Article
Physics, Multidisciplinary
Marc Schenkelberger, Christian Trapp, Timo Mai, Varun Giri, Mina Mohammadi-Kambs, Albrecht Ott
Summary: The specificity of molecular recognition is crucial for molecular self-organization, with better matching molecules prevailing over competitors. Fluorescence-based techniques were used to study the recognition of DNA oligonucleotide single strands, revealing reduced affinity for certain strands in the presence of a better matching competitor.
NEW JOURNAL OF PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
John M. McBride, Jean-Pierre Eckmann, Tsvi Tlusty
Summary: In this study, a model combining chemistry, mechanics, and genetics is presented to explain how these factors interact in the evolution of protein-ligand interactions. The model demonstrates that precision is the key to achieving molecular discrimination, and harder discrimination tasks require more coaction of structure, forces, and movements. The model also suggests that increasing protein size enables the solution of more complicated tasks and makes proteins more evolvable and robust.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Materials Science, Multidisciplinary
Badrinath Jagannath, Madhavi Pali, Kai-Chun Lin, Devangsingh Sankhala, Pejman Naraghi, Sriram Muthukumar, Shalini Prasad
Summary: This work demonstrates the discovery, quantification, and validation of infection prognostic markers, IP-10 and TRAIL, in human sweat using wearable technology. It also shows the potential of a wearable SWEATSENSER device for continuous monitoring of infection markers.
ADVANCED MATERIALS TECHNOLOGIES
(2022)
Article
Chemistry, Multidisciplinary
Andrew T. DeLaitsch, Jacey R. Pridgen, Avery Tytla, Megan L. Peach, Rayleen Hu, David W. Farnsworth, Aislinn K. McMillan, Natalie Flanagan, J. Sebastian Temme, Marc C. Nicklaus, Jeffrey C. Gildersleeve
Summary: Germline antibodies play a critical role in host defense and have important implications for designing vaccines, developing monoclonal antibodies, and understanding antibody evolution. However, there are still many antibody families that have not been studied, and challenges exist in obtaining germline antibodies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Physical
Girgis Obaid, Kimberley Samkoe, Kenneth Tichauer, Shazia Bano, Yeonjae Park, Zachary Silber, Sassan Hodge, Susan Callaghan, Mina Guirguis, Srivalleesha Mallidi, Brian Pogue, Tayyaba Hasan
Summary: This study quantifies the in vivo specificity of receptor targeted nanoliposomes for their target receptors using near-infrared molecular imaging, showing a positive correlation with EGFR expression levels. The findings present an opportunity to address the problematic disconnect between tNL synthesis and in vivo specificity.
Article
Chemistry, Multidisciplinary
Hiroyuki Koide, Chiaki Kiyokawa, Anna Okishima, Kaito Saito, Keiichi Yoshimatsu, Tatsuya Fukuta, Yu Hoshino, Tomohiro Asai, Yuri Nishimura, Yoshiko Miura, Naoto Oku, Kenneth J. Shea
Summary: This article describes a synthetic antibody that binds to HMGB1 and inhibits its interaction with the RAGE receptor, thereby reducing brain damage caused by cerebral ischemia/reperfusion.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Jiaqi Shen, Lequn Geng, Xingyu Li, Catherine Emery, Kayla Kroning, Gwendolyn Shingles, Kerry Lee, Matthias Heyden, Peng Li, Wenjing Wang
Summary: We have developed a pair of chemically activated protein domains (CAPs) that can control the accessibility of short peptides. CAPs are applicable to a range of short peptides and have a chemical dependence up to 156-fold. Our study demonstrates the potential use of CAPs in cell cultures and multiple organs in living animals.
Article
Biochemistry & Molecular Biology
Weiping Lyu, Qihang Li, Yingming Wang, Chenxi Du, Feng Feng, Heng Chi, Yuan Li, Wenyuan Liu, Haopeng Sun
Summary: Cellular autophagy is an intracellular degradation pathway that maintains cell homeostasis, and dysfunctions in autophagy are closely related to various diseases. The protein-protein interaction between LC3 and p62 plays a critical role in autophagosome formation, yet research on inhibitors targeting this interaction is still lacking.
BIOORGANIC CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Jimmy Gaudreault, Yves Durocher, Olivier Henry, Gregory De Crescenzo
Summary: This article discusses the data analysis algorithms and application of Surface Plasmon Resonance (SPR) biosensing. The algorithms can accurately identify kinetic parameters and estimate the composition of mixtures in cases of multiple species interactions, making SPR biosensing a potential tool for bioprocess monitoring.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Edward P. Harvey, Jung-Eun Shin, Meredith A. Skiba, Genevieve R. Nemeth, Joseph D. Hurley, Alon Wellner, Ada Y. Shaw, Victor G. Miranda, Joseph K. Min, Chang C. Liu, Debora S. Marks, Andrew C. Kruse
Summary: In this study, a diverse synthetic camelid antibody fragment library was used to design a set of experiments that allowed machine learning models to accurately assess polyreactivity from protein sequence. The models provided quantitative scoring metrics and predicted the effect of amino acid substitutions on polyreactivity. Experimental tests showed that over 90% of predicted substitutions successfully reduced polyreactivity without compromising the functional properties. A web server was also provided for predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Kenta Morita, Shinano Takeda, Ayumi Yunoki, Takane Tsuchii, Tsutomu Tanaka, Tatsuo Maruyama
Summary: This novel approach involves preparing affinity membranes using azido-containing surfactants and click chemistry, resulting in membranes that display affinity towards specific proteins. The method allows for facile surface functionalization of polymeric materials to produce affinity membranes with different ligands on their surfaces.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2021)
Article
Genetics & Heredity
Olivia P. Duddy, Xiuliang Huang, Justin E. Silpe, Bonnie L. Bassler
Summary: This study highlights the use of quorum sensing for chemical communication between bacteria and phages, specifically in the context of V. cholerae and phage VP882. The research uncovers the molecular mechanisms underlying the asymmetric transcriptional preferences of VqmA proteins, essential for survival and activity of both the pathogen and the phage. The findings shed light on the intricate interplay between bacterial and phage communication systems and their impact on microbial behaviors.
Article
Chemistry, Medicinal
Elif Naz Bingol, Onur Sercinoglu, Pemra Ozbek
Summary: Antigen presentation by major histocompatibility complex (MHC) proteins to T-cell receptors (TCRs) is crucial for triggering the adaptive immune response. Computational biophysics studies have provided insights into dynamic aspects of TCR-peptide-loaded major histocompatibility complex (pMHC) interaction, but there is still a lack of understanding concerning the overall allosteric mechanism behind TCR conformational changes.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Review
Chemistry, Analytical
Weizhi Liu, Qiuyue Wu, Wencheng Wang, Xing Xu, Chaoyong Yang, Yanling Song
Summary: This article reviews the regulation of molecular recognition on a microfluidic affinity interface, focusing on strategies to improve the efficiency of molecular recognition. The strategies discussed include enhancing the encounter rate between target and affinity interface, as well as improving the binding kinetics and thermodynamics. The article also provides perspectives on future research directions and challenges.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Chaehee Park, Jinuk Kim, Seung-Bum Ko, Yeol Kyo Choi, Hyeongseop Jeong, Hyeonuk Woo, Hyunook Kang, Injin Bang, Sang Ah Kim, Tae-Young Yoon, Chaok Seok, Wonpil Im, Hee-Jung Choi
Summary: The study of the interaction mechanism between NPY and its receptor Y1R provides important molecular insights into the role of NPY in physiological processes such as food intake, stress response, and anxiety.
NATURE COMMUNICATIONS
(2022)