Article
Materials Science, Multidisciplinary
Yue Ma, Shangqi Ge, He Yang, Xiaohui Chen
Summary: This paper proposes a new non-equilibrium thermodynamics approach to model multiphysics coupling processes with reactive dissolution, aiming to overcome the potential issues of the Clausius-Duhem Inequality in modeling reactive systems. The effectiveness of the proposed method is demonstrated through numerical simulations.
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS
(2022)
Article
Chemistry, Multidisciplinary
Antonella Ciancetta, Amandeep Kaur Gill, Tianyi Ding, Dmitry S. Karlov, George Chalhoub, Peter J. McCormick, Irina G. Tikhonova
Summary: This study developed a probe confined dynamic mapping protocol to predict allosteric sites on GPCRs, demonstrating the advantage of specific probes derived from GPCR allosteric ligand structures over commonly used cosolvents in allosteric site mapping. The protocol was successfully validated retrospectively on selected receptors and prospectively on the D-2 dopamine receptor, confirming the prediction through subsequent mutagenesis. It provides a fast and efficient prediction of key amino acid residues surrounding allosteric sites in membrane proteins, aiding in the design of allosteric modulators based on protein structure.
ACS CENTRAL SCIENCE
(2021)
Article
Biochemical Research Methods
Shaun T. Lancaster, Thomas Prohaska, Johanna Irrgeher
Summary: This study proposes the use of nitrous oxide (N2O) as a non-corrosive and non-toxic alternative for calcium isotope analysis. Instrument performance testing shows that N2O can achieve equivalent detection limits and background concentrations compared to traditional gases. Further testing with synthetic standards highlights N2O's advantage in separating interferences from potassium and magnesium.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Cell Biology
Jakob Mitgau, Julius Franke, Camilla Schinner, Gabriele Stephan, Sandra Berndt, Dimitris G. Placantonakis, Hermann Kalwa, Volker Spindler, Caroline Wilde, Ines Liebscher
Summary: This study provides information on the structural requirements and forces needed for ECM-mediated activation of the GPR126 receptor. The N terminus of GPR126 acts as an allosteric module that can fine-tune receptor activation in a context-specific manner.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jaina A. Bhayani, Miguel A. Ballicora
Summary: The thermal shift assay is a powerful tool for detecting molecular interactions between proteins and ligands by tracking protein unfolding using temperature and an extrinsic fluorescent dye. A new analysis method based on equilibrium systems and the van't Hoff equation is proposed for determining Kd, showing promising results in testing with different proteins and enzymes. This method has the potential to offer broad applicability across protein classes and detect both active and allosteric site binding compounds.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Benjamin S. Cowan, David L. Beveridge, Kelly M. Thayer
Summary: Allosteric signaling in proteins has been an active area of research, and the importance of electrostatics in long-range signaling has been increasingly recognized. This study focuses on the allosteric dynamics of the PDZ protein, utilizing molecular dynamics trajectories to create networks and exploring the allosteric effect. A new metric is introduced to quantify the volume sampled by a residue in the latent space, providing insights into PDZ and the field of allostery.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Computer Science, Interdisciplinary Applications
Muath Algazlan, Mohammed Abdul Qadeer Siddiqui, Hamid Roshan
Summary: The study investigates the effects of coupled processes and gas sorption on gas flow in shale formations. A sorptive-poroelastic constitutive equation is developed using non-equilibrium thermodynamics and continuum mechanics, and numerical analyses reveal the importance of gas sorption kinetics on gas production, especially in the long term.
COMPUTERS AND GEOTECHNICS
(2022)
Article
Thermodynamics
Kai Wang, Jiahui Zhou, Yue Ma, Aizhong Ding, Xiaohui Chen
Summary: Based on the Mixture-Coupling Theory, this research derives the fully coupled Thermo-Hydro-Mechanical (THM) governing equations for dual-porosity geothermal reservoirs, addressing the interaction between strain, pore/fracture pressure and temperature. Numerical modelling is performed to study the production performance and coupled THM response in an EGS, showing that the production temperature is determined by the coupled THM effects.
APPLIED THERMAL ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Ambuj Kumar, Robert L. Jernigan
Summary: Allostery is a mechanism for transmitting signals through changes in protein fluctuations upon ligand binding, with changes seen at both binding and remote sites. The compensation between energies and entropies of binding varies widely and plays a role in regulating protein function. The allosteric relationship between peptide binding and protein dynamics can impact protein mechanism and function.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Chemistry, Analytical
Pawel Mateusz Nowak, Iwona Biel, Gabriela Kozka, Maria Klag, Michal Wozniakiewicz
Summary: The accuracy of the acid dissociation constant (pK(a)) depends on pH measurement errors. This paper investigates the influence of incorrect pH measurement on pK(a) values obtained by capillary electrophoresis (CE) and microscale thermophoresis (MST). It proposes a self-control procedure to predict the uncertainty of the acidity constant and highlights the need for alternative methods that do not require pH measurement.
MICROCHEMICAL JOURNAL
(2022)
Article
Engineering, Chemical
Zhijie Shen, Jingchun Min
Summary: The non-equilibrium thermodynamics theory is applied to analyze the transmembrane heat and moisture transfer in a membrane-type total heat exchanger. A theoretical model is developed to simulate the coupled heat and mass transfer, and the expressions for the characteristic parameters are derived. The calculations show that the membrane property and air state have significant effects on the coupling transport process.
CHINESE JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Moritz Doeker, Laura Grabowski, Dorte Rother, Andreas Jupke
Summary: Amine transaminase catalyzed reaction systems can efficiently produce metaraminol via extraction-based in situ product removal (ISPR), leading to higher yields and improved enzymatic production. By using l-alanine as an alternative amine donor and oleic acid as a sustainable reactant, a greener production route for metaraminol was established, overcoming thermodynamic limitations and achieving higher conversions.
Article
Biochemical Research Methods
Fanny C. Liu, Mark E. Ridgeway, J. S. Raaj Vellore Winfred, Nicolas C. Polfer, Jusung Lee, Alina Theisen, Christopher A. Wootton, Melvin A. Park, Christian Bleiholder
Summary: The study successfully coupled the separation capabilities of tTIMS/MS with the dissociation capabilities of UVPD for protein structure analysis, demonstrating the feasibility of dissociating intact proteins by UV irradiation at pressure conditions compatible with ion mobility spectrometry. The results highlight the analytical utility of combining tTIMS/MS with UVPD for structural proteomics.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Chemistry, Medicinal
Tianyi Ding, Dmitry S. Karlov, Almudena Pino-Angeles, Irina G. Tikhonova
Summary: In this study, allosteric modulators at the receptor-lipid interface were investigated using molecular dynamics simulations and quantum chemical calculations. The results showed that weak polar interactions and long-range electrostatics contribute to the stability of allosteric modulators at this interface. The presence of allosteric cavities can be detected in different membrane compositions, and lipid tails play a role in ligand binding pose stability and cavity size.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Mathematics, Applied
Alessio Fama, Liliana Restuccia
Summary: This article studies the propagation of coupled porosity, fluid concentration flux, and temperature waves using a model formulated in previous papers for porous media saturated by fluid flow in the framework of non-equilibrium thermodynamics. Three modes of propagation in the one-dimensional and perfect isotropic case are derived and the validity of the model is tested. The results, represented as wave propagation velocities in diagrams as functions of wave number, have applications in technological sectors such as seismology, medical sciences, geology, and nanotechnology.
ELECTRONIC JOURNAL OF DIFFERENTIAL EQUATIONS
(2021)
Article
Biochemistry & Molecular Biology
Caleb B. McDonald, Kenneth L. Seldeen, Brian J. Deegan, Vikas Bhat, Amjad Farooq
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2010)
Article
Biochemistry & Molecular Biology
David C. Mikles, Brett J. Schuchardt, Vikas Bhat, Caleb B. McDonald, Amjad Farooq
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2014)
Article
Biochemistry & Molecular Biology
Kenneth L. Seldeen, Caleb B. McDonald, Brian J. Deegan, Amjad Farooq
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2008)
Article
Biochemistry & Molecular Biology
Alexander J. Abrams, Amjad Farooq, Gaofeng Wang
Article
Biochemistry & Molecular Biology
Brett J. Schuchardt, Vikas Bhat, David C. Mikles, Caleb B. McDonald, Marius Sudol, Amjad Farooq
Article
Biochemistry & Molecular Biology
Kenneth L. Seldeen, Brian J. Deegan, Vikas Bhat, David C. Mikles, Caleb B. McDonald, Amjad Farooq
Review
Biochemistry & Molecular Biology
Marius Sudol, Caleb B. McDonald, Amjad Farooq
Review
Cell Biology
A Farooq, MM Zhou
CELLULAR SIGNALLING
(2004)
Article
Biochemistry & Molecular Biology
KL Manzur, A Farooq, L Zeng, O Plotnikova, AW Koch, Sachchidanand, MM Zhou
NATURE STRUCTURAL BIOLOGY
(2003)
Article
Biochemistry & Molecular Biology
S Mujtaba, Y He, L Zeng, A Farooq, JE Carlson, M Ott, E Verdin, MM Zhou