Article
Biochemistry & Molecular Biology
Michael B. Cory, Allen Li, Christina M. Hurley, Zachary M. Hostetler, Yarra Venkatesh, Chloe M. Jones, E. James Petersson, Rahul M. Kohli
Summary: The SOS response is an important bacterial DNA damage response pathway that is involved in antibiotic resistance. Recent research has shown that as few as three linked RecA units can activate the SOS response, challenging previous models.
Article
Chemistry, Multidisciplinary
Daniel J. Leng, Anja Greule, Max J. Cryle, Manuela Tosin
Summary: Chemical probes were used to capture biosynthetic intermediates generated in the nonribosomal peptide formation of vancomycin in vivo. The putative intercepted intermediates were characterised via HR-LC-MS2, providing insights into the timing of the first chlorination of the peptide backbone by the halogenase VhaA. This information is significant for enzyme engineering towards the production of novel glycopeptides.
CHEMICAL COMMUNICATIONS
(2021)
Article
Energy & Fuels
Zhi-Hao Ma, Sheng Li, Chun Guo, Xue-Qian Dong, Jin-Hu Wang, Min Li, Xian-Hou Guo, Mei-Ling Xu, Xing-Shun Cong, Zhi-Min Zong, Xian-Yong Wei
Summary: A low-temperature coal tar (LTCT) was separated by dual-solvent systems, and the extraction process was intensively characterized using nonlinear fitting, linear fitting, GC/MS, and FTIR. The cumulative extract yield (CEY) conformed to a logistic model with a determination coefficient of 0.97. The highest extract yield was obtained using petroleum ether, followed by methanol and carbon disulfide. The LTCT and extracts contained various compounds categorized into 85 group components. The separation mechanism was explained by hydrogen bonds and van der Waals force, supported by quantum chemical calculations.
Article
Thermodynamics
Wei Li, Tiemin Xuan, Qian Wang, Liming Dai
Summary: Numerical simulation is widely used for developing efficient combustors, but the growing size of chemical kinetic mechanisms increases computation costs. This study proposes an object-oriented directed path screening (OoDPS) method to reduce the size of the mechanism while maintaining accuracy. The OoDPS method demonstrates better performance in predicting combustion characteristics compared to other methods.
COMBUSTION AND FLAME
(2023)
Article
Physics, Multidisciplinary
Huanhuan Su, Hao Sun, Haiyan Hong, Zilong Guo, Ping Yu, Hu Chen
Summary: The study confirmed SRC SH3 protein domain as a typical two-state protein and used stable magnetic tweezers to measure force-dependent unfolding rates and construct a detailed two-state free energy landscape. The results demonstrate the capability of magnetic tweezers in studying protein folding and unfolding dynamics.
Article
Biochemical Research Methods
Ashley Phetsanthad, Gongyu Li, Chae Kyung Jeon, Brandon T. Ruotolo, Lingjun Li
Summary: Structural analysis by native ion mobility-mass spectrometry offers a direct way to characterize protein interactions, stability, and other biophysical properties of disease-associated biomolecules. This study compares two methods for protein gas-phase unfolding and introduces a new data interpretation method.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Physical
Xiaolan Kang, Athanasios Chatzitakis, Thomas Aarholt, Xinwei Sun, Chiara Negri, Truls Norby
Summary: Water adsorption and surface protonic conduction on different crystal facets of nanocrystalline TiO2 have been investigated in wet atmospheres. The adsorption behavior and protonic conductivity vary significantly depending on the crystal facets. The structure of the water layers, coverage of dissociable water, and activation enthalpies for proton migration all contribute to the differences observed in surface properties.
JOURNAL OF MATERIALS CHEMISTRY A
(2021)
Article
Biophysics
Nikhil Thota, Stephen Quirk, Yi Zhuang, Erica R. Stover, Raquel L. Lieberman, Rigoberto Hernandez
Summary: A family of proteins called severing proteins can remodel the actin filament network by modulating the ratio between monomeric and filamentous actin. Mutations in the protein actophorin have been found to increase its thermal and chemical stability. Computer simulations have been used to understand the atomic-level interactions responsible for this stability.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Asmita Dutta, Shimon T. Y. Trolles-Cavalcante, Annie Cleetus, Vered Marks, Alex Schechter, Richard D. Webster, Arie Borenstein
Summary: Fluorescent carbon nanodots have attracted attention as a promising material for electrooptic and bioimaging applications. Chemical modifications and characterization have revealed the correlation between the chemical structure and optical behavior of CNDs, providing insights into controlling their fluorescence for optical applications.
NANOSCALE ADVANCES
(2021)
Article
Engineering, Chemical
Hao-Wei Pang, Michael Forsuelo, Xiaorui Dong, Ryan E. Hawtof, Duminda S. Ranasinghe, William H. Green
Summary: Polymer fouling is a common problem in the separation train downstream of a steam cracker, and a mechanistic understanding of this process is crucial for mitigation. In this study, a multiphase chemical kinetic model was developed to predict the polymer film growth rate in an industrial debutanizer distillation column. The model incorporates thousands of chemical reactions, vapor-liquid equilibria, and phase transport, all of which significantly affect fouling rate. The model was validated using experimental measurements, and the mechanistic details of the fouling process were elucidated, highlighting the challenges in accurately predicting polymer fouling in industrial units.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Engineering, Chemical
Hao-Wei Pang, Michael Forsuelo, Xiaorui Dong, Ryan E. Hawtof, Duminda S. Ranasinghe, William H. Green
Summary: Polymer fouling is a common yet unresolved issue in the separation process downstream of a steam cracker, and a mechanistic understanding is needed to mitigate it. This study introduces a multiphase chemical kinetic model to predict the growth rate of polymer film in an industrial debutanizer distillation column. The model incorporates thousands of chemical reactions, hundreds of species in vapor-liquid equilibria, transport between phases, and flows between trays, which significantly influence fouling rate. The model is validated using experimental measurements, clarifying the mechanistic details of the fouling process and discussing challenges in predicting polymer fouling in industrial units.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Engineering, Environmental
Ping Wu, Niraj R. Rane, Chao Xing, Swapnil M. Patil, Hyun-Seog Roh, Byong-Hun Jeon, Xiaofang Li
Summary: This study investigated the copper sorption and resistance mechanism of Bacillus cereus strain T6, a newly isolated Cu-resistant bacterium, by integrating physiochemistry, genomics, transcriptomics, and metabolomics. The results revealed a complex regulatory network of copper homeostasis in bacteria, involving various genes and metabolites.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Energy & Fuels
Hongwei Yan, Baisheng Nie, Chao Peng, Peijun Liu, Xiaotong Wang, Feifei Yin, Jie Gong, Yueying Wei, Shuangshuang Lin
Summary: This study focuses on the construction of molecular models of coal using C-13 NMR tests and molecular simulations. The results show a positive correlation between the degree of coal metamorphism and structural stability, with the optimized model exhibiting strong spatial three-dimensionality and lower total molecular energy. The more branched C-C bonds have longer bond lengths and lower bond energies, leading to the generation of different types of reactive radicals upon breakage of chemical bonds in coal molecules.
Article
Electrochemistry
Lenaic Madec, Jean-Bernard Ledeuil, Julien Morey, Herve Martinez
Summary: This study proposes the use of Ar+ milling cross-section and nano-Auger/SEM analysis to investigate the chemical and morphological properties of composite materials. These methods allow for the revelation of intrinsic properties such as porosity, distribution, morphological evolution, and interface structure of different composites. The results of this study open up new possibilities for the future development of these techniques in the field of energy storage and beyond.
ELECTROCHIMICA ACTA
(2023)
Article
Engineering, Aerospace
Yonggang Gao, Yang Liu, Dong Ma
Summary: This paper conducts numerical simulation to analyze the effect of operation pressure on the heat release characteristics in the nozzle of a solid rocket motor. The results indicate that the change of operation pressure does not affect the position of the dividing point between equilibrium state and nonequilibrium state, but it does affect the reaction increase rate and reaction progress in the mainstream area and wall.
AEROSPACE SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
April K. Kaneshiro, Karl J. Koebke, Chunyi Zhao, Kyle L. Ferguson, David P. Ballou, Bruce A. Palfey, Brandon T. Ruotolo, E. Neil G. Marsh
Summary: This study identified a new cofactor, prFMN, and revealed the reaction mechanism and kinetic behavior of ferulic acid decarboxylase. The reaction involves an unusual cycloaddition reaction between prFMN and the substrate, followed by decarboxylation after the formation of a cycloadduct. Experimental results suggest that the cycloelimination of the prFMN-styrene cycloadduct determines the catalytic rate of the overall reaction.
Article
Chemistry, Analytical
K. Richardson, D. Langridge, S. M. Dixit, B. T. Ruotolo
Summary: The combination of ion-mobility (IM) separation with mass spectrometry (MS) has revolutionized global measurement efforts in various areas, including food analysis and drug discovery. Traveling Wave Ion Mobility (TWIM) devices, the first commercialized form of IM-MS, operate under low pressures and voltages, making them ideal for hybridization with MS. However, due to the complex motion of ions in TWIM devices, calibration of IM transit times is essential for accurate CCS measurements.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Brandon T. Ruotolo
Summary: Recent advancements have made it possible to comprehensively understand protein structure, oligomeric state, sequence, and modification status, providing new possibilities for treating human diseases. Mass spectrometry (MS) tools, especially those associated with ion mobility (IM) separation, have played a crucial role in this progress. However, the application of collision cross section (CCS) values in native proteomics still has limitations.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Daniel D. Vallejo, Chae Kyung Jeon, Kristine F. Parson, Hayley R. Herderschee, Joseph D. Eschweiler, Dana Filoti, Brandon T. Ruotolo
Summary: In this study, the higher order structure (HOS) of mAb monomers and dimers under different degradation conditions were investigated using IM-MS and CIU technologies. The results showed global HOS changes in both monomers and dimers during degradation, with different changes in collision cross section (CCS) under pH or heat degradation conditions. The differences in CCS changes between IgG1 alpha and IgG1 beta suggest that the complementarity-determining region (CDR) influences the response to degradation and the antibody HOS. CIU fingerprints of IgG1 alpha and IgG1 beta monomers and dimers were dramatically different for both degradation conditions.
ANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Daniel D. Vallejo, Carolina Rojas Ramirez, Kristine F. Parson, Yilin Han, Varun V. Gadkari, Brandon T. Ruotolo
Summary: This review highlights the importance of mass spectrometry in the life sciences, with a focus on recent advancements in assessing protein stability. The article covers various mass spectrometry tools and techniques, as well as applications in areas such as membrane proteins and heat shock proteins.
Article
Biochemistry & Molecular Biology
Sujeet S. Bhoite, Yilin Han, Brandon T. Ruotolo, Matthew R. Chapman
Summary: This study reveals the complex interplay between gut bacterial amyloids and alpha-synuclein, shedding light on the pathogenesis of Parkinson's disease.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Ashley Phetsanthad, Gongyu Li, Chae Kyung Jeon, Brandon T. Ruotolo, Lingjun Li
Summary: Structural analysis by native ion mobility-mass spectrometry offers a direct way to characterize protein interactions, stability, and other biophysical properties of disease-associated biomolecules. This study compares two methods for protein gas-phase unfolding and introduces a new data interpretation method.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biology
Kelly Z. Young, Carolina Rojas Ramirez, Simon G. Keep, John R. Gatti, Soo Jung Lee, Xiaojie Zhang, Magdalena I. Ivanova, Brandon T. Ruotolo, Michael M. Wang
Summary: Specific cysteine residue alterations and quaternary structures are induced by CADASIL mutations in NOTCH3, leading to oligomeric states, altered disulphide bonding, increased free thiols, and reduced protein stability.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shramana Chatterjee, Kristine F. Parson, Brandon T. Ruotolo, John McCracken, Jian Hu, Robert P. Hausinger
Summary: In this study, the LarE sulfur insertase involved in the biosynthesis of NPN was characterized. It was found that LarE functions by transferring sulfur atoms either sacrificially from the protein or noncore sulfide bound to a [4Fe-4S] cluster.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Cara I. D'Amico, Daniel A. Polasky, Daniel J. Steyer, Brandon T. Ruotolo, Robert T. Kennedy
Summary: This study explores the high-throughput capabilities of CIU fingerprinting and applies it to compound screening against Sirtuin-S. The results identify novel Sirtuin-S binders and demonstrate that Sirtuin-S inhibitors stabilize specific gas-phase conformations. The study demonstrates the feasibility of droplet-CIU as a high-throughput biophysical characterization approach.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Varun V. Gadkari, Brock R. Juliano, Christopher S. Mallis, Jody C. May, Ruwan T. Kurulugama, John C. Fjeldsted, John A. McLean, David H. Russell, Brandon T. Ruotolo
Summary: Through comparing three laboratories, the reproducibility of collision-induced unfolding (CIU) in protein studies was evaluated. The results showed that within the same laboratory, CIU fingerprints were repeatable with an RMSD value of less than 5%. The collision cross section (CCS) values of CIU intermediates were consistent across the laboratories, but the activation potentials required for protein CIU transitions varied between the three laboratories.
Article
Biochemical Research Methods
Carolina Rojas Ramirez, Rayan Murtada, Jinshan Gao, Brandon T. Ruotolo
Summary: Native top-down proteomics enables identification of proteoforms and characterization of cellular protein complexes. However, the efficiency of tandem MS-based fragmentation for such targets is low. This study optimizes the use of free-radical-initiated peptide sequencing (FRIPS) for native top-down sequencing experiments, resulting in significant improvements in sequence coverage for protein complexes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemistry & Molecular Biology
Joshua D. Jones, Monika K. Franco, Tyler J. Smith, Laura R. Snyder, Anna G. Anders, Brandon T. Ruotolo, Robert T. Kennedy, Kristin S. Koutmou
Summary: Chemical modifications to protein encoding messenger RNAs influence their localization, translation, and stability within cells. Over 15 different types of mRNA modifications have been observed by sequencing and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) approaches. LC-MS/MS is the most essential tool for studying mRNA modifications, but it has been limited by the difficulty of obtaining pure mRNA and limited sensitivities for modified nucleosides.
RSC CHEMICAL BIOLOGY
(2023)
Meeting Abstract
Biochemistry & Molecular Biology
Iliana Levesque, Kristine Parson, Sarah Fantin, Brandon Ruotolo
Article
Biochemistry & Molecular Biology
Jessica J. Waninger, Tyler S. Beyett, Varun V. Gadkari, Ronald F. Siebenaler, Carson Kenum, Sunita Shankar, Brandon T. Ruotolo, Arul M. Chinnaiyan, John J. G. Tesmer
Summary: Oncogenic mutations in the KRAS gene result in a constitutively active form, making direct targeting of KRAS challenging. A study identified AGO2 as a protein that interacts with RAS-driven oncogenesis. While purified AGO2 was shown to co-immunoprecipitate with KRAS, the complex between FL AGO2 and KRAS could not be isolated, indicating further research is needed to understand the interaction of KRAS with purified AGO2 forms.
BIOCHEMISTRY AND BIOPHYSICS REPORTS
(2022)