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Micikas RJ, Acharyya A, Smith AB, Gai F. Synthesis and characterization of the fluorescence utility of two Visible-Light-Absorbing tryptophan derivatives. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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Marklund E, Mao G, Yuan J, Zikrin S, Abdurakhmanov E, Deindl S, Elf J. Sequence specificity in DNA binding is mainly governed by association. Science 2022; 375:442-445. [PMID: 35084952 DOI: 10.1126/science.abg7427] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Sequence-specific binding of proteins to DNA is essential for accessing genetic information. We derive a model that predicts an anticorrelation between the macroscopic association and dissociation rates of DNA binding proteins. We tested the model for thousands of different lac operator sequences with a protein binding microarray and by observing kinetics for individual lac repressor molecules in single-molecule experiments. We found that sequence specificity is mainly governed by the efficiency with which the protein recognizes different targets. The variation in probability of recognizing different targets is at least 1.7 times as large as the variation in microscopic dissociation rates. Modulating the rate of binding instead of the rate of dissociation effectively reduces the risk of the protein being retained on nontarget sequences while searching.
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Affiliation(s)
- Emil Marklund
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
| | - Jinwen Yuan
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
| | - Spartak Zikrin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
| | - Eldar Abdurakhmanov
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, 75124, Uppsala, Sweden
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Gober IN, Riemen AJ, Villain M. Sequence sensitivity and pH dependence of maleimide conjugated N-terminal cysteine peptides to thiazine rearrangement. J Pept Sci 2021; 27:e3323. [PMID: 33786923 PMCID: PMC8243948 DOI: 10.1002/psc.3323] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022]
Abstract
Thiazine formation during the conjugation of N‐terminal cysteine peptides to maleimides is an underreported side reaction in the peptide literature. When the conjugation was performed at neutral and basic pH, we observed the thiazine isomer as a significant by‐product. Nuclear magnetic resonance (NMR) spectroscopy confirmed the structure of the six‐membered thiazine and ultra‐high performance liquid chromatography (UHPLC) combined with tandem mass spectrometry (MS/MS) allowed for facile, unambiguous detection due to a unique thiazine mass fragment. Furthermore, substitution of various amino acids adjacent to the N‐terminal cysteine in a tripeptide model system resulted in different rates of thiazine formation, albeit within the same order of magnitude. We also determined that varying the N‐substitution of the maleimide affects the thiazine conversion rate. Altogether, our findings suggest that thiazine rearrangement for N‐terminal cysteine‐maleimide adducts is a general side reaction that is applicable to other peptide or protein systems. Performing the conjugation reaction under acidic conditions or avoiding the use of an N‐terminal cysteine with a free amino group prevents the formation of the thiazine impurity.
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Affiliation(s)
- Isaiah N Gober
- Research and Development Department, Bachem Americas, Inc., Torrance, California, USA
| | - Alexander J Riemen
- Research and Development Department, Bachem Americas, Inc., Torrance, California, USA
| | - Matteo Villain
- CMC Development Group, Bachem Americas, Inc., Torrance, California, USA
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Ali MZ, Parisutham V, Choubey S, Brewster RC. Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif. eLife 2020; 9:56517. [PMID: 32808926 PMCID: PMC7505660 DOI: 10.7554/elife.56517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of asymmetry depends on network features such as network size and TF-binding affinities. Intriguingly, asymmetry disappears when the growth rate is too fast or too slow and is most significant for typical growth conditions. These results highlight the importance of accounting for network architecture in quantitative models of gene expression.
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Affiliation(s)
- Md Zulfikar Ali
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Vinuselvi Parisutham
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sandeep Choubey
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Robert C Brewster
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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Liao Q, Lüking M, Krüger DM, Deindl S, Elf J, Kasson PM, Lynn Kamerlin SC. Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition. J Phys Chem B 2019; 123:3576-3590. [PMID: 30952192 DOI: 10.1021/acs.jpcb.8b12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse-grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (LacI), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein-DNA interactions, as well as the behavior of the helix-turn-helix motif of LacI when interacting with the DNA. Our simulations suggest that stable LacI binding occurs primarily to bent A-form DNA, with a loss of LacI conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA-protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.
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Affiliation(s)
- Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Malin Lüking
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden.,Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, Bioinformatics Unit , German Center for Neurodegenerative Diseases, Göttingen , von Siebold Strasse 3A , 37075 Göttingen , Germany
| | - Sebastian Deindl
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Johan Elf
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
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