Article
Chemistry, Applied
Wenfei Xiong, Ya Li, Cong Ren, Jing Li, Bin Li, Fang Geng
Summary: Investigating the thermodynamic parameters in the formation process of protein-polysaccharide complex coacervates is crucial for understanding the binding mechanism. pH, salt ion strength, and temperature were found to influence the thermodynamic parameters of gelatin (G)-pectin (P) complex coacervation. The binding between G and P involves electrostatic bonding, hydrogen bonding, and hydrophobic interactions.
FOOD HYDROCOLLOIDS
(2021)
Review
Pharmacology & Pharmacy
Iago Dillion Lima Cavalcanti, Francisco Humberto Xavier Junior, Nereide Stela Santos Magalhaes, Mariane Cajuba de Britto Lira Nogueira
Summary: Isothermal titration calorimetry (ITC) is a technique for evaluating the thermodynamic profiles of connection between two molecules, allowing the experimental design of nanoparticles systems with drugs and/or biological molecules. In the field of pharmaceutical nanotechnology, ITC has been increasingly used to understand the interaction mechanisms in the formation of nanoparticles and the behavior of nanocarriers in in vivo studies. This technique provides quick and easy results to optimize the formulation process of nano-systems.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Fanrui Sha, Tzu-Yi Tai, Madeleine A. Gaidimas, Florencia A. Son, Omar K. Farha
Summary: Isothermal titration calorimetry (ITC) is a technique for measuring the thermodynamic parameters of binding events, which has applications not only in biological macromolecules but also in synthetic systems like metal-organic frameworks (MOFs). Utilizing ITC in MOFs can provide insights into small molecule adsorption mechanisms and the formation of MOF-based composite materials through non-covalent interactions, with specific experimental considerations discussed. Furthermore, underexplored research directions related to MOFs that could benefit from ITC are highlighted.
Article
Biochemistry & Molecular Biology
Adam Jugl, Miloslav Pekar
Summary: The interactions between hyaluronan and cecropin B were investigated using high-resolution ultrasonic spectroscopy and isothermal titration calorimetry. The study found that the molecular weight of hyaluronan played a significant role in the interactions, particularly the transition between different conformations. In water, interactions were saturated at a molar charge ratio of 1.5, possibly due to steric hinderance or functional group interactions. However, in PBS, no interactions were observed, regardless of the molecular weight of hyaluronan, indicating that the interactions were suppressed at higher ionic strength.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Applied
Jingbo Liu, Jiale Chai, Ting Zhang, Yixin Yuan, Ramesh Kumar Saini, Menglei Xu, Shanle Li, Xiaomin Shang
Summary: The complexation between ovalbumin (OVA) and highly charged dextran sulfate (DS) is mainly driven by strong electrostatic interactions, with the addition of salt having diverse effects on coacervate formation. Isothermal titration calorimetry (ITC) results show that DS binds to native OVA through electrostatic forces, forming coacervates with high viscoelasticity.
FOOD HYDROCOLLOIDS
(2021)
Article
Biochemistry & Molecular Biology
Eva S. Cobos, Ignacio E. Sanchez, Lucia B. Chemes, Jose C. Martinez, Javier Murciano-Calles
Summary: PDZ domains play a crucial role in cell signaling and cell-cell junctions, being able to recognize various natural targets. The study reveals a basic specificity in each PDZ domain, with host partners mostly being able to bind their corresponding PDZ domain. Additionally, viral ligands show the ability to bind most of the studied PDZ domains, including those not previously described.
Article
Biochemistry & Molecular Biology
Shilpa Mohanakumar, Namkyu Lee, Simone Wiegand
Summary: In this study, we compared data obtained from the non-equilibrium process of thermal diffusion forced Rayleigh scattering (TDFRS) with data obtained from the equilibrium process of isothermal titration calorimetry (ITC). The results showed that the thermophoretic behavior quantified by the Soret coefficient S_T agreed with the Gibb's free energy Delta G determined in the ITC experiment. We also investigated the influence of fluorescent labeling on the binding behavior and found that the dye had a significant impact.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Falin He, Shanshan Chu, Ning Sun, Xiangxiang Li, Mingyang Jing, Jingqiang Wan, Wansong Zong, Jingchun Tang, Rutao Liu
Summary: Acrylamide interacts with lysozyme under physiological conditions, affecting the structure and function of lysozyme by unfolding polypeptide chains and decreasing alpha-helical content. The interaction is primarily driven by acrylamide's interactions with lysozyme's tryptophan and tyrosine residues, and directly affects the enzyme's active center and fluorescence sensitization phenomenon.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Engineering, Environmental
Min-Ji Kim, Yuliia Herchenova, Jaeshik Chung, Sang-Heon Na, Eun-Ju Kim
Summary: This study systematically investigates the aggregation behavior of polystyrene nanoplastics (PS NPs) under different electrolyte conditions and the impact of environmental factors on NP stability. The results show that solvation entropy plays a significant role in NP aggregation, and the stability of PS NPs is influenced by ionic strength and the presence of natural colloids.
Article
Thermodynamics
Federica D'Aria, Bruno Pagano, Concetta Giancola
Summary: Cyclodextrins (CDs) have been shown to improve the stability, solubility, and bioavailability of various molecules, with low toxicity for different routes of administration. Isothermal titration calorimetry (ITC) is a key method for studying cyclodextrin/guest interaction, providing important thermodynamic parameters simultaneously.
JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY
(2022)
Article
Biotechnology & Applied Microbiology
Shams T. A. Islam, Jie Zhang, Fabio Tonin, Renske Hinderks, Yanthi N. Deurloo, Vlada B. Urlacher, Peter-Leon Hagedoorn
Summary: Lignin valorization through laccase catalysis can release aromatic products, but different enzymes exhibit significant variations in conversion efficiency and rate. Trametes versicolor laccase follows Michaelis-Menten kinetics in converting Kraft lignin, with specific thermodynamic and kinetic parameters, making it a promising tool for guiding enzymatic lignin valorization strategies.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Chemistry, Physical
Pablo F. Garrido, Margarida Bastos, Adrian Velazquez-Campoy, Alfredo Amigo, Philippe Dumas, Angel Pineiro
Summary: The injection of air into an isothermal titration calorimeter's sample cell allows for accurate determination of the surface tension of the target liquid, despite the periodic contribution from bubbles. The new algorithm successfully identifies and analyzes these contributions, improving the analysis of calorimetric signals.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Robert Kerep, Tino Seba, Valentina Borko, Tin Weitner, Toma Keser, Gordan Lauc, Mario Gabricevic
Summary: Human serum alpha-1 acid glycoprotein is involved in the binding and transport of many drugs. Sialic acid groups play a major role in drug binding. The study found that different sialylation can result in different binding affinities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Aaron M. N. Joiner, Ben P. Phillips, Kumar Yugandhar, Ethan J. Sanford, Marcus B. Smolka, Haiyuan Yu, Elizabeth A. Miller, J. Christopher Fromme
Summary: The study revealed the regulation of Rab1 activation by the TRAPPIII complex, with the Trs85 subunit serving as a membrane anchor for the entire complex via its amphipathic helix. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
Article
Biochemistry & Molecular Biology
Kiran S. Toti, John R. Jimah, Veronica Salmaso, Jenny E. Hinshaw, Kenneth A. Jacobson
Summary: This study investigates the impact of the North and South conformations of guanine nucleotides on dynamin-mediated membrane constriction and reveals that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, natural dynamin structures predominantly exhibit the (S)-conformation, presenting a mismatch with the required (N) vs. (S) for GTP analogues in the dynamin-mediated process.
Article
Biochemistry & Molecular Biology
Mervi T. Hyvonen, Olga A. Smirnova, Vladimir A. Mitkevich, Vera L. Tunitskaya, Maxim Khomutov, Dmitry S. Karpov, Sergey P. Korolev, Merja R. Hakkinen, Marko Pietila, Marina B. Gottikh, Jouko Vepsalainen, Leena Alhonen, Alexander A. Makarov, Sergey N. Kochetkov, Heather M. Wallace, Tuomo A. Keinanen, Alex R. Khomutov
Summary: The polyamines spermine and spermidine are crucial for cell growth and function. This study demonstrates that a protein called OAZ1 inhibits polyamine uptake and targets an enzyme involved in polyamine biosynthesis for degradation. The study also reveals that polyamines induce the dimerization of OAZ1 and this dimerization is modulated by certain chemicals. These findings provide new insights into the regulation of polyamine homeostasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra V. Petrovskaya, Artem M. Tverskoi, Evgeny P. Barykin, Kseniya B. Varshavskaya, Alexandra A. Dalina, Vladimir A. Mitkevich, Alexander A. Makarov, Irina Yu. Petrushanko
Summary: The breakdown of the blood-brain barrier in Alzheimer's disease promotes the accumulation of beta-amyloid peptide in the brain. Different forms of this peptide have varying effects on the redox status and mitochondrial function of brain endothelial cells, which play a role in BBB breakdown.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Hedvig Tamman, Karin Ernits, Mohammad Roghanian, Andres Ainelo, Christina Julius, Anthony Perrier, Ariel Talavera, Hanna Ainelo, Remy Dugauquier, Safia Zedek, Aurelien Thureau, Javier Perez, Gipsi Lima-Mendez, Regis Hallez, Gemma C. Atkinson, Vasili Hauryliuk, Abel Garcia-Pino
Summary: Stringent factors regulate bacterial cell reprogramming by increasing the level of (p)ppGpp. This study presents the crystal structure of the hydrolase-only SpoT from Acinetobacter baumannii and reveals the intramolecular regulation mechanism of 'long'-stringent factors. The Core subdomain plays a key role in determining the specialization of long RelA-SpoT homologs towards synthesis or hydrolysis.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Andres Ainelo, Julien Caballero-Montes, Ondrej Bulvas, Karin Ernits, Kyo Coppieters't Wallant, Hiraku Takada, Sophie Z. Craig, Gabriel Mazzucchelli, Safia Zedek, Iva Pichova, Gemma C. Atkinson, Ariel Talavera, Chloe Martens, Vasili Hauryliuk, Abel Garcia-Pino
Summary: In this study, the crystal structure of the DarB2:RelNTD2 complex was determined to uncover how DarB interacts with the SYNTH domain of Rel to stimulate (p)ppGpp synthesis directly. Binding to c-di-AMP rigidifies DarB, imposing an entropic penalty that precludes DarB-mediated control of Rel during normal growth. These experiments provide insights into the allosteric regulation mechanism of Rel stringent factors independent of amino acid starvation.
Article
Oncology
Olga A. Smirnova, Olga N. Ivanova, Irina T. Fedyakina, Gaukhar M. Yusubalieva, Vladimir P. Baklaushev, Dmitry V. Yanvarev, Olga I. Kechko, Vladimir A. Mitkevich, Pavel O. Vorobyev, Vyacheslav S. Fedorov, Birke Bartosch, Vladimir T. Valuev-Elliston, Anastasiya L. Lipatova, Alexander V. Ivanov
Summary: This study found that the novel coronavirus can infect liver cancer cells and certain types of brain tumor cells, but not normal liver cells. Additionally, the study found that viral infection may lead to a decrease in the differentiation level of liver cells. Overall, these results suggest that liver dysfunction during COVID-19 is not caused by SARS-CoV-2 infection, and tumors may potentially serve as reservoirs for the virus during infection.
Article
Biology
Evgeny P. Barykin, Dmitry V. Yanvarev, Maria A. Strelkova, Vladimir T. Valuev-Elliston, Kseniya B. Varshavskaya, Vladimir A. Mitkevich, Alexander A. Makarov
Summary: Phosphorylation of beta-amyloid peptide affects its neurotoxicity, oligomerisation, amyloidogenicity, and other pathogenic properties. The production and regulation of phosphorylated A beta have not been studied in detail previously. This study demonstrated that HEK293 cells can robustly phosphorylate A beta, likely with contribution from casein kinase 2, whereas in bEnd.3 cells, the activity of A beta phosphorylation is relatively low.
Article
Biochemistry & Molecular Biology
Viktoriia E. Baksheeva, Veronika V. Tiulina, Elena N. Iomdina, Sergey Yu. Petrov, Olga M. Filippova, Nina Yu. Kushnarevich, Elena A. Suleiman, Remi Eyraud, Francois Devred, Marina V. Serebryakova, Natalia G. Shebardina, Dmitry V. Chistyakov, Ivan I. Senin, Vladimir A. Mitkevich, Philipp O. Tsvetkov, Evgeni Yu. Zernii
Summary: Primary open-angle glaucoma (POAG) is a common neurodegenerative disorder that causes blindness and is characterized by optic nerve and retinal ganglion cell damage. Early detection and treatment of the disease are crucial, but difficult due to its asymptomatic nature and lack of objective diagnostic approaches. Recent studies have shown that glaucoma involves complex metabolomic and proteomic changes in eye liquids, including tear fluid. However, the analysis of tear fluid is technically challenging and not suitable for clinical practice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Yaroslava M. M. Chalenko, Daria A. A. Slonova, Olga I. I. Kechko, Egor V. V. Kalinin, Vladimir A. A. Mitkevich, Svetlana A. A. Ermolaeva
Summary: The virulence factor InlB of Listeria monocytogenes interacts specifically with the receptors c-Met and gC1q-R. This study examines the effects of different isoforms of InlB on L. monocytogenes uptake and intracellular proliferation in human macrophages. The isoform idInlB(CC1) exhibits the highest efficiency in macrophage proliferation compared to other isoforms. Pretreatment of macrophages with idInlB(CC1) impairs macrophage functions, decreasing pathogen uptake and improving its intracellular multiplication.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Nozomu Obana, Hiraku Takada, Caillan Crowe-McAuliffe, Mizuki Iwamoto, Artyom A. Egorov, Kelvin J. Y. Wu, Shinobu Chiba, Victoriia Murina, Helge Paternoga, Ben I. C. Tresco, Nobuhiko Nomura, Andrew G. Myers, Gemma C. Atkinson, Daniel N. Wilson, Vasili Hauryliuk
Summary: This study investigates genome-encoded antibiotic resistance ABC proteins from different bacteria and discovers their resistance spectrum and mechanisms, which are important for understanding the diversity of intrinsic antibiotic resistance in bacteria.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Engineering, Environmental
Veljo Kisand, Peeter Laas, Kadi Palmik-Das, Kristel Panksep, Helen Tammert, Leena Albreht, Hille Allemann, Lauri Liepkalns, Katri Vooro, Christian Ritz, Vasili Hauryliuk, Tanel Tenson
Summary: Taking advantage of Estonia's small size and population, a wastewater-based epidemiology approach was used to monitor the spread of SARS-CoV-2, with weekly nation-wide updates released. Results showed that the concentration of the virus in wastewater correlated with the number of COVID-19 infections in the population, and the increase in virus concentration preceded the increase in positive cases by approximately 1.25 weeks (9 days). The surveillance system in Estonia helped inform public health policies and interventions during the COVID-19 pandemic.
Article
Microbiology
Anna Maria Giuliodori, Riccardo Belardinelli, Melodie Duval, Raffaella Garofalo, Emma Schenckbecher, Vasili Hauryliuk, Eric Ennifar, Stefano Marzi
Summary: Escherichia coli CspA is an RNA binding protein that stimulates translation, including its own, during cold-shock. It specifically promotes the translation of cspA mRNA at low temperature by interacting with the folded conformation less accessible to the ribosome without inducing large structural rearrangements. This interaction allows the progression of ribosomes during the transition from translation initiation to elongation, and a similar mechanism may be responsible for CspA-dependent translation stimulation observed with other probed mRNAs.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maxim A. Khomutov, Arthur I. Salikhov, Vladimir A. Mitkevich, Vera L. Tunitskaya, Olga A. Smirnova, Sergey P. Korolev, Alexander O. Chizhov, Marina B. Gottikh, Sergey N. Kochetkov, Alex R. Khomutov
Summary: The biogenic polyamines, spermidine (Spd) and spermine (Spm), are essential for regulating vital cellular functions and are present in high concentrations in all eukaryotic cells. In this study, convenient gram-scale syntheses of C-methylated analogs of Spd were described, which could be used to investigate the cellular functions of polyamines and their metabolism. The biochemical properties of these compounds and the potential for regulating their activity by modifying their structure were discussed.
Article
Multidisciplinary Sciences
Janani Durairaj, Andrew M. Waterhouse, Toomas Mets, Tetiana Brodiazhenko, Minhal Abdullah, Gabriel Studer, Gerardo Tauriello, Mehmet Akdel, Antonina Andreeva, Alex Bateman, Tanel Tenson, Vasili Hauryliuk, Torsten Schwede, Joana Pereira
Summary: The AlphaFold database provides millions of predicted protein structures, covering almost all known proteins. By utilizing deep learning techniques, these structures can be accurately predicted, shedding light on the functions and roles of these proteins in biology. This study further explores the discovery of new protein families through these predicted structures.
Article
Biochemical Research Methods
Lucia Dominguez-Molina, Ariel Talavera, Albinas Cepauskas, Tatsuaki Kurata, Dannele Echemendia-Blanco, Vasili Hauryliuk, Abel Garcia-Pino
Summary: This study reports the production, biophysical analysis, and crystallization of the aTfaRel2/faRel2 operon from Coprobacillus sp. D7, which encodes a bicistronic type II toxin-antitoxin module. The structures of the antitoxin ATfaRel2, toxin FaRel2, and the ATfaRel2-FaRel2 complex were determined through crystallography. These findings provide insights into the structure and function of this TA module.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Infectious Diseases
Tetiana Brodiazhenko, Kathryn Jane Turnbull, Kelvin J. Y. Wu, Hiraku Takada, Ben I. C. Tresco, Tanel Tenson, Andrew G. Myers, Vasili Hauryliuk
Summary: In this study, we found that the newly developed lincosamide iboxamycin showed high activity against Listeria monocytogenes and could overcome the resistance caused by VgaL/Lmo0919 ABCF ATPase. Iboxamycin displayed a pronounced post-antibiotic effect and showed potential as a novel antilisterial agent. However, the emergence and spread of ABCF ARE variants capable of defeating next-generation lincosamides should be closely monitored.
JAC-ANTIMICROBIAL RESISTANCE
(2022)