Review
Engineering, Biomedical
Jean -Daniel Malcor, Frederic Mallein-Gerin
Summary: This review article discusses the use of triple-helical peptides as efficient tools to improve cell-biomaterial interactions in tissue engineering. Triple-helical peptides are bioactive molecules that mimic the architectural and biological properties of collagen. They have been successfully used to specifically recognize cell-surface receptors and provide cells seeded on biomaterials with controlled biological cues. Functionalization with triple-helical peptides has enabled researchers to improve cell function for regenerative medicine applications, such as tissue repair. However, this approach still remains under-explored and most functionalization strategies reported in the literature are unable to address collagen-binding receptors.
ACTA BIOMATERIALIA
(2022)
Article
Biochemistry & Molecular Biology
Wagner A. Muller, Paul A. Beales, Andrei R. Muniz, Lars J. C. Jeuken
Summary: Hybrid vesicles combining natural phospholipids and synthetic amphiphilic copolymers have great potential in biotechnology due to their unique material properties. Molecular dynamics simulations and experiments have been used to investigate the interactions between lipids and copolymers, as well as the effects on membrane protein reconstitution and resistance to destabilization by detergents.
Article
Multidisciplinary Sciences
Katrina M. Hawley, Rachel J. Eclov, Mathew R. Schnorenberg, Yu Tian, Rhea N. Shah, Anika T. Thomas-Toth, Marie Fefferman, Gregory H. Bird, Loren D. Walensky, Matthew V. Tirrell, James L. LaBelle
Summary: Researchers investigated the use of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3 and disrupt its protein-protein interaction. They demonstrated that these peptides could inhibit Treg cell function and alter gene expression, suggesting their potential as a therapeutic approach to enhance immune responsiveness.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Qiang Shao, Muya Xiong, Jiameng Li, Hangchen Hu, Haixia Su, Yechun Xu
Summary: This study investigated the proteolysis mechanism of SARS-CoV-2 PLpro and found that the C270R mutation affects the structural dynamics and catalytic function, leading to an inhibitory effect on the enzyme.
Article
Multidisciplinary Sciences
Peng-Kai Kao, Bryan J. VanSaders, Sharon C. Glotzer, Michael J. Solomon
Summary: This research demonstrates that cyclically applied electric fields can improve the quality of colloidal crystals by annealing local disorder. The optimal off-duration for maximum annealing is found to be approximately half of the characteristic melting half lifetime of the crystalline phase. Local six-fold bond orientational order grows more rapidly than global scattering peaks, indicating that local restructuring leads to global annealing.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Analytical
Yuhong Duan, Xinrui Qiao, Lu Xu, Lina Sun, Fen Ma
Summary: A novel sandwich structure electrogenerated chemiluminescence biosensor was developed for determination of matrix metalloproteinase and its expressing cancer cells. The biosensor exhibited excellent sensitivity and a wide linear range.
MICROCHEMICAL JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Ta-Chou Huang, Wolfgang B. Fischer
Summary: A novel algorithm is proposed for assembling bitopic transmembrane domains of membrane proteins. The algorithm is tested with viral channel forming proteins and shows promising results in generating structures based on a 7-dimensional space. The assembly of TMDs can be achieved through simultaneous or sequential docking, and scoring is obtained using estimated binding energies. The algorithm improves data when using polypeptides with adapted amino acid coordinates.
Article
Chemistry, Multidisciplinary
Seung-Eun Chong, Jae Hoon Oh, Kyungjin Min, Sohyun Park, Sejong Choi, Joon Hyung Ahn, Dahyun Chun, Hyung Ho Lee, Jaehoon Yu, Yan Lee
Summary: A new vehicle is designed for intracellular delivery of antibodies at nanomolar concentrations by combining Z domain with LK sequences. The delivered IgGs can control targeted intracellular signaling pathway, showing potential for future therapeutic development.
JOURNAL OF CONTROLLED RELEASE
(2021)
Article
Chemistry, Physical
Ningning Zhang, Jan Philipp Bittner, Marius Fiedler, Thomas Beretta, Pablo Dominguez de Maria, Sven Jakobtorweihen, Selin Kara
Summary: This paper explores the effects of organic solvents on horse liver alcohol dehydrogenase (HLADH) using experimental and computational studies. The results show that different solvents have different toxicities to the enzyme, with toluene and 2-methyltetrahydrofuran being detrimental, while methyl tert-butyl ether is the optimal option. The combination of experiments and simulations can be used as useful tools to study the effects of reaction media and guide solvent selection.
Article
Chemistry, Physical
Xiufang Song, Yuxiang Bu
Summary: This study systematically investigates the effects of applied electric fields on electron transfer along peptide chains, revealing that different intensities of the electric field can modulate electron-binding abilities, molecular orbital energies, and dipole moments of alpha-helical oligopeptides. Additionally, it demonstrates that longer peptides exhibit more significant effects of the electric field, and provides new insights for modulating electron migration behaviors in protein electronics engineering.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biology
Maria C. Oliveira, Maksudbek Yusupov, Rodrigo M. Cordeiro, Annemie Bogaerts
Summary: The study reveals that hydrophilic RONS have lower barriers for permeation through nitrated membranes compared to hydrophobic RONS, indicating that nitrated membranes are more permeable during nitro-oxidative stress.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Douglas R. Walker, Ali A. Alizadehmojarad, Anatoly B. Kolomeisky, Jeffrey D. Hartgerink
Summary: There is a lack of well-understood and controllable interactions for directing the organization of collagen triple helices. Amide-pi interactions are a relatively understudied charge-free interaction that has the potential to be harnessed for triple-helix design.
Article
Chemistry, Multidisciplinary
Christopher A. Ryan, Vladislavs Baskevics, Martins Katkevics, Eriks Rozners
Summary: In triplex-forming peptide nucleic acid, a novel 2-guanidyl pyridine nucleobase (V) can recognize up to two cytosine interruptions in polypurine tracts of dsRNA by engaging the entire Hoogsteen face of C-G base pair. Insights from ab initio and molecular dynamics simulations revealed the H-bonding interactions that stabilize V · C-G triplets. Our findings provide guidance for future design of improved nucleobases, advancing the goal of recognizing any sequence of dsRNA.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Xinming Xu, Long Su, Fei Lu, Zuobing Yin, Yanan Gao, Liqiang Zheng, Xinpei Gao
Summary: This work investigates the impact of anion size and symmetry on the coordination and dynamics of lithium ions (Li+) in ionic liquid (IL) electrolytes through molecular dynamics simulations. The study finds that the formation of Li+ aggregates enhances Li+ transport in concentrated IL electrolytes, and asymmetric anions exhibit superior performance compared to symmetric anions. Additionally, dual-anion based electrolytes show faster Li+ diffusion coefficients than mono-anion based electrolytes due to the synergistic effect between mixed anions. The research highlights the role of anion structures and synergism in the design of concentrated IL-based electrolytes.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Polymer Science
Renata Ruskova, Dusan Racko
Summary: Through coarse-grained molecular dynamics simulations, the chiral sensitivity of helical channels to polymer knots was explored, showing varying levels of stereoselectivity depending on the type of knot. The magnitude of the effect can be adjusted by changing the radius of the helix, the pitch of the helix, and the strength of the pulling force. The model has applications in designing nanotechnological devices, preparing gels with tailor-made properties, and studying the diffusion of knotted DNA in biological conditions.
Article
Chemistry, Medicinal
Natalia Diaz, Dimas Suarez
Summary: This research investigates the conformational properties of unguisin A and its difluorinated stereoisomers using NMR experiments and enhanced MD techniques. The study reveals that fluorination significantly alters the secondary structure of the macrocycle, except for one diastereomer, suggesting that fluorination can select conformations accessible to the unsubstituted peptide. Computational characterization of macrocyclic peptides may thus aid in the rational design of stereoselective fluorinated peptides with fine-tuned conformation and activity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Chemistry, Physical
Fernando Jimenez-Gravalos, Dimas Suarez
Summary: In this study, a conceptual and theoretical framework of short-range electrostatic interactions is presented based on the Interacting Quantum Atoms approach. By performing energy decomposition and dispersion corrections, a pairwise approximation to the total binding energy is derived along with energetic descriptors at varying distances. This framework also proposes a consistent definition of charge penetration energy within quantum chemical topology, primarily characterized by intramolecular electrostatic energy.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Applied
Ismael Marcet, Jaime Delgado, Natalia Diaz, Manuel Rendueles, Mario Diaz
Summary: This study hydrolyzed lipoproteins using trypsin and evaluated the bioactivity of resulting peptides through in silico analysis. The transmission of valuable peptides through PES and SC membranes at different pHs was also assessed. The most promising antihypertensive peptide, K.VQWGIIPSWIK.K, was found in the permeates.
Article
Chemistry, Medicinal
Roberto Lopez, Natalia Diaz, Evelio Francisco, Angel Martin-Pendas, Dimas Suarez
Summary: The interacting quantum atoms (IQA) method allows for the decomposition of the quantum mechanical (QM) energy of a molecular system using the quantum theory of atoms in molecules framework. This method, enhanced with molecular mechanics (MM) and Poisson-Boltzmann surface-area (PBSA) solvation methods, can be extended to hybrid QM/MM methodologies. The IQA QM/MM approach has been demonstrated to successfully characterize metal-water interactions and QM/MM boundary artifacts, as well as describe covalent and noncovalent bonding interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Dimas Suarez, Natalia Diaz
Summary: Amphiphilic cyclodextrins can spontaneously form supramolecular assemblies with potential applications in drug release. Molecular dynamics simulations were used to characterize the structure, dynamics, binding properties, and aggregation capabilities of several amphiphilic derivatives of beta-cyclodextrin. The length of alkyl side chains in these derivatives plays a crucial role in determining their complexing abilities and aggregation tendencies.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Analytical
F. J. Pereira, R. Lopez, D. Suarez, A. J. Aller
Summary: This study compares the experimental Raman spectra of inorganic arsenic oxoacids in different aqueous solutions with the dry precipitates obtained from these solutions. The ability of quantum chemical methods to model the Raman spectra of the arsenic oxoacids in solution is also explored. It was found that hydrogen bridges and the coexistence of arsenic oxoacids contribute to strong overlapping in the Raman spectra of As-(III) aqueous samples compared to As-(V) samples. Furthermore, some Raman shifts of the dry arsenic precipitates correlate well with the corresponding Raman spectra of the same arsenic species in aqueous solutions, allowing for practical use of Raman spectroscopy in indirect screening of arsenic speciation in condensed phases.
MICROCHEMICAL JOURNAL
(2022)
Article
Chemistry, Analytical
R. Lopez, F. J. Pereira, D. Suarez, A. J. Aller
Summary: This study provides a comparative evaluation of the Raman spectra of four organoarsenicals in aqueous solutions under different pH conditions. It also examines the proficiency of computational chemistry in obtaining theoretical Raman spectra for these compounds. The results show that Raman spectrometry and computational chemistry can effectively identify the species and spectral features of organoarsenicals under different pH conditions.
MICROCHEMICAL JOURNAL
(2022)
Article
Chemistry, Physical
Natalia Diaz, Dimas Suarez
Summary: This study demonstrates the accuracy of estimating the entropy of flexible molecules using a partitioning approach based on rigid-rotor-harmonic-oscillator (RRHO) entropy and Gibbs-Shannon entropy. By employing discretization and expansion techniques that capture the correlation effects among torsional motions, the entropy of single molecules of varying sizes can be accurately computed. Extensive sampling, such as classical molecular dynamics simulations, is crucial for reliable entropy estimation.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Angel Martin Pendas, Evelio Francisco, Dimas Suarez, Aurora Costales, Natalia Diaz, Julen Munarriz, Tomas Rocha-Rinza, Jose Manuel Guevara-Vela
Summary: In this study, recent advances in the concept of atoms-in-molecules are reviewed from a real space perspective. The general formalism of atomic weight factors, which unifies fuzzy and non-fuzzy decompositions, is introduced. The use of reduced density matrices and their cumulants for partitioning quantum mechanical observables into atomic or group contributions is discussed. The importance of this study is 9 out of 10.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Natalia Diaz, Dimas Suarez
Summary: While computational simulations support a neutral state for the catalytic dyad of the SARS-CoV-2 main protease, a recently-reported neutron structure shows a zwitterionic form. Molecular Dynamics study reveals that the enzyme charge configuration from the neutron structure is not compatible with a catalytically-competent binding mode for peptide substrates.
CHEMICAL COMMUNICATIONS
(2021)
