• NMR CBEC
  • OSU CBEC
  • CBEC Lab

Aggregator

Coil-Library-Derived Amino-Acid-Specific Side-Chain χ<sub>1</sub> Dihedral Angle Potentials for AMBER-Type Protein Force Field

2 weeks ago
The successful simulation of proteins by molecular dynamics (MD) critically depends on the accuracy of the applied force field. Here, we modify the AMBER-family ff99SBnmr2 force field through improvements to the side-chain χ(1) dihedral angle potentials in a residue-specific manner using conformational dihedral angle distributions from an experimental coil library as targets. Based on significant deviations observed for the parent force field with respect to the coil library, the χ(1) dihedral...
Eric Fagerberg

Coil-Library-Derived Amino-Acid-Specific Side-Chain χ<sub>1</sub> Dihedral Angle Potentials for AMBER-Type Protein Force Field

2 weeks ago
The successful simulation of proteins by molecular dynamics (MD) critically depends on the accuracy of the applied force field. Here, we modify the AMBER-family ff99SBnmr2 force field through improvements to the side-chain χ(1) dihedral angle potentials in a residue-specific manner using conformational dihedral angle distributions from an experimental coil library as targets. Based on significant deviations observed for the parent force field with respect to the coil library, the χ(1) dihedral...
Eric Fagerberg

Dendritic Molecular Baskets for Selective Binding of Toxic Methotrexate

1 month 2 weeks ago
We describe the preparation, assembly, recognition characteristics, and bioactivity of dendritic basket 6^(12-). This novel cavitand has a deep aromatic pocket with three (S)-glutamic acid dendrons at the rim to amplify water solubility and prevent self-association. ¹H NMR spectroscopy, calorimetry (ITC), and mass spectrometry (ESI-MS) measurements validate the formation of an inclusion complex between 6^(12-) and anticancer drug methotrexate (MTX^(2-)) in water (K(d)=9.2 μM). To identify the...
Nitesh Kumar

Dendritic Molecular Baskets for Selective Binding of Toxic Methotrexate

1 month 2 weeks ago
We describe the preparation, assembly, recognition characteristics, and bioactivity of dendritic basket 6^(12-). This novel cavitand has a deep aromatic pocket with three (S)-glutamic acid dendrons at the rim to amplify water solubility and prevent self-association. ¹H NMR spectroscopy, calorimetry (ITC), and mass spectrometry (ESI-MS) measurements validate the formation of an inclusion complex between 6^(12-) and anticancer drug methotrexate (MTX^(2-)) in water (K(d)=9.2 μM). To identify the...
Nitesh Kumar

COLMAR1d: A Web Server for Automated, Quantitative One-Dimensional Nuclear Magnetic Resonance-Based Metabolomics at Arbitrary Magnetic Fields

2 months 1 week ago
The field of metabolomics, which is quintessential in today's omics research, involves the large-scale detection, identification, and quantification of small-molecule metabolites in a wide range of biological samples. Nuclear magnetic resonance spectroscopy (NMR) has emerged as a powerful tool for metabolomics due to its high resolution, reproducibility, and exceptional quantitative nature. One of the key bottlenecks of metabolomics studies, however, remains the accurate and automated analysis...
Da-Wei Li

COLMAR1d: A Web Server for Automated, Quantitative One-Dimensional Nuclear Magnetic Resonance-Based Metabolomics at Arbitrary Magnetic Fields

2 months 1 week ago
The field of metabolomics, which is quintessential in today's omics research, involves the large-scale detection, identification, and quantification of small-molecule metabolites in a wide range of biological samples. Nuclear magnetic resonance spectroscopy (NMR) has emerged as a powerful tool for metabolomics due to its high resolution, reproducibility, and exceptional quantitative nature. One of the key bottlenecks of metabolomics studies, however, remains the accurate and automated analysis...
Da-Wei Li

Supramolecular Motion Enables Chondrogenic Bioactivity of a Cyclic Peptide Mimetic of Transforming Growth Factor-β1

5 months ago
Transforming growth factor (TGF)-β1 is a multifunctional protein that is essential in many cellular processes that include fibrosis, inflammation, chondrogenesis, and cartilage repair. In particular, cartilage repair is important to avoid physical disability since this tissue does not have the inherent capacity to regenerate beyond full development. We report here on supramolecular coassemblies of two peptide amphiphile molecules, one containing a TGF-β1 mimetic peptide, and another which is one...
Shelby C Yuan

Supramolecular Motion Enables Chondrogenic Bioactivity of a Cyclic Peptide Mimetic of Transforming Growth Factor-β1

5 months ago
Transforming growth factor (TGF)-β1 is a multifunctional protein that is essential in many cellular processes that include fibrosis, inflammation, chondrogenesis, and cartilage repair. In particular, cartilage repair is important to avoid physical disability since this tissue does not have the inherent capacity to regenerate beyond full development. We report here on supramolecular coassemblies of two peptide amphiphile molecules, one containing a TGF-β1 mimetic peptide, and another which is one...
Shelby C Yuan

Thermodynamic coupling of the tandem RRM domains of hnRNP A1 underlie its pleiotropic RNA binding functions

5 months 2 weeks ago
The functional properties of RNA binding proteins (RBPs) require allosteric regulation through interdomain communication. Despite the importance of allostery to biological regulation, only a few studies have been conducted to describe the biophysical nature by which interdomain communication manifests in RBPs. Here, we show for hnRNP A1 that interdomain communication is vital for the unique stability of its amino-terminal domain, which consists of two RNA recognition motifs (RRMs). These RRMs...
Jeffrey D Levengood

CCIC Mass Spectrometry and Proteomics Summer Workshop

6 months ago
A Mass Spectrometry and Proteomics Summer Workshop will be held on July 15-16 in DHLRI 170, located at 473 W. 12th Ave, on the OSU campus in Columbus, OH. The two-day workshop is presented by faculty and staff of the OSU Campus Chemical Instrument Center Mass Spectrometry and Proteomics Facility. All students, postdocs, faculty, and […]
Laura VanArsdale

April 19 @12:30pm

8 months 1 week ago
Fred Strathman, Sr. VP of US Business, MOBILion Systems “The Duality of Ion Mobility: From Practical Applications to Novel Insights” Date: Friday, April 19, 2024 Time: 12:30pm Location: James L045
Laura VanArsdale

April 5 @12:30pm

9 months 3 weeks ago
Dr. John Sausen, Agilent Technologies, Director of Strategic Initiatives — Mass Spectrometry “Advancing Ion Mobility into Lipidomics, Metabolomics, Exposomics, and Protein Characterization” Date: Friday, April 5, 2024 Time: 12:30pm Location: 014 University Hall Abstract Laboratories conducting Multi-Omics analysis have challenging requirements to better define isomeric and isoberic structures across a broad mass range in a […]
Laura VanArsdale

February 23 @12:30pm

10 months 1 week ago
Ms. Kristie Baker, Wysocki Group, Ohio State “Characterizing a Surface Bridge in the Four-Helix Bundle Rop by Surface- and Collision-Induced Activation” and Philip Lacey, Wysocki Group, Ohio State “Heterogeneous Non-Canonical Inflammasome Oligomerization Probed by Narrow Quadrupole Selections and Electron Capture Charge Reduction” Date: Friday, February 23, 2024 Time: 12:30pm Location: 0035 Hitchcock Hall
Laura VanArsdale

January 26 @12:30pm

11 months ago
Mr. Alex Grooms, Badu Group, Ohio State “Uncatalyzed Hydrazine Cross Coupling via Plasma-Microdroplet Fusion Enables Programmable C–N Bond Formation” Date: January 26, 2024 Time: 12:30 PM Location 0035 Hitchcock Hall
Laura VanArsdale

COLMARppm: A Web Server Tool for the Accurate and Rapid Prediction of (1)H and (13)C NMR Chemical Shifts of Organic Molecules and Metabolites

1 year ago
Despite rapid progress in metabolomics research, a major bottleneck is the large number of metabolites whose chemical structures are unknown or whose spectra have not been deposited in metabolomics databases. Nuclear magnetic resonance (NMR) spectroscopy has a long history of elucidating chemical structures from experimentally measured ¹H and ^(13)C chemical shifts. One approach to characterizing the chemical structures of an unknown metabolite is to predict the ¹H and ^(13)C chemical shifts of...
Nick Rigel

COLMARppm: A Web Server Tool for the Accurate and Rapid Prediction of (1)H and (13)C NMR Chemical Shifts of Organic Molecules and Metabolites

1 year ago
Despite rapid progress in metabolomics research, a major bottleneck is the large number of metabolites whose chemical structures are unknown or whose spectra have not been deposited in metabolomics databases. Nuclear magnetic resonance (NMR) spectroscopy has a long history of elucidating chemical structures from experimentally measured ¹H and ^(13)C chemical shifts. One approach to characterizing the chemical structures of an unknown metabolite is to predict the ¹H and ^(13)C chemical shifts of...
Nick Rigel

December 12 @5:30pm

1 year ago
Ms. Ayesha Seth, Badu Group, Ohio State “Revolutionizing Malaria Detection: Pioneering Chemical Signal Amplification for Asymptomatic Cases with Mass Spectrometry” and Mr. Joseph Holbrook, Hummon Group, Ohio State “Enhancement of Lipid Signals in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry with Ammonium Fluoride as a Matrix Additive” Date: Dec 12, 2023 Time: 5:30 PM Location: BRT 105
Laura VanArsdale

Meeting — November 14 @5:30pm

1 year 1 month ago
Ms. Ariana Shannon (Hummon/Searle Group) “Generating fit-for-purpose targeted mass-spectrometry based proteomics assays from a global proteome catalog” Date: Nov 14, 2023 (TODAY) Time: 5:30 PM Location: BRT 105
Laura VanArsdale

NMR (1)H, (13)C, (15)N backbone resonance assignments of wild-type human K-Ras and its oncogenic mutants G12D and G12C bound to GTP

1 year 1 month ago
Human K-Ras protein, which is a member of the GTPase Ras family, hydrolyzes GTP to GDP and concomitantly converts from its active to its inactive state. It is a key oncoprotein, because several mutations, particularly those at residue position 12, occur with a high frequency in a wide range of human cancers. The K-Ras protein is therefore an important target for developing therapeutic anti-cancer agents. In this work we report the almost complete sequence-specific resonance assignments of...
Chunhua Yuan

NMR (1)H, (13)C, (15)N backbone resonance assignments of wild-type human K-Ras and its oncogenic mutants G12D and G12C bound to GTP

1 year 1 month ago
Human K-Ras protein, which is a member of the GTPase Ras family, hydrolyzes GTP to GDP and concomitantly converts from its active to its inactive state. It is a key oncoprotein, because several mutations, particularly those at residue position 12, occur with a high frequency in a wide range of human cancers. The K-Ras protein is therefore an important target for developing therapeutic anti-cancer agents. In this work we report the almost complete sequence-specific resonance assignments of...
Chunhua Yuan