Article
Nanoscience & Nanotechnology
Quanyong Cheng, Jingyi Chen, Chuchu Wan, Yuhang Song, Caili Huang
Summary: This study reports a facile route to prepare Janus droplets and hydrogels via aqueous two-phase systems (ATPS). The Janus droplets with different morphologies can be well controlled by manipulating the concentrations of polymers on the phase diagram. The introduction of monomers and/or nanoparticles in ATPS droplets followed by photopolymerization enables the synthesis of Janus hydrogel particles with diverse functionalities.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Biochemistry & Molecular Biology
Pedro P. Madeira, Amber R. Titus, Luisa A. Ferreira, Alexander I. Belgovskiy, Elizabeth K. Mann, Jay Adin Mann, William V. Meyer, Anthony E. Smart, Vladimir N. Uversky, Boris Y. Zaslavsky
Summary: Analysis using attenuated total reflection-Fourier transform infrared spectroscopy revealed that each coexisting phase in aqueous two-phase systems has a unique arrangement of hydrogen bonds. The specific arrangements vary depending on the solutes present in the system, and are correlated with the differences in hydrophobic and electrostatic properties of the phases in the systems studied. This suggests that the arrangement of hydrogen bonds may play a significant role in phase separation.
Article
Chemistry, Physical
Samaneh Fathi Darani, Farzaneh Ghazizadeh Ahsaie, Gholamreza Pazuki, Shiva Abdolrahimi
Summary: This study investigated the potential use of copolymers in aqueous two-phase systems, and the effect of UCON copolymer ATPS on the partitioning of doxorubicin. The results showed that the molecular weight of dextran affects the partition coefficient, while pH has minimal impact, and increasing the weight fraction of UCON enhances the partitioning of doxorubicin.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Green & Sustainable Science & Technology
Dipak Kumar Kanaujiya, Kannan Pakshirajan
Summary: This study investigates the biodegradation of DMP and DEP using a TPPB system. The results demonstrate that Cellulosimicrobium funkei can efficiently degrade these endocrine disrupting chemicals, highlighting the potential of the TPPB system for detoxification in the environment.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Biotechnology & Applied Microbiology
Antonina dos Santos, Paula Gabrielly Campos Gomes, Filipe Smith Buarque, Cleide Mara Faria Soares, Thiago Rodrigues Bjerk, Alvaro Silva Lima
Summary: This study investigated the effect of different extracting agents on the extraction of phenolic compounds from agro-industrial residues of seriguela. The results showed that 1,3-dioxolane and [C2mim][CH3SO3] were the best organic solvent and ionic liquid, respectively, and phase separation could be achieved by adding an organic solvent.
FOOD AND BIOPRODUCTS PROCESSING
(2023)
Article
Chemistry, Multidisciplinary
Raagya Arora, Umesh Waghmare, C. N. R. Rao
Summary: This study investigates various 2D lattices of Group IV chalcogenides to understand the nature of metavalent bonding (MVB). It is found that honeycomb lattices adhere to the 8-N rule and exhibit covalent bonding, while square and orthorhombic structures display in-plane MVB driven by p-p orbital interactions, with cationic lone pairs inducing out-of-plane puckering.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Kirill S. Nikolsky, Liudmila I. Kulikova, Denis V. Petrovskiy, Vladimir R. Rudnev, Kristina A. Malsagova, Anna L. Kaysheva
Summary: Protein modifications can affect protein structure and function. Phosphorylation, a common modification, can cause local structural changes in proteins. This study compared protein structural changes in different amino acid residues near the modification site and found that phosphorylation can lead to pronounced local structural changes.
Article
Materials Science, Multidisciplinary
Qingbin Yang, Jing Ge, Mengmeng Qin, Hui Wang, Xiaoyu Yang, Xinlei Zhou, Bo Zhang, Yiyu Feng, Wei Feng
Summary: This study investigated the characteristics of three asymmetric alkoxy-substituted azobenzene molecules in terms of crystallization and isomerization. It was found that by optimizing molecular structures and interactions, phase-change azobenzene derivatives can be designed for ideal energy storage systems at different temperatures.
SCIENCE CHINA-MATERIALS
(2023)
Article
Biochemical Research Methods
Gregor Urban, Christophe N. Magnan, Pierre Baldi
Summary: Accurate prediction of protein secondary structure and solvent accessibility is crucial for studying protein evolution, structure, and predicting 3D protein structure. This study presents an improved version of SSpro/ACCpro predictors that utilize deep learning and enhanced features to achieve higher accuracy compared to previous versions.
Article
Computer Science, Interdisciplinary Applications
Mehdi Vahab, Mark Sussman, Kourosh Shoele
Summary: This paper presents a numerical approach for the modeling and simulation of fluid-structure interaction in multi-material and multi-phase systems with potential phase-changes dynamics. The method couples the Eulerian multi-material solver to the Lagrangian structural solver using an immersed boundary technique to enforce boundary conditions at the interface between fluids and structures, maintaining efficiency of the solution algorithm. The technique includes modeling phase-change dynamics and a systematic stability criterion for the coupled problems, tested with multiple canonical problems.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Kohki Fujikawa, Youjung Han, Tsukiho Osawa, Shoko Mori, Kaoru Nomura, Maki Muramoto, Ken-ichi Nishiyama, Keiko Shimamoto
Summary: MPIase is a glycolipid involved in membrane protein integration in Escherichia coli's inner membrane. To address the limitations of natural MPIase, we synthesized MPIase analogs and studied their structure-activity relationship. Our findings showed the role of distinctive functional groups and the effect of MPIase glycan length on membrane protein integration activity. Furthermore, we observed the synergistic effects of these analogs with the membrane chaperone/insertase YidC, as well as the chaperone-like activity of the phosphorylated glycan. These results confirm a translocon-independent membrane integration mechanism in E. coli's inner membrane, where MPIase captures hydrophobic nascent proteins, prevents aggregation, attracts proteins to the membrane surface, and delivers them to YidC to regenerate its own integration activity.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Multidisciplinary Sciences
Hsi-En Tsao, Shu Nga Lui, Anthony Hiu-Fung Lo, Shuai Chen, Hiu Yan Wong, Chi-Kin Wong, Liwen Jiang, Kam-Bo Wong
Summary: In Arabidopsis, vacuolar sorting receptor isoform 1 (VSR1) plays a key role in directing 12S globulins and other storage proteins to the protein storage vacuoles during seed development. The crystal structure of VSR1-PA in complex with the C-terminal pentapeptide of cruciferin 1 sheds light on the molecular mechanisms involved in the sorting process. The study provides insights into how VSR1 recognizes and interacts with the C-terminal sorting determinants of various storage proteins, which could potentially aid in targeting recombinant proteins to seed storage vacuoles.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Jaran Patchimpet, Kanokphorn Sangkharak, Apiluck Eiad-ua, Sappasith Klomklao
Summary: The study investigated the recovery and partitioning of lipase from Nile tilapia viscera using a T-ATPS system, achieving high yield and partial purification of lipase by optimizing different partitioning parameters and conditions. Ultrasound was found to enhance the activity of lipase, demonstrating its potential as a technology for lipase recovery.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Green & Sustainable Science & Technology
Qian Li, Keping Zhang, Liangcheng Yang, Lichao Lu, Xianwang Kong, Xiangyu Zhao, Jianmeng Chen, Dongzhi Chen
Summary: Two-phase partitioning biotechnology is an effective method for enhancing the purification of hydrophobic waste-gas. However, current non-aqueous phases have limitations such as difficulty in recovery and low affinity for hydrophobic pollutants. In this study, a nano silicon oil-based ferrofluid was synthesized and used as an innovative non-aqueous phase liquid for the removal of gaseous n-hexane, achieving high removal efficiency and easy recovery.
JOURNAL OF CLEANER PRODUCTION
(2023)
Article
Biochemical Research Methods
Menglian Wu, Xiangcen Chen, Kaifeng Du
Summary: This study proposes a novel method for preparing cellulose monoliths using an aqueous two-phase system without any organic solvents and surfactants. The obtained cellulose monolith exhibits a porous structure with a large surface area. Functionalized cellulose monoliths show potential as adsorbents.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemistry & Molecular Biology
Ilaria Camponeschi, Achille Damasco, Vladimir N. Uversky, Alessandro Giuliani, Michele M. Bianchi
Summary: The interaction between environment and life is a key topic in biological sciences, with biological rhythms existing across all levels of organisms. This study demonstrates a significant increase in heritable phenotypic changes in yeast growing under 12-hour light/dark cycles, suggesting a potential role of intrinsic disorder-driven interactions in mediating environment/biological resonance phenomena.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Review
Biochemistry & Molecular Biology
Raied A. Badierah, Vladimir N. Uversky, Elrashdy M. Redwan
Summary: Extracellular vesicles, including exosomes, are membrane-encapsulated particles released by cells with diverse biological functions. Disease-specific exosomes may facilitate pathological cell-cell communication. Viruses can manipulate the exosome biogenesis system to promote infection spread.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Eduard Y. Kostetsky, Vladimir N. Uversky
Summary: This study discusses the formation of the matrix mechanism in protocells, focusing on the involvement of mineral complexes and gas phase radicals. The structures of apatite and carbonate-apatite play a role in determining the formation of DNA and RNA, while organic matter gradually replaces the mineral matrix. The study provides a detailed description of the preparation and launch of the matrix mechanism, as well as discussing several related issues.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Letter
Biochemistry & Molecular Biology
Vladimir N. Uversky, Fatma Elrashdy, Abdullah Aljadawi, Elrashdy M. Redwan
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Zhihua Du, Xiangdong Xiao, Vladimir N. Uversky
Summary: In this article, the authors propose a new deep learning method called DeepA-RBPBS for predicting the binding site of RNA-binding proteins (RBP) using RNA sequences and structural features. The performance of DeepA-RBPBS is found to be better than the state-of-the-art predictor iDeepS in terms of MCC and AUC scores. The method is also successfully applied to predict target RNA data of RBPs related to diabetes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Gerard Kian-Meng Goh, Vladimir N. Uversky
Summary: This article discusses the significant impact of intrinsic disorder in the outer shell of HIV on vaccine development and proposes a new model for vaccine design. Traditional viruses typically do not have high levels of intrinsic disorder in their outer shells, allowing for successful establishment of effective vaccines.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Agriculture, Dairy & Animal Science
Elrashdy M. Redwan, Abdullah A. Aljadawi, Vladimir N. Uversky
Summary: Egg yolk immunoglobulin Y (IgY) is not only a common food component but also has essential therapeutic potentials in fighting infections. This study developed a fast, simple, cost-effective, and efficient protocol for IgY isolation from chicken egg yolks, which can contribute to the control and passive cure of infectious diseases of bacterial and viral origin in humans and animals.
Review
Chemistry, Multidisciplinary
Angel Serrano-Aroca, Kazuo Takayama, Alberto Tunon-Molina, Murat Seyran, Sk Sarif Hassan, Pabitra Pal Choudhury, Vladimir N. Uversky, Kenneth Lundstrom, Parise Adadi, Giorgio Palu, Alaa A. A. Aljabali, Gaurav Chauhan, Ramesh Kandimalla, Murtaza M. Tambuwala, Amos Lal, Tarek Mohamed Abd El-Aziz, Samendra Sherchan, Debmalya Barh, Elrashdy M. Redwan, Nicolas G. Bazan, Yogendra Kumar Mishra, Bruce D. Uhal, Adam Brufsky
Summary: There is an urgent need for therapeutic options for COVID-19, caused by the highly pathogenic SARS-CoV-2, particularly for viral pneumonia and respiratory distress syndrome. Current treatments have limited efficacy, and antibiotic resistance in pneumonia treatment is escalating rapidly. Carbon-based nanomaterials show promise as alternative therapeutics with their broad-spectrum antimicrobial activity and low risk of resistance.
Editorial Material
Cell Biology
Sarah E. Bondos, A. Keith Dunker, Vladimir N. Uversky
Summary: The sequence -> structure -> function paradigm is primarily applicable to enzymes, transmembrane proteins, and signaling domains, while the sequence -> IDP/IDR ensemble -> function paradigm is primarily applicable to signaling and regulatory proteins and regions. Disorder contributes to signaling in a broad spectrum of species, playing diverse roles in responding to signals and orchestrating organismal processes.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Environmental Sciences
Sk Sarif Hassan, Pallab Basu, Elrashdy M. Redwan, Kenneth Lundstrom, Pabitra Pal Choudhury, Angel Serrano-Aroca, Gajendra Kumar Azad, Alaa A. A. Aljabali, Giorgio Palu, Tarek Mohamed Abd El-Aziz, Debmalya Barh, Bruce D. Uhal, Parise Adadi, Kazuo Takayama, Nicolas G. Bazan, Murtaza Tambuwala, Amos Lal, Gaurav Chauhan, Wagner Baetas-da-Cruz, Samendra P. Sherchan, Vladimir N. Uversky
Summary: This study tracked the emergence of mutations in SARS-CoV-2 proteins globally and in six model countries, revealing that since October 2020, frequent mutations have been observed mainly in ORF7b and ORF8. Interestingly, no high-frequency mutations were found in the UK, India, and Brazil, which does not correlate with the virus's transmission in these countries.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Faisal Nabi, Owais Ahmad, Yawar Ali Khan, Anas Nabi, Hashmi Md Amiruddin, Faizan Abul Qais, Aiman Masroor, Malik Hisamuddin, Vladimir N. Uversky, Rizwan Hasan Khan
Summary: The study screened FDA-approved drugs against SARS-CoV-2 proteins and found potential interactions with anticancer, antipsychotic, and antiviral drugs. Molecular dynamics simulations revealed protein evolution upon drug interaction, and a phylogenetic analysis was conducted on 43 coronavirus strains infecting 12 mammalian species.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Review
Biochemistry & Molecular Biology
Liberato Marzullo, Maria C. Turco, Vladimir N. Uversky
Summary: The Bcl-2 associated athanogene (BAG) family of proteins in humans exhibit exceptional multifunctionality and binding promiscuity, playing a role in the pathogenesis of various diseases. The presence of multiple isoforms and extensive posttranslational modifications can be explained through the concept of intrinsic disorder, which allows for a broad spectrum of interactions with diverse binding partners. Understanding the functional roles of BAG proteins from a perspective of protein intrinsic disorder provides insights into their multifunctionality and relation to disease pathogenesis.
JOURNAL OF CELLULAR BIOCHEMISTRY
(2022)
Review
Biochemistry & Molecular Biology
Oyku Irem Balli, Vladimir N. Uversky, Serdar Durdagi, Orkid Coskuner-Weber
Summary: Experimenters face challenges in analyzing glycoproteins due to their structural complexity, but computational studies have been used to complement experimental results. However, recent investigations have shown that computational studies also have significant challenges. Future developments in computational biochemistry and biology are necessary to provide more accurate analyses of glycoprotein structures.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Kenneth Lundstrom, Debmalya Barh, Bruce D. Uhal, Kazuo Takayama, Alaa A. A. Aljabali, Tarek Mohamed Abd El-Aziz, Amos Lal, Elrashdy M. Redwan, Parise Adadi, Gaurav Chauhan, Samendra P. Sherchan, Gajendra Kumar Azad, Nima Rezaei, Angel Serrano-Aroca, Nicolas G. Bazan, Sk Sarif Hassan, Pritam Kumar Panda, Pabitra Pal Choudhury, Damiano Pizzol, Ramesh Kandimalla, Wagner Baetas-da-Cruz, Yogendra Kumar Mishra, Giorgio Palu, Adam M. Brufsky, Murtaza M. Tambuwala, Vladimir N. Uversky
Summary: The European Medicines Agency has approved four different types of COVID-19 vaccines, which play an important role in preventing COVID-19. However, in some individuals, adverse reactions such as thrombosis with associated thrombocytopenia may occur. These events may be related to interactions between viral proteins and receptors, viral vector interactions with antibodies, and individual immune mechanisms, especially requiring validation in risk groups.
Article
Chemistry, Physical
Pedro P. Madeira, Ines L. D. Rocha, Marguerita E. Rosa, Mara G. Freire, Joao A. P. Coutinho
Summary: This study used size-exclusion high-performance liquid chromatography and dynamic light scattering to investigate the aggregation behavior of bovine serum albumin and its modulation by salt ions. The results show that albumin dissociates in solution to form macromolecular ions, which then bind with each other to form large aggregates. The chemical equilibria established between salt ions and the charges present in the macromolecular ions' backbone play a crucial role in promoting or preventing aggregation. These aggregation behaviors and their modulation can be explained by chemical concepts, with chemical equilibrium being essential.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
