Article
Immunology
Zehua Sun, Wei Li, John W. Mellors, Rimas Orentas, Dimiter S. Dimitrov
Summary: A large size human antibody VH domain library was constructed based on thermo-stable, aggregation-resistant scaffolds, and binders against various viral and tumor targets were isolated. This study demonstrates the potential applications of antibody domains derived from library screens in therapeutics.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Huziel E. Sauceda, Valentin Vassilev-Galindo, Stefan Chmiela, Klaus-Robert Mueller, Alexandre Tkatchenko
Summary: Nuclear quantum effects (NQE) can enhance both intra- and intermolecular interactions, leading to dynamic stabilization of molecules at finite temperature. This includes strengthening of specific interactions, localization of molecular rotors, and enhanced van der Waals forces, resulting in unique bonding patterns, hindered rotor dynamics, and molecular stiffening.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Xiaojie Chu, Wei Li, Margaret G. Hines, Ilya Lyakhov, John W. Mellors, Dimiter S. Dimitrov
Summary: The high expression of uPAR is associated with tumor progression, invasion, and metastasis in various types of cancer. Our study identified two anti-uPAR domain antibodies that exhibit potent killing of uPAR-positive cancer cells, making them promising candidates for treating uPAR positive cancers.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biology
Zahra Bahrami Dizicheh, I-Ling Chen, Patrick Koenig
Summary: By analyzing variable domain structures from llamas and alpacas, it was found that VHHs can be classified into two large structural clusters based on their CDR-H3 conformation. Extended CDR-H3 loops protrude into the solvent, while kinked CDR-H3 loops fold back onto framework regions. The CDR-H3 conformation of VHHs correlates with the germline from which the antibodies are derived.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Rishika Rai, Ravichandran Khazeber, Kana M. Sureshan
Summary: A covalent helical polymer was synthesized by biomimicry, which exhibited high strength and load-bearing capacity in its single crystals, making it suitable for various technological applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Analytical
Jinhua Dong, Bhagat Banwait, Hiroshi Ueda, Peter Kristensen
Summary: Quenchbodies, a type of biosensor, use antibodies labeled with a fluorescent dye to detect proteins. The dye is quenched in the absence of an antigen, but de-quenched in its presence. This study demonstrates the development of mini Q-bodies using a single-domain heavy chain V-H antibody and different dyes. The results confirm the applicability of this method in detecting proteins.
Article
Medicine, Research & Experimental
Xiaojie Chu, Wei Li, Margaret G. Hines, Ilya Lyakhov, John W. Mellors, Dimiter S. Dimitrov
Summary: The elevated expression of GPNMB and VCAM-1 has been associated with poor prognosis and increased cancer metastasis in various types of cancer. In this study, two high-affinity specific human VH domain antibody candidates, 87 (GPNMB) and 1B2 (VCAM-1), were isolated and converted to VH-Fc to increase avidity. Domain-based bispecific T-cell engagers (DbTE) based on these antibodies showed potent killing against GPNMB and VCAM-1-positive cancer cells. Therefore, these domain antibodies are promising therapeutic candidates for cancers expressing GPNMB or VCAM-1.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Physical
Heng Sun, Yichen Tian, Yuna Fu, Yongrong Lei, Yani Wang, Xinrui Yan, Jianhua Wang
Summary: In this study, the protein-protein interactions (PPIs) between Bcl-2 and BAX were investigated using atomic force microscopy-based single-molecule force spectroscopy (SMFS) and in silico approaches. The researchers found that the binding between BAX and Bcl-2 is mediated by specific and non-specific forces, leading to the formation of stable complexes. This study provides valuable insights into the molecular mechanisms of BAX-Bcl-2 interactions and has implications for the design of PPI inhibitors.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Geochemistry & Geophysics
Christine V. Putnis, Encarnacion Ruiz-Agudo
Summary: The rapid increase of nanoparticles in the environment is largely due to anthropogenic activities such as industrialization, accelerated mining activities, plastic waste manufacturing, overuse of fertilizers and pesticides, and pharmaceutical production. Recent research focuses on the formation of nanoparticles via non-classical growth mechanisms and potential environmental remediation strategies. Advances in analytical techniques allow for the imaging of nanoparticles as presented in this review.
Article
Chemistry, Multidisciplinary
Kingshuk Dutta, Pintu Kanjilal, Ritam Das, Sankaran Thayumanavan
Summary: An electrostatics-enhanced covalent self-assembly strategy was developed to generate polymer-protein/antibody nanoassemblies, which efficiently encapsulated proteins and antibodies and delivered functional antibodies to the cytosol, exerting their biological activity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Editorial Material
Crystallography
Alexander S. Novikov
Summary: This editorial announces a special issue on the theoretical investigation of non-covalent interactions in crystals. The special issue covers the latest progress in data science, artificial intelligence, quantum and computational chemistry, and highlights the main successes in the field of fundamental theoretical studies of non-covalent interactions over the past year.
Article
Materials Science, Multidisciplinary
Lazar Novakovic, Dean Sayre, Daniel Schacher, Ranga P. Dias, Ashkan Salamat, Keith Lawler
Summary: Recent developments in high temperature superconducting materials have highlighted the importance of numerical evaluation of the superconducting transition temperature (Tc) as a means of identification. Existing methods often do not agree with each other or experiment, possibly due to the neglect of dispersion interactions. This study evaluates the effect of dispersion interactions on the predicted superconducting properties of covalent superhydride materials and finds that dispersion has a sizable effect on increasing the electron-phonon coupling.
Article
Chemistry, Physical
Dominic A. Sirianni, Xiao Zhu, Doree F. Sitkoff, Daniel L. Cheney, C. David Sherrill
Summary: High-level quantum chemical computations provide significant insight into the nature of non-covalent interactions. Previous studies have mainly focused on gas-phase computations, but non-covalent interactions frequently occur in complex chemical environments. This study examines the pi-pi interactions in an aqueous solution and analyzes how the solvent molecules affect these interactions. The results show that the nearby solvent molecules have little effect on the direct solute-solute interactions, except for charged solutes, indicating that the differences in binding energies between the gas phase and solution phase are primarily due to the competition between solute-solute and solute-solvent interactions.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Debanjana Chakraborty, Chao Yang, Lijuan Wang, Dongping Zhong
Summary: The repair of a CPD structural isomer with a sugar replacement was investigated, and a decrease in binding efficiency and repair quantum yield was observed. Using femtosecond spectroscopy and molecular dynamics simulations, it was found that the sugar replacement disrupted the lesion binding configuration and weakened the electronic coupling between the cofactor and lesion. These findings highlight how CPD photolyases have optimized their interactions to maximize repair yields.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Analytical
Lidia N. Gomez-Arribas, Augusto Juste-Dolz, Riikka Peltomaa, David Gimenez-Romero, Sergi Morais, Rodrigo Barderas, Carmen Cuadrado, Angel Maquieira, Elena Benito-Pena, Maria C. Moreno-Bondi
Summary: Phage display technology has become a powerful tool for antibody discovery, selecting specific binders for a given antigen from combinatorial libraries. High-affinity VH antibody fragments identified as PHA binders (with apparent association constants ranging from 108 to 1010 M^-1) through QCM-D measurements and PCA, enable evaluation and identification of clone clusters with similar binding characteristics and molecular interaction mechanisms with capabilities beyond conventional techniques.
SENSORS AND ACTUATORS B-CHEMICAL
(2021)
