Fábio C. Gozzo
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View article: Effect of Lys84 carbamylation and chloride ion on OXA-143 dynamics and catalytic efficiency
Effect of Lys84 carbamylation and chloride ion on OXA-143 dynamics and catalytic efficiency Open
Carbapenem-hydrolyzing Class-D β-lactamase OXA-143 is known as an efficient carbapenemase, and the number of clinically isolated Acinetobacter baumannii carrying the OXA-143 gene has risen significantly since it was first identified in 200…
View article: Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics
Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics Open
View article: RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control
RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control Open
We present RawVegetable 2.0, a software tailored for assessing mass spectrometry data quality and fine-tuned for cross-linking mass spectrometry (XL-MS) applications. Building upon the capabilities of its predecessor, RawVegetable 2.0 intr…
View article: Contents list
Contents list Open
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View article: PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS
PROTEOME-SCALE RECOMBINANT STANDARDS AND A ROBUST HIGH-SPEED SEARCH ENGINE TO ADVANCE CROSS-LINKING MS-BASED INTERACTOMICS Open
A bstract Advancing data analysis tools for proteome-wide cross-linking mass spectrometry (XL-MS) requires ground-truth standards that mimic biological complexity. Here, we develop wellcontrolled XL-MS standards comprising hundreds of reco…
View article: PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification
PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification Open
Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding…
View article: DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters
DiagnoMass: A proteomics hub for pinpointing discriminative spectral clusters Open
DiagnoMass and related documentation, including a usage protocol, are available at http://www.diagnomass.com.
View article: Mechanism of high-mannose N-glycan breakdown and metabolism by Bifidobacterium longum
Mechanism of high-mannose N-glycan breakdown and metabolism by Bifidobacterium longum Open
View article: Increasing confidence in proteomic spectral deconvolution through mass defect
Increasing confidence in proteomic spectral deconvolution through mass defect Open
Motivation Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. Results In general, all deconvolution algorithms m…
View article: Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom
Molecular Architecture of the Antiophidic Protein DM64 and its Binding Specificity to Myotoxin II From Bothrops asper Venom Open
DM64 is a toxin-neutralizing serum glycoprotein isolated from Didelphis aurita , an ophiophagous marsupial naturally resistant to snake envenomation. This 64 kDa antitoxin targets myotoxic phospholipases A 2 , which account for most local …
View article: New Intracellular Peptide Derived from Hemoglobin Alpha Chain Induces Glucose Uptake and Reduces Blood Glycemia
New Intracellular Peptide Derived from Hemoglobin Alpha Chain Induces Glucose Uptake and Reduces Blood Glycemia Open
Intracellular peptides were shown to derive from proteasomal degradation of proteins from mammalian and yeast cells, being suggested to play distinctive roles both inside and outside these cells. Here, the role of intracellular peptides pr…
View article: Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors
Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors Open
View article: Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition
Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition Open
Motivation Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing wi…
View article: Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations
Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations Open
View article: Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry Open
View article: Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry
Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry Open
Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformati…
View article: Publisher Correction: Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family
Publisher Correction: Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family Open
View article: Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family
Structural insights into β-1,3-glucan cleavage by a glycoside hydrolase family Open
View article: The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity
The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity Open
Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction…
View article: C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly
C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly Open
Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X‐interacting protein (HBXIP; LAMTOR 1—5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, …
View article: First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study
First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study Open
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during…
View article: Understanding mechanisms of oocyte development by follicular fluid lipidomics
Understanding mechanisms of oocyte development by follicular fluid lipidomics Open
View article: Identification of multi-crosslinked species by mass spectrometry
Identification of multi-crosslinked species by mass spectrometry Open
A search for multiple crosslinking reaction products was conducted using processed raw data of the protein SALBIII obtained by LC/MS-MS. In parallel, new compounds containing three reactive terminal groups were used with myoglobin and cyto…
View article: Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution
Structural Complementarity of Distance Constraints Obtained from Chemical Crosslinking and Amino Acid Coevolution Open
View article: Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines
Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines Open
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has largely increase…
View article: The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans
The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans Open
View article: Author Index
Author Index Open
View article: Ovarian environment aging: follicular fluid lipidomic and related metabolic pathways
Ovarian environment aging: follicular fluid lipidomic and related metabolic pathways Open
View article: Structural basis of exo-β-mannanase activity in the GH2 family
Structural basis of exo-β-mannanase activity in the GH2 family Open
The classical microbial strategy for depolymerization of β-mannan polysaccharides involves the synergistic action of at least two enzymes, endo-1,4-β-mannanases and β-mannosidases. In this work, we describe the first exo-β-mannanase from t…
View article: Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints
Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints Open
Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These con…