incorporation of non-canonical amino acids (ncAAs) into proteins via amber suppression provides access to novel protein properties, structures, and functions. Historically, poor protein expression yields resulting from release factor 1 (RF1) competition has limited this technology. To address this limitation, we develop a high-yield, one-pot cell-free platform for synthesizing proteins bearing ncAAs based on genomically recoded Escherichia coli lacking RF1. A key feature of this platform is the independence on the addition of purified T7 DNA-directed RNA polymerase (T7RNAP) to catalyze transcription. Extracts derived from our final strain demonstrate high productivity, synthesizing 2.67 ± 0.06 g/L superfolder GFP in batch mode without supplementation of purified T7RNAP. Using an optimized one-pot platform, we demonstrate multi-site incorporation of the ncAA p-acetyl-L-phenylalanine into an elastin-like polypeptide with high accuracy of incorporation and yield. Our work has implications for chemical and synthetic biology.
    MeSH term(s) Bacteriophage T7/enzymology ; Cell-Free System ; DNA-Directed RNA Polymerases/metabolism ; Elastin/biosynthesis ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Peptide Termination Factors/deficiency ; Peptide Termination Factors/genetics ; Phenylalanine/analogs & derivatives ; Phenylalanine/metabolism ; Protein Biosynthesis ; Viral Proteins/metabolism
    Chemical Substances Escherichia coli Proteins ; Peptide Termination Factors ; Viral Proteins ; prfA protein, E coli ; Phenylalanine (47E5O17Y3R) ; acetylphenylalanamide (7376-90-1) ; Elastin (9007-58-3) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2019-11-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2451-9448
    ISSN (online) 2451-9448
    DOI 10.1016/j.chembiol.2019.10.008
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  7. Article ; Online: Biotin Identification Proteomics in Three-Dimensional Organotypic Human Skin Cultures.

    Cable, Calvin J / Kaplan, Nihal / Getsios, Spiro / Thomas, Paul M / Perez White, Bethany E

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 2109, Page(s) 185–197

    Abstract: Biotin identification (BioID) proteomics facilitates the unbiased detection of protein interaction neighborhoods in live cells. The BioID technique relies on the covalent biotin alteration of vicinal proteins by a modified bacterial biotin ligase. The ... ...

    Abstract Biotin identification (BioID) proteomics facilitates the unbiased detection of protein interaction neighborhoods in live cells. The BioID technique relies on the covalent biotin alteration of vicinal proteins by a modified bacterial biotin ligase. The biotin ligase is fused to a protein of interest to identify putative protein-protein interactions. Here, we describe the adaptation of this technique for use in three-dimensional epidermal cultures. Due to the covalent biotin modification of proteins, our protocol allows for the complete solubilization of the total cellular protein content in differentiated keratinocytes. Thus, a comprehensive network of potential interactors of a protein of interest can be mapped.
    MeSH term(s) Biotin/chemistry ; Humans ; Organ Culture Techniques/methods ; Protein Interaction Mapping ; Proteomics/methods ; Skin/cytology ; Skin/metabolism
    Chemical Substances Biotin (6SO6U10H04)
    Language English
    Publishing date 2019-05-23
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/7651_2019_239
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  8. Article: Characterization of a Copper-Chelating Natural Product from the Methanotroph Methylosinus sp. LW3

    Park, Yun Ji / Roberts, Gerri M. / Montaser, Rana / Kenney, Grace E. / Thomas, Paul M. / Kelleher, Neil L. / Rosenzweig, Amy C.

    Biochemistry. 2021 Sept. 12, v. 60, no. 38

    2021  

    Abstract: Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptidic natural products that bind copper with high affinity. Methanotrophic bacteria use Mbns to acquire copper needed for enzymatic methane oxidation. Despite the presence ... ...

    Abstract Methanobactins (Mbns) are ribosomally produced, post-translationally modified peptidic natural products that bind copper with high affinity. Methanotrophic bacteria use Mbns to acquire copper needed for enzymatic methane oxidation. Despite the presence of Mbn operons in a range of methanotroph and other bacterial genomes, few Mbns have been isolated and structurally characterized. Here we report the isolation of a novel Mbn from the methanotroph Methylosinus (Ms.) sp. LW3. Mass spectrometric and nuclear magnetic resonance spectroscopic data indicate that this Mbn, the largest characterized to date, consists of a 13-amino acid backbone modified to include pyrazinedione/oxazolone rings and neighboring thioamide groups derived from cysteine residues. The pyrazinedione ring is more stable to acid hydrolysis than the oxazolone ring and likely protects the Mbn from degradation. The structure corresponds exactly to that predicted on the basis of the Ms. sp. LW3 Mbn operon content, providing support for the proposed role of an uncharacterized biosynthetic enzyme, MbnF, and expanding the diversity of known Mbns.
    Keywords Methylosinus ; acid hydrolysis ; biosynthesis ; copper ; cysteine ; enzymes ; mass spectrometry ; methane ; methanotrophs ; nuclear magnetic resonance spectroscopy ; operon ; oxidation ; spectral analysis
    Language English
    Dates of publication 2021-0912
    Size p. 2845-2850.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.1c00443
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  9. Article: Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics

    Gerbasi, Vincent R / Melani, Rafael D / Abbatiello, Susan E / Belford, Michael W / Huguet, Romain / McGee, John P / Dayhoff, Dawson / Thomas, Paul M / Kelleher, Neil L

    Analytical chemistry. 2021 Apr. 12, v. 93, no. 16

    2021  

    Abstract: Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical ... ...

    Abstract Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.
    Keywords analytical chemistry ; chromatography ; electric potential difference ; mass spectrometry ; molecular weight ; proteomics
    Language English
    Dates of publication 2021-0412
    Size p. 6323-6328.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.1c00402
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  10. Article: Update on comparison of current prediction imaging programs.

    Thomas, Paul M

    American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics

    2005  Volume 127, Issue 2, Page(s) 160

    MeSH term(s) Humans ; Image Processing, Computer-Assisted ; Microcomputers ; Software
    Language English
    Publishing date 2005-01-18
    Publishing country United States
    Document type Comment ; Letter
    ZDB-ID 356699-7
    ISSN 1097-6752 ; 0889-5406 ; 0002-9416
    ISSN (online) 1097-6752
    ISSN 0889-5406 ; 0002-9416
    DOI 10.1016/j.ajodo.2004.12.012
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