Article
Plant Sciences
Xia Li, Geng Chen, Qing-Qing Gao, Chun-Fan Xiang, Cheng-Xiao Yuan, Xiao-Ning Li, Yan-Yu Shu, Guang-Hui Zhang, Yan-Li Liang, Sheng-Chao Yang, Chen-Xi Zhai, Yan Zhao
Summary: This study explored the key enzymes involved in cucurbitacins biosynthesis in the Chinese traditional medicinal plant Hemsleya chinensis. Using AlphaFold2 and molecular docking, the researchers successfully predicted the 3D structure of HcOSC6 and its binding features to 2,3-oxidosqualene. Mutagenesis experiments identified three key amino acid residues, E246, M261, and D490, which significantly affected the activity of HcOSC6. This study not only characterized three potential key residues for producing cucurbitacins, but also provided insights into their significant role in metabolic engineering.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Delilah Jewel, Rachel E. E. Kelemen, Rachel L. L. Huang, Zeyu Zhu, Bharathi Sundaresh, Xiaofu Cao, Kaitlin Malley, Zeyi Huang, Muhammad Pasha, Jon Anthony, Tim van Opijnen, Abhishek Chatterjee
Summary: Virus-assisted directed evolution of tRNAs (VADER) allows for the efficient enrichment of active and orthogonal tRNA mutants from naive libraries in mammalian cells. Using this method, improved mutants of Methanosarcina mazei pyrrolysyl-tRNA and a bacterial tyrosyl-tRNA were obtained. The most efficient mutant pyrrolysyl-tRNA showed specific activity for mammalian cells, suggesting improved interaction with the unique mammalian translation machinery.
Article
Biochemical Research Methods
Huiyong Jia, Ricardo Couto-Rodriguez, Sharon Johnson, Stephanie Medina, Brianna Novillo, Peter Huynh, Matt Kim, Cade Cooper, Meagan Michalik, Benjamin Siew, Elise Turesson, Julie A. Maupin-Furlow
Summary: This study reports two new methods for site-directed mutagenesis of plasmids, which overcome the current issues of low efficiency, complexity, and time consumption. Both methods have high efficiency and can generate and isolate the appropriate DNA products with site-directed mutations.
Article
Biochemistry & Molecular Biology
Jenny W. Cheung, William D. Kinney, Joshua S. Wesalo, Megan Reed, Eve M. Nicholson, Alexander Deiters, T. Ashton Cropp
Summary: The use of light to control protein function is a critical tool in chemical biology. In this paper, we describe the addition of a photocaged histidine to the genetic code, allowing for the optical control of enzymes. By genetically encoding photocaged histidine in mammalian cells, we were able to successfully manipulate and control firefly and Renilla luciferases using light.
Article
Microbiology
Purnendu Bhowmik, Nagakumar Bharatham, Satoshi Murakami, Vasanthi Ramachandran, Santanu Datta
Summary: OqxB, a member of the RND efflux pump family, is widely recognized as a major contributor to antimicrobial resistance. It is predominantly present in Klebsiella spp. and contributes to resistance against antibiotics like nitrofurantoin, quinolones, b-lactams, and colistin. In addition to Klebsiella spp., oqxB has been found to occur via horizontal gene transfer in other bacterial genera. The crystal structure and key amino acid residues involved in the substrate binding domain of OqxB have been characterized, revealing their importance in efflux and resistance development against fluoroquinolones.
RESEARCH IN MICROBIOLOGY
(2023)
Article
Microbiology
Emily C. Hoedt, Francesca Bottacini, Nora Cash, Roger S. Bongers, Kees van Limpt, Kaouther Ben Amor, Jan Knol, John MacSharry, Douwe van Sinderen
Summary: Members of the genus Bifidobacterium are difficult to genetically manipulate due to their extensive and variable Restriction-Modification systems. A modified suicide vector, pFREM28, was developed to target specific genes in B. breve by removing known restriction sites, reducing the time, effort, and resources required for generating site-directed mutants. This approach could be applied to other (bifido)bacterial species as well.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Su-Jin Jun, Jung-A Lee, Young-Wan Kim, Sang-Ho Yoo
Summary: Through site-directed mutagenesis, a robust mutant Bifidobacterium thermophilum (BtAS) strain BtAS(Y414F/P200R) with enhanced turanose productivity was successfully developed, showing an increase in turanose yield by two times compared to the wild type BtAS and completing the reaction in half the time.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Engineering, Chemical
Zhien Zhang, Shraavya Rao, Yang Han, Ruizhi Pang, W. S. Winston Ho
Summary: In this study, facilitated transport membranes with PVAm as fixed carrier and various amino acid salts as mobile carriers were synthesized for post-combustion capture. The CO2 separation performance was compared among different AAS carriers, with PZEA-Pro showing the highest effectiveness in facilitating CO2 transport. By adjusting the ratio of PVAm and mobile carriers, the membranes achieved improved CO2 permeance and selectivity, along with good thermal stability and consistent membrane thickness. The membranes developed in this study surpassed the Robeson upper bound and demonstrate great potential for CO2 capture applications.
JOURNAL OF MEMBRANE SCIENCE
(2021)
Review
Biotechnology & Applied Microbiology
Li Xie, Rong Liu, Xin Chen, Mei He, Yi Zhang, Shuyi Chen
Summary: This review highlights the common approaches to designing functional polymeric micelles based on basic amino acids and their applications as drug carriers for cancer therapy. Different polypeptide architectures are developed for efficient drug loading and delivery, with polylysine- and polyhistidine-based micelles enabling pH-responsive drug release. Additionally, polyarginine can enhance membrane penetration and gas therapy through generating metabolites of nitric oxide (NO).
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Lena Goshayeshi, Sara Yousefi Taemeh, Nima Dehdilani, Mohammadreza Nasiri, Mohammad M. Ghahramani Seno, Hesam Dehghani
Summary: The study demonstrates the use of an RNA-guided piggyBac transposase and dual sgRNAs for site-directed integrations in the human ROSA26 safe harbor region. This methodology shows promise for targeting specific genomic regions, such as in cancer cells for inserting sequences into target regions or activating tumor suppressor genes.
Article
Agriculture, Multidisciplinary
Cheng-Hua Wang, Wu-Ping Xiong, Cheng Huang, Xiao-Ming Li, Qing-Yan Wang, Ri-Bo Huang
Summary: This study successfully increased the catalytic activity and efficiency of an exoinulinase under acidic conditions through rational site-directed mutagenesis. The mutants showed improved substrate preference for inulin and may serve as promising candidates for industrial inulin hydrolysis. The study demonstrates the potential of mutating non-conserved substrate recognition residues for industrial enzyme improvements.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Review
Plant Sciences
Olawale Samuel Adeyinka, Bushra Tabassum, Brice Landry Koloko, Ifedayo Victor Ogungbe
Summary: The improvement of CRISPR-Cas gene editing technology has facilitated genetic modification of desirable agronomic traits in crops, such as resistance to pathogens, drought tolerance, nutritional value, and yield-related traits. This presents a significant opportunity for precise genetic diversification in plants.
Article
Biochemistry & Molecular Biology
Satoru Watanabe, Masahiro Ito, Takanori Kigawa
Summary: DiRect is a novel PCR-based mutagenesis method that achieves high quality product (>99% substitution) without the use of recombinant DNA technology. It has been successfully applied in the study of an industrially relevant enzyme, showing simplicity, efficiency, and potential scalability in site-directed mutagenesis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Chemistry, Organic
Houchao Xu, Jeroen S. Dickschat
Summary: In the past three decades, numerous terpene synthases have been characterized from various life kingdoms. The mechanisms of terpene synthases have been investigated through site-directed mutagenesis, providing valuable insights into their catalysis and resulting in mutants with improved yields.
SYNTHESIS-STUTTGART
(2022)
Article
Biochemistry & Molecular Biology
Philipp Grad, Katarina Edwards, Lars Gedda, Victor Agmo Hernandez
Summary: This study investigates the effects of polyethylene glycol-(PEG) modified lipids and gangliosides on the Ca2+ induced interaction between liposomes composed of palmitoyl-oleoyl phosphatidylethanolamine (POPE) and palmitoyl-oleoyl phosphatidylserine (POPS) at physiological ionic strength. The results show that naked liposomes tend to adhere, rupture, and collapse on each other's surfaces upon addition of Ca2+, eventually resulting in the formation of large multilamellar aggregates and bilayer sheets. However, the presence of gangliosides or PEGylated lipids leads to the formation of small, long-lived bilayer fragments/disks. PEGylated lipids seem to be more effective than gangliosides at stabilizing these structures. The study suggests that direct liposome-liposome fusion is not the dominating process triggered by Ca2+ in the systems studied.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Saurabh Saraswat, Archana Chugh
Summary: Cell penetrating peptides (CPP) are important tools for intracellular delivery of molecules. In this study, a novel marine-derived CPP from Engraulis japonicus, called Engraulisin, was reported. Engraulisin demonstrated successful cellular uptake and selective antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA), making it a potential candidate for drug delivery.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Emanuela Efodili, Ashlynn Knight, Maryem Mirza, Cedric Briones, Il-Hyung Lee
Summary: This study demonstrates the spontaneous transfer of small membrane-bound peptides between a supported lipid bilayer and giant unilamellar vesicles in vitro. The transfer occurs through the formation of hemi-fusion stalks and is limited to small peptides due to the highly curved structure of the stalk. This system provides a synthetic platform for studying peptide trafficking between synthetic membranes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Yueqi Niu, Si Jia Chen, Jeffery B. Klauda
Summary: Macrophage membranes in the activated state are more tightly packed, exhibit increased chain order across lipid species, and form specific lipid clusters. These findings provide physiologically accurate models for future computational studies of macrophage membranes and their proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Niki Baccile, Vincent Chaleix, Ingo Hoffmann
Summary: This study measured the bending rigidity of self-assembled structures formed by a new biobased glucolipid bioamphiphile using neutron spin-echo (NSE) technology. The results showed that the bending rigidity of these structures is lower or higher compared to phospholipid membranes, providing a new theoretical basis for the application of these new molecular systems.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Alain Bolano Alvares, Pablo E. A. Rodriguez, Gerardo D. Fidelio
Summary: The behavior of amphiphilic molecules at the air/water interface was studied to evaluate the arrangement formed in a confined area. The surface properties of zwitterionic DPPC lipid and A beta(1-40) amyloid peptide in mixed films were investigated at different temperatures. DPPC undergoes a phase transition depending on temperature and lateral pressure, which allows for the study of its influence on amyloid structure formation.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Lukasz Plachta, Marzena Mach, Magdalena Kowalska, Pawel Wydro
Summary: Resveratrol, a popular phytoalexin found in grapes and red wine, has beneficial effects on the cardiovascular system, exhibits antiviral, antibacterial, and antifungal properties, and may have therapeutic effects against cancer. This study investigates the interaction of resveratrol with model cell membranes, demonstrating changes in their physicochemical parameters and highlighting the role of cholesterol content in resveratrol incorporation. The findings suggest that the molecular mechanism of action of resveratrol may involve interactions with lipid rafts.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Edurne Rujas, Beatriz Apellaniz, Johana Torralba, David Andreu, Jose M. M. Caaveiro, Shixia Wang, Shan Lu, Jose L. Nieva
Summary: This study investigates the role of fusion peptide and Trp-rich membrane proximal external region in HIV-1 fusion and demonstrates that liposome-based formulations containing FP-MPER hybrid peptides can induce the production of specific neutralizing antibodies in rabbits. The results support the use of liposomes as vaccine carriers and the inclusion of lipid membranes in immunogens to elicit specific humoral responses.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Dailin Li, Dingyuan Shi, Lei Wang
Summary: G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in regulating cell excitability. This study investigated the ion permeation mechanism in GIRK2 mutants using molecular dynamic simulations and QM/MM methods. The results revealed the importance of a multi-ion distribution for ion conduction.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Max J. den Uijl, Arnold J. M. Driessen
Summary: Membrane protein insertion into and translocation across the bacterial cytoplasmic membrane are essential processes facilitated by the Sec translocon. The phospholipid dependence of membrane protein insertion has remained mostly unknown. This study reveals that the insertion of the mannitol permease MtlA into the membrane depends on the presence of phosphatidylglycerol and is stimulated by phosphatidylethanolamine.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick Allen, Adam C. Smith, Vernon Benedicto, Abbas Abdulhasan, Vasanthy Narayanaswami, Enrico Tapavicza
Summary: We explore the stability, size, and structure of nanodiscs formed by the N-terminal domain of apolipoprotein E3 and a variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine molecules. Our simulations suggest that nanodiscs containing 240 to 420 DMPC molecules are stable. The antiparallel configuration shows more protein-protein interactions and ionic contacts, as well as greater stability and rigidity compared to the parallel configuration.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick M. Keating, Nicholas P. Schifano, Xinrui Wei, Matthew Y. Kong, Jinwoo Lee
Summary: Lassa virus (LASV) infection is dependent on the fusion of its viral membrane with the host cell membrane, and our study reveals that this fusion process involves pH-dependent conformational changes in the transmembrane domain of LASV. These findings provide valuable insights into the fusion mechanism of LASV and can be utilized in the design of therapeutics to combat Lassa virus infections and prevent its potential spread.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Ashley L. Bennett, Kristen N. Cranford, Austin L. Bates, Christopher R. Sabatini, Hee-Seung Lee
Summary: This study employed molecular dynamics simulations to elucidate the binding, folding, and insertion details of TP10W in the cell membrane. The simulations revealed that TP10W can translocate across the lipid membrane as a monomer, and the charged amino acid side chains can move between lipid leaflets. Comparison with point mutated variants demonstrated significant conformational changes due to charge distribution.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Jessica H. van Wonderen, Jason C. Crack, Marcus J. Edwards, Thomas A. Clarke, Gerhard Saalbach, Carlo Martins, Julea N. Butt
Summary: Electrogenic bacteria transfer excess respiratory electrons to metal oxide particles and electrodes through the MtrCAB complex. The crystal structure of MtrCAB from S. baltica OS185 was resolved, and liquid chromatography mass spectrometry was used to determine the mass values of the three proteins in purified MtrCAB complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Review
Biochemistry & Molecular Biology
Yi-Ming Chen, Ching-Tai Lu, Chia-Wen Wang, Wolfgang B. Fischer
Summary: A series of dye ligands were ranked based on docking experiments, selecting the most suitable ligands for binding with different proteins. Additionally, a comparison study was conducted on a series of repurposing drugs and known antivirals.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)