Article
Multidisciplinary Sciences
Michael R. Lawson, Laura N. Lessen, Jinfan Wang, Arjun Prabhakar, Nicholas C. Corsepius, Rachel Green, Joseph D. Puglisi
Summary: Through single-molecule fluorescence assays, researchers found that in the termination process of yeast translation, the two release factors eRF1 and eRF3 bind together to rapidly recognize stop codons and induce termination through a tightly regulated, multistep process that resembles transfer RNA selection during translation elongation.
Article
Biochemistry & Molecular Biology
Jacob H. Schroader, Lindsey A. Jones, Ryan Meng, Hannah K. Shorrock, Jared Richardson, Sharon M. Shaughnessy, Qishan Lin, Thomas J. Begley, J. Andrew Berglund, Gabriele Fuchs, Mark T. Handley, Kaalak Reddy
Summary: ITPase deficiency results in the accumulation of ITP, leading to misincorporation of inosine into RNA. This misincorporation perturbs translation, causing developmental anomalies and pathogenesis.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Lorenzo Eugenio Leiva, Sara Elgamal, Sebastian A. A. Leidel, Omar Orellana, Michael Ibba, Assaf Katz
Summary: This study characterized the effects of oxidative stress on translation elongation by constructing a library of plasmids coding for GFP fused to different sets of identical codons. The results showed significant variations in GFP production levels under oxidative stress, with translation initiation rates affecting the overall output of translation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Florian Mayer, Monika Cserjan-Puschmann, Benedikt Haslinger, Anton Shpylovyi, Thomas Dalik, Christian Sam, Rainer Hahn, Gerald Striedner
Summary: This study aimed to investigate the impact of scale-related process inhomogeneities on the misincorporation of non-canonical amino acids into recombinant target proteins and whether strain-specific properties may play a role. The results showed significant differences between two E. coli strains in terms of norleucine misincorporation, especially under heterogeneous cultivation conditions. Furthermore, differences in biomass and Fab production were observed between the strains during scale-down cultivations.
MICROBIAL CELL FACTORIES
(2022)
Article
Biochemistry & Molecular Biology
Heejo Choi, Markus W. Covert
Summary: In this study, a whole-cell model was used to investigate the inconsistencies between in vitro tRNA aminoacylation measurements and in vivo protein synthesis demands in E. coli. The results showed that kinetic measurements of aminoacyl-tRNA synthetase were insufficient for cellular proteome maintenance, leading to significant impacts on cellular phenotypes. This study deepens our understanding of translation in an in vivo context.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Engineering, Multidisciplinary
Ionut-Gabriel Farcas, Benjamin Peherstorfer, Tobias Neckel, Frank Jenko, Hans-Joachim Bungartz
Summary: Multi-fidelity Monte Carlo methods leverage low-fidelity and surrogate models for variance reduction to make uncertainty quantification tractable. This work proposes a context-aware multi-fidelity Monte Carlo method that optimizes the balance between training costs and sampling costs. The method applies to hierarchies of different types of low-fidelity models and allows for optimal trade-offs between training and sampling to minimize mean-squared errors of estimators.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Microbiology
Daniel Goncalves-Carneiro, Paul D. Bieniasz
Summary: The development of safe and effective vaccines against viruses is crucial for disease control. Recent advancements in DNA synthesis technology have fueled research efforts in generating attenuated viruses through synonymous mutations. Understanding the molecular mechanisms of attenuation by genetic recoding of viruses could provide insights for vaccine development.
Article
Multidisciplinary Sciences
Yavuz T. Durmaz, Alankrit Shatadal, Kyle Friend
Summary: Messenger RNA translation and the presence of certain codons can affect mRNA stability and protein folding, with ribosomes playing a role in mRNA decay and ribosomal collisions potentially promoting mRNA decay and protein misfolding.
Article
Multidisciplinary Sciences
Alec C. Gleason, Ghanashyam Ghadge, Jin Chen, Yoshifumi Sonobe, Raymond P. Roos
Summary: This study improves the accuracy and prediction capability of identifying translation initiation sites in genes associated with neurologic repeat expansion disorders by optimizing feature selection, data sampling, and machine learning algorithms.
Article
Biochemistry & Molecular Biology
Goro Terai, Kiyoshi Asai
Summary: This paper proposes a method for extracting secondary structure features that affect the functional activity of RNA from sequence-activity data. The method is applied to different experimental systems and provides detailed insights into the structure-activity relationships of RNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Immunology
Michael J. Hogan, Nikita Maheshwari, Bridget E. Begg, Annalisa Nicastri, Emma J. Hedgepeth, Hiromi Muramatsu, Norbert Pardi, Michael A. Miller, Shanelle P. Reilly, Laurent Brossay, Kristen W. Lynch, Nicola Ternette, Laurence C. Eisenlohr
Summary: This study identifies an unconventional epitope that drives T cell immunity against influenza virus and is restricted by the nonclassical Qa-1 class I molecule.
Article
Biochemical Research Methods
Daniel A. Nissley, Anna Carbery, Mark Chonofsky, Charlotte M. Deane
Summary: This study found that in yeast, the ribosome occupancy profiles of paralogous domains tend to be significantly more similar to one another than to profiles of non-paralogous domains. This indicates that entire ribosome occupancy profiles are conserved between even distantly related domains, supporting the hypothesis that translation schedule is conserved between structurally related domains to retain folding pathways and facilitate efficient folding.
Article
Biochemical Research Methods
Mark C. Jenkins, Carolyn Parker, Celia O'Brien, Philip Campos, Matt Tucker, Katarzyna Miska
Summary: The objective of this study was to compare the expression levels of recombinant proteins from three Eimeria genes in Escherichia coli before and after codon optimization. Codon optimization alone did not necessarily lead to higher expression levels, as the outcomes varied with some proteins showing higher, lower, or no change in yield. The codon usage analysis revealed that Eimeria, like other organisms, uses both rare and frequently used codons in its protein-coding sequences, but there was no correlation between codon usage and protein structure.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Article
Biochemistry & Molecular Biology
Monika Witzenberger, Sandra Burczyk, David Settele, Wieland Mayer, Luisa M. Welp, Matthias Heiss, Mirko Wagner, Thomas Monecke, Robert Janowski, Thomas Carell, Henning Urlaub, Stefanie M. Hauck, Aaron Voigt, Dierk Niessing
Summary: 5-Methyluridine (m(5)U) is a common RNA modification in cytosolic tRNA, and tRNA methyltransferase 2 homolog A (hTRMT2A) is the enzyme responsible for m(5)U formation at position 54 of tRNA. Through structural and sequence analysis, it has been determined that hTRMT2A achieves specificity for tRNA modification through a combination of binding preference and the presence of a uridine at position 54. Additionally, hTRMT2A has been found to interact with proteins involved in RNA biogenesis and its knockdown has been shown to reduce translation fidelity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Michael Yarus
Summary: The study showed that minimally evolved codes retain qualities of the standard genetic code but constrain the possibility of evolution. The shape and size of wobble domains significantly affect the accuracy of codon assignments. Additionally, a plausible pathway to limited randomness is necessary to fit a highly ordered, degenerate code into a preset three-dimensional space.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Zhongqi Zhang, Bhavana Shah, Xiaoyan Guan
ANALYTICAL CHEMISTRY
(2019)
Article
Biochemical Research Methods
Glenn R. Masson, John E. Burke, Natalie G. Ahn, Ganesh S. Anand, Christoph Borchers, Sebastien Brier, George M. Bou-Assaf, John R. Engen, S. Walter Englander, Johan Faber, Rachel Garlish, Patrick R. Griffin, Michael L. Gross, Miklos Guttman, Yoshitomo Hamuro, Albert J. R. Heck, Damian Houde, Roxana E. Iacob, Thomas J. D. Jorgensen, Igor A. Kaltashov, Judith P. Klinman, Lars Konermann, Petr Man, Leland Mayne, Bruce D. Pascal, Dana Reichmann, Mark Skehel, Joost Snijder, Timothy S. Strutzenberg, Eric S. Underbakke, Cornelia Wagner, Thomas E. Wales, Benjamin T. Walters, David D. Weis, Derek J. Wilson, Patrick L. Wintrode, Zhongqi Zhang, Jie Zheng, David C. Schriemer, Kasper D. Rand
Article
Medicine, Research & Experimental
Zhongqi Zhang, Bhavana Shah, Jason Richardson
Article
Chemistry, Analytical
Zhongqi Zhang
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Medicinal
Jian Liu, Michael Ronk, Yanxin Luo, Jette Wypych, Zhongqi Zhang, Joel Perez-Pacheco, Ellen Jin, Bhavana Shah, Jason Richardson, Kim Li, David Semin, Yasser Nashed-Samuel
Summary: Battery-powered drug delivery devices were assessed for extractable and leachables (E&L) concerns, identifying novel compounds from device batteries but toxicology assessment showed acceptable levels. A control strategy was established based on assessments to mitigate potential risks, leading to successful qualification of a new battery for delivery devices. The study highlights the importance of understanding materials on a case-by-case basis for successful development and qualification.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Sebasthian Santiago Gonzalez, Omer Ad, Bhavana Shah, Zhongqi Zhang, Xizi Zhang, Abhishek Chatterjee, Alanna Schepartz
Summary: The commercial strain Vibrio natriegens (Vmax X2) shows robust unnatural amino acid mutagenesis and can generate exceptional yields of soluble protein. Compared to other expression strains, Vmax X2 cells not only exhibit higher yields but also reduce levels of misincorporated natural amino acids.
ACS CENTRAL SCIENCE
(2021)
Article
Chemistry, Analytical
Zhongqi Zhang, Bhavana Shah
Summary: A new workflow has been established to assess the impact of various variants on conformational stability simultaneously without the need for enrichment, using limited proteolysis and MS detection. This methodology allows for the evaluation of approximately 100 variants within a short period of time.
ANALYTICAL CHEMISTRY
(2021)
Review
Biochemical Research Methods
Izydor Apostol, Pavel Bondarenko, Da Ren, David J. Semin, Chao-Hsiang Wu, Zhongqi Zhang, Chetan T. Goudar
Summary: Mass spectrometers have become central to the development, characterization, and regulatory filings of biopharmaceuticals, with rapid technological advances improving their capabilities. These improvements have enabled their application across the entire drug development continuum and beyond, leading to a broader understanding of product quality and attribute-focused product development.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Chemistry, Medicinal
Zhongqi Zhang, Sih-Yao Chow, Ronandro De Guzman, Nathan H. Joh, Marisa K. Joubert, Jason Richardson, Bhavana Shah, Mats Wikstrom, Zhaohui Sunny Zhou, Jette Wypych
Summary: This study characterizes light-induced modifications on therapeutic proteins through irradiation experiments and identifies a list of potential modifications. The findings provide a database for routine characterization of light-induced modifications on therapeutic proteins.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2022)
Article
Chemistry, Medicinal
Bhavana Shah, Ming Li, Jette Wypych, Marisa K. Joubert, Zhongqi Zhang
Summary: Therapeutic IgG monoclonal antibodies expressed from Chinese hamster ovary (CHO) cells contain C-terminal variants in their heavy chains, including C-terminal amidation. These variants are commonly found in IgG of all subclasses and are more prevalent in recombinant IgG expressed from CHO cell lines compared to murine cell lines. The presence of a small amount of C-terminal amidation in therapeutic IgGs does not pose a safety concern.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Riley Fricke, Cameron V. Swenson, Leah Tang Roe, Noah Xue Hamlish, Bhavana Shah, Zhongqi Zhang, Elise Ficaretta, Omer Ad, Sarah Smaga, Christine L. Gee, Abhishek Chatterjee, Alanna Schepartz
Summary: The absence of orthogonal aminoacyl-transfer RNA (tRNA) synthetases that accept non-l-a-amino acids is a primary bottleneck hindering the in vivo translation of sequence-defined hetero-oligomers and biomaterials. Pyrrolysyl-tRNA synthetase (PylRS) and certain PylRS variants have been found to accept a-hydroxy, a-thio and N-formyl-l-a-amino acids, as well as a-carboxy acid monomers that are precursors to polyketide natural products. This discovery highlights the potential of PylRS-derived enzymes in expanding the range of monomers used in protein synthesis.
Article
Biochemical Research Methods
Zhongqi Zhang, Jason Richardson, Bhavana Shah
Summary: LC-MS based multi-attribute methods (MAM) are highly valued for their ability to simultaneously monitor numerous quality attributes of biopharmaceutical products. To successfully implement MAM, it is crucial for the method to detect new or missing peaks in the sample compared to a control. This report presents a statistical method for detecting rare differences between two similar samples without replicate analyses, which greatly reduces false positive rate without a significant increase of false negative rate.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Chemistry, Analytical
Jason Richardson, Zhongqi Zhang
Summary: This paper presents a novel method for fully automated online protein digestion and LC-MS peptide mapping, which is efficient and produces fewer artifacts compared to manually prepared digests.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Medicinal
Bhavana Shah, YaXing Zhu, Jette Wypych, Zhongqi Zhang
Summary: Therapeutic IgG mAbs can have three variations of their heavy chain C-termini, including unprocessed C-terminal lysine, processed C-terminal lysine, and C-terminal amidation. These variants are also found in endogenous human IgGs, with a very low level of unprocessed C-terminal lysine. A new heavy-chain C-terminal variant, called des-GK truncation, has been discovered in both recombinant and endogenous human IgG4. The presence of des-GK truncation in endogenous human IgG4 suggests that its low level in therapeutic IgG4 is unlikely to be a safety concern.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2023)
Article
Medicine, Research & Experimental
Zhongqi Zhang, Pik K. Chan, Jason Richardson, Bhavana Shah