Article
Multidisciplinary Sciences
Anna A. Shiriaeva, Konstantin Kuznedelov, Ivan Fedorov, Olga Musharova, Timofey Khvostikov, Yuliya Tsoy, Elena Kurilovich, Gerald R. Smith, Ekaterina Semenova, Konstantin Severinov
Summary: CRISPR-Cas systems provide prokaryotes with adaptive immunity against foreign nucleic acids. In E. coli, the integration of 33-bp spacers into CRISPR arrays leads to the acquisition of immunity. During the process called primed adaptation, DNA targets complementary to spacers are degraded and serve as a source of new spacers. This study identifies RecJ as the main exonuclease involved in trimming the 5' ends of prespacer precursors, and reveals the functional interactions between genome maintenance proteins and CRISPR interference and adaptation machineries.
Article
Multidisciplinary Sciences
Khanh Vu Huu, Rene Zangl, Jan Hoffmann, Alicia Just, Nina Morgner
Summary: The study investigates the assembly process of F-1 complex from Acetobacterium woodii using laser induced liquid bead ion desorption mass spectrometry. The results indicate that nucleotide binding is crucial for in vitro assembly of F-1, while ATP hydrolysis is less critical. The study also proposes a model for the assembly pathway of a functional F-1 complex, correlating the results with activity measurements.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Claudio Castillo-Caceres, Eva Duran-Meza, Esteban Nova, Raul Araya-Secchi, Octavio Monasterio, Rodrigo Diaz-Espinoza
Summary: Novel functional roles of amyloids have been increasingly reported, with recent findings showing that amyloids formed from small peptides can exhibit catalytic reactivity, particularly towards ribonucleotides. The observed catalytic activity is dependent on binding of divalent metals like manganese (Mn2+), and a single aspartate per peptide is sufficient for enabling the hydrolytic activity towards phosphoanhydride bonds of nucleotides.
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
(2021)
Article
Biochemistry & Molecular Biology
Jie Zhou, Mengfen Wei, Lijun You
Summary: In this study, peptides from Pinctada martensii meat were prepared and the structures were identified. The potential antioxidant peptides were synthesized and their activities were verified using HepG2 cells. The results showed that the peptides exhibited antioxidant effects and could be used as candidates in functional foods.
Article
Biochemistry & Molecular Biology
Han-Ha Chai, Tae-Hun Kim, Young Ran Kim, Dajeong Lim
Summary: The study predicted the structure of the pig TAP transporter and its inhibition complex by the herpes simplex virus-encoded ICP47 inhibitor, revealing the specificity determinants and functional effects of the ICP47 inhibitor on TAP. The research also demonstrated the specialized structure-function relationship of the pig TAP exporter and its implications for antiviral resistance and disease susceptibility.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Nutrition & Dietetics
Xiao Hu, Jing Liu, Jun Li, Yuqiong Song, Shengjun Chen, Shaobo Zhou, Xianqing Yang
Summary: In this study, antioxidant peptides were obtained by hydrolyzing Gracilariopsis lemaneiformis protein with alkaline protease. The optimal enzymatic hydrolysis conditions were determined through experiments. Three novel antioxidant peptides were identified and one of them exhibited the best antioxidant activity. Molecular docking results showed that this peptide had better binding ability and inhibition than the others. Cell viability assay confirmed the protective effect of the antioxidant peptide against oxidative damage. These findings highlight the potential of using antioxidant peptides from Gracilariopsis lemaneiformis as antioxidants.
FRONTIERS IN NUTRITION
(2022)
Article
Engineering, Chemical
Steffen Zobel-Roos, Florian Vetter, Daniel Scheps, Marcus Pfeiffer, Matthias Gunne, Oliver Boscheinen, Jochen Strube
Summary: This study proposes a combined approach to optimize the process design of a separation task by applying experiments and statistical analysis. The best buffer composition and crucial model parameters were obtained through early-stage buffer screening and optimization experiments, allowing the establishment of a digital twin model. The digital twin model predicts the optimal buffer composition and applies model-predicted control to maintain the process at the optimal productivity at a predetermined purity.
Article
Biology
Jesus Herrera-Bravo, Lisandra Herrera Belen, Jorge G. Farias, Jorge F. Beltran
Summary: This study evaluated fifteen machine learning algorithms for the classification of tumor antigens, with the quadratic discriminant classifier showing the best performance. A new immunoinformatic tool called TAP 1.0 was developed for tumor antigen prediction.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2021)
Article
Biology
Xue Zhang, Jingcheng Wu, Joseph Baeza, Katie Gu, Yichun Zheng, Shuqing Chen, Zhan Zhou
Summary: This study provides a comprehensive analysis of TAP-binding peptide sequences and develops a novel method called DeepTAP for accurate prediction of TAP-binding peptides. DeepTAP outperforms other baseline models and improves the prediction accuracy of high-confidence neoantigens, making it a valuable tool for antigen presentation research and T-cell epitope screening.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Food Science & Technology
Haisheng Lin, Wan Li, Ruikun Sun, Cheng Xu, Chaohua Zhang, Jialong Gao, Wenhong Cao, Xiaoming Qin, Saiyi Zhong, Yibin Chen
Summary: This study purified and identified an immunoregulatory peptide named SNLP from Sipunculus nudus L., which showed dual immunomodulatory activities including immunostimulatory and anti-inflammatory effects.
FOOD SCIENCE & NUTRITION
(2023)
Article
Biochemistry & Molecular Biology
Jiahui Guo, Yihan Lu, Xiaoqing He, Jiashu Li, Chenling Fan, Hongmei Zhang, Weiping Teng, Zhongyan Shan, Jing Li
Summary: Our recent study found that ENO1Ab expression in an experimental AIT mouse model was induced by thyroglobulin (Tg) immunization. In this study, we investigated the potential roles of ENO1Ab in miscarriage occurrence among AIT women and the specific epitopes of ENO1 targeted by ENO1Ab. The results showed that serum ENO1Ab was an independent risk factor for miscarriage, especially among AIT females, and the autoantibody specific to the P6 epitope of ENO1 may be more specifically related to this disorder.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Defne I. Dayi, Ursula Eschenhagen, Henrike Seidinger, Holger Schneider, Magnus S. Schmidt
Summary: In this study, we demonstrated the immobilization of a technical-grade & beta;-d-galactosidase on amino-functionalized microtiter plates and transferred the results to a resin-based approach. The enzyme was covalently bound to an amino-functionalized microtiter plate prefunctionalized with 1,4-phenylendiisothiocyanate. The cleavage of the substrate 5-bromo-4-chloro-3-indoxyl-& beta;-d-galactopyranoside (X-Gal) produced a deep blue dye, which was quantified in a microtiter plate reader at 595 nm. The maximum reaction rates and the Michaelis-Menten constant were calculated, and optimization of the experiments minimized the formation of unwanted blue precipitate.
Article
Multidisciplinary Sciences
Armin Mirzapour-Kouhdasht, Marzieh Moosavi-Nasab, Chul Won Lee, Hyosuk Yun, Jong-Bang Eun
Summary: Fish gelatin hydrolysates exhibit multifunctional properties with antibacterial and ACE/DPP-IV enzyme inhibitory activities. The synthesized PEP1, PEP2, and PEP3 peptides demonstrate this multifunctionality, confirmed through in vitro and in silico experiments. The binding energies of these peptides are sufficient to inhibit both ACE and DPP-IV enzymes with excellent three-dimensional conformation in all six docking mechanisms.
SCIENTIFIC REPORTS
(2021)
Article
Food Science & Technology
Aliaa M. A. Hashem, Anushma Venmarath, Tanaji G. G. Kudre
Summary: The study focused on the preparation, purification, and identification of novel antioxidant peptides from Piaractus brachypomus fish meat. The RPMPH-IF fraction, obtained by ultrafiltration, displayed significantly higher antioxidant activities. After purification by gel filtration and reversed-phase liquid chromatography, the RPH-8 fraction showed the highest antioxidant activities. The peptide sequences of RPH-8 fraction were identified using LC-MS/MS and MASCOT software.
FOOD SCIENCE AND BIOTECHNOLOGY
(2023)
Article
Oncology
Koen A. Marijt, Lisa Griffioen, Laura Blijleven, Sjoerd. H. van der Burg, Thorbald van Hall
Summary: TEIPP is a novel category of cancer antigens that emerge on cancers with functional loss of peptide pump TAP, evoking CD8 T cell immune response. By studying LRPAP1(21-30)-specific CD8 T cells, it was found that replacing the serine anchor with valine in the signal sequence enhances HLA-A2 binding affinity and T cell stimulation.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2022)
Article
Multidisciplinary Sciences
Sunesh Sethumadhavan, Marie Barth, Robbert M. Spaapen, Carla Schmidt, Simon Trowitzsch, Robert Tampe
Summary: This study reveals that surface presentation of MHC I is differently affected by viral factors ICP47 and US6, indicating the impact of antigenic differences. The findings suggest that different inhibitory mechanisms and conformational states influence MHC I surface presentation across allotypes.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Eike F. Joest, Christian Winter, Joshua S. Wesalo, Alexander Deiters, Robert Tampe
Summary: Genetic code expansion is a versatile method for synthesis of modified proteins, allowing site-specific incorporation of non-canonical amino acids. By overcoming limitations caused by ribosomal inaccuracy, a new suppression concept based on ribosomal skipping was designed to successfully synthesize nanobodies with photoactivated target binding capabilities. This flexible intrabody concept establishes an ideal platform for modulating target protein function in photopharmacology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nicole Koller, Philipp Hoellthaler, Martina Barends, Marius Doering, Christoph Spahn, Veronica Duran, Bibiana Costa, Jennifer Becker, Mike Heilemann, Ulrich Kalinke, Robert Tampe
Summary: Dendritic cells (DCs) translate innate immune responses into adaptive immunity, but the spatial organization of underlying processes is not well understood. By studying human monocyte-derived DCs, we discovered a nanoscale organization of antigen-loading machinery and observed an increase in density during DC maturation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Multidisciplinary Sciences
Alexander Domnick, Christian Winter, Lukas Susac, Leon Hennecke, Mario Hensen, Nicole Zitzmann, Simon Trowitzsch, Christoph Thomas, Robert Tampe
Summary: In this study, the authors determine the structure of the editing module of the peptide loading complex (PLC) and reveal the communication between peptide-MHC I assembly and glycan processing. These findings are important for understanding the initiation of adaptive immune responses and the coordination of events in endoplasmic reticulum quality control.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Christian Winter, Alexander Domnick, Darja Cernova, Robert Tampe
Summary: This study developed a semi-synthetic immune modulator that can be controlled by light, revealing key events in antigen processing. A new assay was established to monitor the activity of the antigen processing machinery in native cell membranes.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemistry & Molecular Biology
Lukas Susac, Mai T. Vuong, Christoph Thomas, Soren von Bulow, Caitlin O'Brien-Ball, Ana Mafalda Santos, Ricardo A. Fernandes, Gerhard Hummer, Robert Tampe, Simon J. Davis
Summary: This study reveals the structure of a tumor-reactive TCR complex bound to a melanoma-specific human class I pMHC, providing insights into the initiation of TCR signaling when the receptor binds to pMHC molecules.
Review
Biochemistry & Molecular Biology
M. Florencia Sanchez, Robert Tampe
Summary: Cell-surface receptors play a crucial role in mediating communication between cells and their environment. The organization of receptors on the cell membrane and the formation of dynamic receptor clusters are important for signal transduction and cell signaling. Recent studies have shown that receptor clustering can modulate transmembrane signaling even in the absence of natural ligands. This review discusses the latest findings on how ligand-independent receptor clustering regulates signaling, focusing on the biological relevance and unraveling of this phenomenon using advanced technologies such as DNA nanotechnology, optogenetics, and optochemistry.
TRENDS IN BIOCHEMICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Samoil Sekulovski, Lukas Susac, Lukas S. Stelzl, Robert Tampe, Simon Trowitzsch
Summary: The heterotetrameric human tRNA splicing endonuclease TSEN and its associated RNA kinase CLP1 are essential for intron excision from pre-tRNAs. This study presents cryo-EM reconstructions of human TSEN with intron-containing pre-tRNAs and reveals the molecular principles of pre-tRNA recognition and cleavage. Disease mutations are also rationalized, providing insights into the pathogenesis of pontocerebellar hypoplasia.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Correction
Multidisciplinary Sciences
Rong Zhu, Daniel Canena, Mateusz Sikora, Miriam Klausberger, Hannah Seferovic, Ahmad Reza Mehdipour, Lisa Hain, Elisabeth Laurent, Vanessa Monteil, Gerald Wirnsberger, Ralph Wieneke, Robert Tampe, Nikolaus F. Kienzl, Lukas Mach, Ali Mirazimi, Yoo Jin Oh, Josef M. Penninger, Gerhard Hummer, Peter Hinterdorfer
NATURE COMMUNICATIONS
(2023)
Article
Biology
Lina Sagert, Christian Winter, Ina Ruppert, Maximilian Zehetmaier, Christoph Thomas, Robert Tampe
Summary: Adaptive immune responses are triggered by antigenic peptides presented on MHC I. The stability of peptide-MHC I complexes is facilitated by tapasin and TAPBPR, and the folding status of glycoproteins in the ER is monitored by UGGT1. In this study, the function of TAPBPR during the UGGT1-catalyzed quality control and reglucosylation of MHC I was investigated using a reconstituted in-vitro system.
Article
Chemistry, Multidisciplinary
Michael Rudolph, Robert Tampe, Benesh Joseph
Summary: ATP-binding cassette (ABC) transporters are responsible for transporting various substances across biological membranes. The transition between inward-facing (IF) and outward-facing (OF) conformations of transmembrane domains (TMDs) is crucial for the transport process. This study investigated the functional role of asymmetric nucleotide-binding sites (NBSs) in ABC transporters using pulsed electron-electron double-resonance spectroscopy. The results showed that ATP hydrolysis at the consensus NBS accelerates the reverse transition, and the degenerate NBS may regulate the kinetics of this process.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biotechnology & Applied Microbiology
Eike F. Joest, Robert Tampe
Summary: Engineered antibodies are crucial tools in research and advanced pharmacy, as they offer both target recognition and modulation. Using light-activated antibody fragments, high spatiotemporal control over spontaneous antigen interaction can be achieved. Recent developments in optogenetic and optochemical engineering concepts have provided strategies for conditional antigen binding. These novel design approaches serve as complementary tools to enhance current and upcoming antibody technologies.
TRENDS IN BIOTECHNOLOGY
(2023)
Article
Cell Biology
Jasper Fuk-Woo Chan, Yoo Jin Oh, Shuofeng Yuan, Hin Chu, Man-Lung Yeung, Daniel Canena, Chris Chung-Sing Chan, Vincent Kwok-Man Poon, Chris Chun-Yiu Chan, Anna Jinxia Zhang, Jian-Piao Cai, Zi-Wei Ye, Lei Wen, Terrence Tsz-Tai Yuen, Kenn Ka-Heng Chik, Huiping Shuai, Yixin Wang, Yuxin Hou, Cuiting Luo, Wan-Mui Chan, Zhenzhi Qin, Ko-Yung Sit, Wing-Kuk Au, Maureen Legendre, Rong Zhu, Lisa Hain, Hannah Seferovic, Robert Tampe, Kelvin Kai-Wang To, Kwok-Hung Chan, Dafydd Gareth Thomas, Miriam Klausberger, Cheng Xu, James J. Moon, Johannes Stadlmann, Josef M. Penninger, Chris Oostenbrink, Peter Hinterdorfer, Kwok-Yung Yuen, David M. Markovitz
Summary: Researchers have designed pan-coronavirus antivirals that target conserved viral components, and have identified H84T-BanLec as a potential inhibitor of Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (including Omicron), and other human-pathogenic coronaviruses. H84T-BanLec exhibits potent antiviral activity at nanomolar concentrations and protects against MERS-CoV and SARS-CoV-2 infection in vivo. Mechanistic assays reveal that H84T-BanLec targets virus entry by binding to high-mannose glycans on the viral spike protein, competing with SARS-CoV-2 spike for binding to cellular ACE2. This drug compound's broad-spectrum antiviral activity is attributed to its multiple binding sites on the spike protein, which likely prevents the emergence of resistant mutants.
CELL REPORTS MEDICINE
(2022)
Meeting Abstract
Immunology
J. Becker, L. Krajewski, B. Costa, V. Duran, B. Bosnjak, N. Koller, M. Barends, K. Laib-Sampaio, P. Larsen, Z. Fneish, M. M. Santamorena, S. Tischer-Zimmermann, R. Foerster, B. Eiz-Vesper, R. Tampe, U. Kalinke
EUROPEAN JOURNAL OF IMMUNOLOGY
(2022)
Article
Materials Science, Multidisciplinary
Heike Krueger, Marvin Asido, Josef Wachtveitl, Robert Tampe, Ralph Wieneke
Summary: This study demonstrates the 3D patterning of proteins in photoresponsive hydrogels and the potential to dynamically modify the biofunctional properties of materials at specific subvolumes.
COMMUNICATIONS MATERIALS
(2022)