Article
Multidisciplinary Sciences
Oana N. Antonescu, Andreas Rasmussen, Nicole A. M. Damm, Ditte F. Heidemann, Roman Popov, Alexander Nesterov-Mueller, Kristoffer E. Johansson, Jakob R. Winther
Summary: A novel platform for functional analysis of leave-one-out split fluorescent proteins (LOO-FPs) was established and validated, with over 12,000 variants of β-strand split fragment screened using high-density peptide microarrays. The effects of peptide length and different linkers on solid support, as well as amino acid substitutions on each position, were studied. Results indicate that the signal intensity on the peptide microarray faithfully reflects the binding affinity between split fragments, with a 9-fold higher affinity peptide identified.
Article
Biochemical Research Methods
Richard A. Stein, Hassane S. Mchaourab
Summary: This study presents a general approach to drive Alphafold2 to model alternate protein conformations through manipulation of the multiple sequence alignment. The applicability of this approach is demonstrated through the investigation of membrane proteins, expanding the potential uses of Alphafold2.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ibuki Nakamura, Hiroshi Amesaka, Mizuho Hara, Kento Yonezawa, Keisuke Okamoto, Hironari Kamikubo, Shun-ichi Tanaka, Takashi Matsuo
Summary: This study investigates the applicability of synthetic binding proteins, specifically monobodies, in regulating the functions of proteins that undergo large conformational changes. The results show that monobodies can capture and stabilize specific conformational states of proteins, thereby affecting their functions. This suggests that monobody-based modulators can regulate the functions of proteins with significant conformational changes.
Article
Biochemistry & Molecular Biology
Ozge Ugurlu, Serap Evran
Summary: YopM, an essential effector protein of Yersinia, shows immunosuppressive effect through protein-protein interactions in host cells. This study investigated the protein-protein interactions of YopM with T3SS components LcrV and LcrG, and found that YopM interacts with LcrG. BiFC assay is proposed as a simple method to screen novel interaction partners of YopM.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Haiyan Jin, Jongwan Kim, Onju Lee, Hyein Kim, Kyoung Tai No
Summary: In this study, we used the fragment molecular orbital (FMO) method to explore the molecular mechanisms of small-molecule inhibitors binding to PLK1. The findings provide valuable insights for designing potent and selective PLK1 inhibitors, which can have significant implications for developing anti-cancer therapeutics.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Adam L. Poti, Laura Denes, Kinga Papp, Csaba Bato, Zoltan Banoczi, Attila Remenyi, Anita Alexa
Summary: Protein kinases are essential for cell signaling and have been targeted for therapeutic purposes for many years. Inhibiting kinase activity or interfering with kinase docking can be alternative strategies for controlling kinases. The development of phosphorylation-assisted luciferase complementation (PhALC) sensors allows for the quantitative analysis of kinase activity or kinase docking, making it a useful tool in research and high-throughput screening.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pharmacology & Pharmacy
Monika Saini, Che Julius Ngwa, Manisha Marothia, Pritee Verma, Shakeel Ahmad, Jyoti Kumari, Sakshi Anand, Vandana Vandana, Bharti Goyal, Soumyananda Chakraborti, Kailash C. Pandey, Swati Garg, Soumya Pati, Anand Ranganathan, Gabriele Pradel, Shailja Singh
Summary: This study characterizes the PHBs genes in Plasmodium falciparum and demonstrates their expression in both asexual and sexual stages of the parasite. The study also confirms that PfPHB1 and PfPHB2 are mitochondrial proteins in the parasite and interact with each other. Functional studies show that these proteins are involved in stabilizing mitochondrial DNA and cell growth.
BIOCHEMICAL PHARMACOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Yusuke Fujino, Takero Miyagawa, Masayuki Torii, Masao Inoue, Yuki Fujii, Hiroki Okanishi, Yoshikatsu Kanai, Ryoji Masui
Summary: A study found that a thermophilic Ser/Thr protein kinase completely unfolds at high temperatures, but is significantly stabilized by its natural ligands ATP and ADP, increasing the melting temperature to 80 degrees Celsius. This striking effect of a substrate on the thermostability of thermophilic proteins has not been reported before.
Article
Infectious Diseases
Guoqing Shao, Ruiqi Hua, Hongyu Song, Yanxin Chen, Xiaowei Zhu, Wei Hou, Shengqiong Li, Aiguo Yang, Guangyou Yang
Summary: The study demonstrates that the six recombinant proteins have significant protective efficacy in dogs against E. granulosus infection, reducing worm biomass and inhibiting growth. The vaccinated dogs also showed an increased level of IgG, indicating an enhanced immune response.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Genetics & Heredity
Limin Shang, Yuehui Zhang, Yuchen Liu, Chaozhi Jin, Yanzhi Yuan, Chunyan Tian, Ming Ni, Xiaochen Bo, Li Zhang, Dong Li, Fuchu He, Jian Wang
Summary: In this study, a high-efficiency BiFC-seq method coupled with next-generation DNA sequencing was used for genome-wide interactome mapping. By applying this method to investigate the intraviral network of the Ebola virus and the interactome of the tumor protein p53, as well as screening potential interactors in a more complex background, satisfactory results were obtained.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Virology
Tucker Hansen, Jodie Baris, Min Zhao, Richard E. Sutton
Summary: This study developed both cell-intact and cell-free systems that can reliably, rapidly, and reproducibly quantify Rev-Rev interaction. The results of mutant Revs tested in the cell-based assay correlated strongly with the results of a functional Rev trans-complementation infectivity assay. These assays may be useful in screening and identifying compounds that inhibit Rev function on a high throughput basis.
Article
Chemistry, Multidisciplinary
Zsofia Hegedus, Fruzsina Hobor, Deborah K. Shoemark, Sergio Celis, Lu-Yun Lian, Chi H. Trinh, Richard B. Sessions, Thomas A. Edwards, Andrew J. Wilson
Summary: This study describes an alternative approach using dynamic ligation screening to identify small-molecule replacements for beta-strand mediated protein-protein interactions. The findings demonstrate the effectiveness of this method in identifying and validating peptide hybrids with selective inhibitory effects.
Article
Chemistry, Physical
Takumi Washio, Ryo Kanada, Xiaoke Cui, Jun-ichi Okada, Seiryo Sugiura, Shoji Takada, Toshiaki Hisada
Summary: The semi-implicit Hessian correction (SimHec) scheme proposed in this study allows for significantly larger time steps in molecular dynamics simulations compared to traditional implicit methods. By introducing a hybrid method (SimHec-H) that combines explicit time steps, the drawbacks of increased transition dynamics and reduced fluctuations in bonded potentials can be corrected. This scheme results in a speedup factor of 7-30, making simulations more efficient and accurate.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Biochemistry & Molecular Biology
Leszek A. Kleczkowski, Abir U. Igamberdiev
Summary: Free magnesium (Mg2+) functions as a signal of adenylate (ATP+ADP+AMP) status in cells, controlled by the equilibrium of adenylate kinase (AK) and membrane-bound adenylate- and Mg2+-translocators. Changes in [Mg2+] impact enzyme activities, metabolism, and processes like photosynthesis, under normal and stress conditions. Magnesium signaling is likely widespread in all eukaryotic and prokaryotic organisms due to the ubiquitous nature of AK and its role in adenylate equilibration.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Alexis Voegele, Mirko Sadi, Darragh Patrick O'Brien, Pauline Gehan, Dorothee Raoux-Barbot, Maryline Davi, Sylviane Hoos, Sebastien Brule, Bertrand Raynal, Patrick Weber, Ariel Mechaly, Ahmed Haouz, Nicolas Rodriguez, Patrice Vachette, Dominique Durand, Sebastien Brier, Daniel Ladant, Alexandre Chenal
Summary: The P454 segment of the CyaA toxin is capable of translocating across membranes and interacting with calmodulin, with key residues involved in membrane destabilization and calmodulin binding. Inhibitors of calmodulin can efficiently block CyaA internalization. This suggests a potential mechanism for the vectorial translocation of the toxin into host cells.
Article
Materials Science, Biomaterials
Noemie-Manuelle Dorval Courchesne, Anna Duraj-Thatte, Pei Kun R. Tay, Peter Q. Nguyen, Neel S. Joshi
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2017)
Article
Biochemical Research Methods
Pei Kun R. Tay, Peter Q. Nguyen, Neel S. Joshi
ACS SYNTHETIC BIOLOGY
(2017)
Review
Chemistry, Multidisciplinary
Peter Q. Nguyen, Noemie-Manuelle Dorval Courchesne, Anna Duraj-Thatte, Pichet Praveschotinunt, Neel S. Joshi
ADVANCED MATERIALS
(2018)
Article
Biochemical Research Methods
Pichet Praveschotinunt, Noemie-Manuelle Dorval Courchesne, Ilona den Hartog, Chaochen Lu, Jessica J. Kim, Peter Q. Nguyen, Neel S. Joshi
ACS SYNTHETIC BIOLOGY
(2018)
Article
Multidisciplinary Sciences
Ally Huang, Peter Q. Nguyen, Jessica C. Stark, Melissa K. Takahashi, Nina Donghia, Tom Ferrante, Aaron J. Dy, Karen J. Hsu, Rachel S. Dubner, Keith Pardee, Michael C. Jewett, James J. Collins
Article
Multidisciplinary Sciences
Jessica C. Stark, Ally Huang, Peter Q. Nguyen, Rachel S. Dubner, Karen J. Hsu, Thomas C. Ferrante, Mary Anderson, Ada Kanapskyte, Quinn Mucha, Jessica S. Packett, Palak Patel, Richa Patel, Deema Qaq, Tyler Zondor, Julie Burke, Thomas Martinez, Ashlee Miller-Berry, Aparna Puppala, Kara Reichert, Miriam Schmid, Lance Brand, Lander R. Hill, Jemima F. Chellaswamy, Nuhie Faheem, Suzanne Fetherling, Elissa Gong, Eddie Marie Gonzalzles, Teresa Granito, Jenna Koritsaris, Binh Nguyen, Sujud Ottman, Christina Palffy, Angela Patel, Sheila Skweres, Adriane Slaton, TaRhonda Woods, Nina Donghia, Keith Pardee, James J. Collins, Michael C. Jewett
Article
Biochemical Research Methods
Jessica C. Stark, Ally Huang, Karen J. Hsu, Rachel S. Dubner, Jason Forbrook, Suzanne Marshalla, Faith Rodriguez, Mechelle Washington, Grant A. Rzimicky, Peter Q. Nguyen, Brenna Hasselbacher, Ramah Jabri, Rijha Kamran, Veronica Koralewski, Will Wightkin, Thomas Martinez, Michael C. Jewett
ACS SYNTHETIC BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Max A. English, Luis R. Soenksen, Raphael V. Gayet, Helena de Puig, Nicolaas M. Angenent-Mari, Angelo S. Mao, Peter Q. Nguyen, James J. Collins
Article
Biotechnology & Applied Microbiology
Jaeyoung K. Jung, Khalid K. Alam, Matthew S. Verosloff, Daiana A. Capdevila, Morgane Desmau, Phillip R. Clauer, Jeong Wook Lee, Peter Q. Nguyen, Pablo A. Pasten, Sandrine J. Matiasek, Jean-Francois Gaillard, David P. Giedroc, James J. Collins, Julius B. Lucks
NATURE BIOTECHNOLOGY
(2020)
Article
Biochemical Research Methods
Raphael Gayet, Helena de Puig, Max A. English, Luis R. Soenksen, Peter Q. Nguyen, Angelo S. Mao, Nicolaas M. Angenent-Mari, James J. Collins
Article
Biotechnology & Applied Microbiology
Peter Q. Nguyen, Luis R. Soenksen, Nina M. Donghia, Nicolaas M. Angenent-Mari, Helena de Puig, Ally Huang, Rose Lee, Shimyn Slomovic, Tommaso Galbersanini, Geoffrey Lansberry, Hani M. Sallum, Evan M. Zhao, James B. Niemi, James J. Collins
Summary: This study demonstrates the development of wearable devices functionalized with freeze-dried, cell-free synthetic circuits for noninvasive detection of biomolecules, including virus nucleic acids, without the need for living engineered bacteria. The technology shows promise for expanding opportunities in physiological status monitoring and disease detection.
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Evan M. Zhao, Angelo S. Mao, Helena de Puig, Kehan Zhang, Nathaniel D. Tippens, Xiao Tan, F. Ann Ran, Isaac Han, Peter Q. Nguyen, Emma J. Chory, Tiffany Y. Hua, Pradeep Ramesh, David B. Thompson, Crystal Yuri Oh, Eric S. Zigon, Max A. English, James J. Collins
Summary: The use of eukaryotic toehold switches (eToeholds) allows for efficient induction of gene translation in eukaryotic cells, capable of distinguishing the presence of RNA transcripts under various circumstances. Through optimization of RNA annealing, up to 16-fold induction of transgene expression was achieved.
NATURE BIOTECHNOLOGY
(2022)
Review
Nanoscience & Nanotechnology
H. Ceren Ates, Peter Q. Nguyen, Laura Gonzalez-Macia, Eden Morales-Narvaez, Firat Guder, James J. Collins, Can Dincer
Summary: Wearable sensors that access biophysical and biochemical information can monitor physiological state and aid in diagnosis. These devices can be worn in various forms and have shown potential in early detection and monitoring of diseases. Future wearable sensors are expected to enable multimodal and real-time continuous measurement.
NATURE REVIEWS MATERIALS
(2022)
Article
Chemistry, Physical
Martin G. Nussbaumer, Peter Q. Nguyen, Pei K. R. Tay, Alexander Naydich, Erisa Hysi, Zsofia Botyanszki, Neel S. Joshi
Review
Biochemistry & Molecular Biology
Peter Q. Nguyen
BIOCHEMICAL SOCIETY TRANSACTIONS
(2017)