Article
Biochemistry & Molecular Biology
Darren M. Gordon, Stephen H. Hong, Zachary A. Kipp, Terry D. Hinds
Summary: This study revealed that bilirubin interacts with threonine 283 (T283) and alanine 333 (A333) in the ligand-binding pocket of PPAR alpha. Mutational analysis showed significantly reduced bilirubin binding with T283 and A333 mutations. Bilirubin did not show any interaction with PPAR gamma.
Article
Biochemistry & Molecular Biology
Wilford Tse, Nathan Whitmore, Myles R. Cheesman, Nicholas J. Watmough
Summary: By studying the binding of nitrite to recombinant wild-type Sperm Whale myoglobin, researchers discovered a different mode of nitrite binding compared to the traditional nitro binding. Substitution of the proximal heme ligand can enhance reactivity towards nitrite, influencing the distal pocket environment and leading to an increase in reaction rate. The thermal equilibrium of spin-states plays a crucial role in this process.
BIOCHEMICAL JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Marina A. Semenova, Rita V. Chertkova, Mikhail P. Kirpichnikov, Dmitry A. Dolgikh
Summary: Neuroglobin, a heme protein predominantly expressed in nervous tissue, has been shown to promote neuronal survival. However, the molecular mechanisms underlying its neuroprotective function remain unclear. Recent experimental and computational work suggests that the interaction between neuroglobin and mitochondrial cytochrome c may contribute to neuroglobin-mediated neuroprotection, both in the cytoplasm and within the mitochondria.
Article
Microbiology
Hua Li, Qianqian Bao, Jianfeng Zhao, Yinbiao Xu, Shengyu Yang, Weishi Xue, Yang Sun, Yupeng Liu
Summary: This study analyzes the interactions between eight GDH mutants and NADP(+) using AlphaFold2 and Discovery Studio 3.0 and verifies the catalytic efficiency of one mutant (P45A) through site-directed mutagenesis. The study also reveals a positive correlation between the enzyme activity of GDH and its pocket hydrophobicity. In addition, mutant P45A exhibits improved catalytic ability in organic solvents, albeit with altered substrate affinity.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Indrek Kalvet, Mary Ortmayer, Jingming Zhao, Rebecca Crawshaw, Nathan M. Ennist, Colin Levy, Anindya Roy, Anthony P. Green, David Baker
Summary: In this study, a high-affinity heme-binding protein, dnHEM1, was designed with an axial histidine ligand, a vacant coordination site, and a tunable distal pocket. This protein was converted into a proficient peroxidase and enantiocomplementary carbene transferases by reconfiguring the distal pocket. This approach allows for the custom design of enzymes with a variety of shapes and functionalities.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(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
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
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
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
Computer Science, Software Engineering
Madhavi Latha Yadav Bangaru, Ravi Kumar Medabalimi, Sobhan Babu, Nidhanapati K. Raghavendra
Summary: Silent mutations allowing for restriction site modification can aid in screening successful mutants during site-directed mutagenesis. However, introducing a new restriction site requires the analysis of degenerate sequences within mutant primers, which becomes increasingly laborious, time-consuming, and prone to errors as the number of degenerate codons increases. A software named 'REMP' was developed to instantly generate degenerate sequences with restriction sites that are 6-8 base pairs in length, allowing users to edit the list of restriction sites without the need for writing computer code or knowing a program language.
Article
Biochemistry & Molecular Biology
Elizabeth R. Rochon, Maria Azzurra Missinato, Jianmin Xue, Jesus Tejero, Michael Tsang, Mark T. Gladwin, Paola Corti
ANTIOXIDANTS & REDOX SIGNALING
(2020)
Article
Biochemistry & Molecular Biology
Jason J. Rose, Kaitlin A. Bocian, Qinzi Xu, Ling Wang, Anthony W. DeMartino, Xiukai Chen, Catherine G. Corey, Danielle A. Guimaraes, Ivan Azarov, Xueyin N. Huang, Qin Tong, Lanping Guo, Mehdi Nouraie, Charles F. McTiernan, Christopher P. O'Donnell, Jesus Tejero, Sruti Shiva, Mark T. Gladwin
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Hematology
Anthony W. DeMartino, Jason J. Rose, Matthew B. Amdahl, Matthew R. Dent, Faraaz A. Shah, William Bain, Bryan J. McVerry, Georgios D. Kitsios, Jesus Tejero, Mark T. Gladwin
Article
Medicine, Research & Experimental
Tolani F. Olonisakin, Tomeka Suber, Shekina Gonzalez-Ferrer, Zeyu Xiong, Hernan F. Penaloza, Rick van der Geest, Yuting Xiong, David O. Osei-Hwedieh, Jesus Tejero, Matthew R. Rosengart, Wendy M. Mars, Daria Van Tyne, Andreas Perlegas, Samuel Brashears, Daniel B. Kim-Shapiro, Mark T. Gladwin, Michael A. Bachman, Eldad A. Hod, Claudette St Croix, Yulia Y. Tyurina, Valerian E. Kagan, Rama K. Mallampalli, Anuradha Ray, Prabir Ray, Janet S. Lee
Summary: Macrophages play a crucial role in heme metabolism and immune defense, but excessive heme can lead to immunosuppression. The clearance of senescent RBCs by macrophages impairs immunity and is independent of bacterial iron acquisition.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Hematology
Ravi Vats, Tomasz W. Kaminski, Eun-Mi Ju, Tomasz Brozska, Egemen Tutuncuoglu, Jesus Tejero, Enrico M. Novelli, Prithu Sundd, Tirthadipa Pradhan-Sundd
Summary: The chronic deficiency of P-selectin attenuates liver ischemia but fails to prevent hepatobiliary injury in SCD mice, possibly due to an increase in cellular senescence and reduced epithelial cell proliferation in the liver. This highlights the importance of investigating the long-term effects of chronic P-selectin inhibition therapy on liver pathophysiology in patients with SCD.
Article
Cardiac & Cardiovascular Systems
Jeffrey Wang, Willard N. Applefeld, Junfeng Sun, Steve B. Solomon, Jing Feng, Zoe G. Couse, Thomas F. Risoleo, Robert L. Danner, Jesus Tejero, Juan Lertora, Elmira Alipour, Swati Basu, Vandana Sachdev, Daniel B. Kim-Shapiro, Mark T. Gladwin, Harvey G. Klein, Charles Natanson
Summary: The study found that elevated CFH levels in septic shock lead to various pathophysiological changes, including increased pulmonary arterial pressures and right ventricular afterload, depressed cardiac function, worsening shock, lactate levels, metabolic acidosis, and multiorgan failure. These effects are mainly attributed to nitric oxide scavenging and iron supply promoting bacterial growth.
AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY
(2021)
Article
Chemistry, Inorganic & Nuclear
Matthew R. Dent, Anthony W. DeMartino, Jesus Tejero, Mark T. Gladwin
Summary: Interdisciplinary research has revealed the essential roles of nitric oxide (NO) as a signaling molecule in various physiological pathways relevant to human health and disease. Hemeproteins, including hemoglobin and myoglobin, play central roles in generating and maintaining NO as well as serving as a stable reservoir for NO in the form of nitrite. These pathways involve complex chemical and biochemical reactions that govern NO and nitrite signaling in vivo, presenting potential therapeutic targets for treating a wide range of diseases.
INORGANIC CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Courtney E. Sparacino-Watkins, Jack R. Lancaster
Summary: NO CLDs are specialized and sensitive spectroscopic instruments capable of directly measuring NO flux rates, instrumental in characterizing mammalian nitrite-dependent NO synthases. Guidelines for measuring NO production rates and potential pitfalls related to NO flux measurements are provided in this detailed review.
NITRIC OXIDE-BIOLOGY AND CHEMISTRY
(2021)
Article
Hematology
Ravi Vats, Tomasz W. Kaminski, Tomasz Brzoska, John A. Leech, Egemen Tutuncuoglu, Omika Katoch, Jude Jonassaint, Jesus Tejero, Enrico M. Novelli, Tirthadipa Pradhan-Sundd, Mark T. Gladwin, Prithu Sundd
Summary: This study reveals for the first time that the sterile inflammatory milieu in SCD promotes caspase-4/11-dependent activation of GSDMD, and facilitates the liver-to-lung embolic translocation of NETs, leading to the development of acute lung injury.
Article
Biochemistry & Molecular Biology
Stefan J. Kaliszuk, Natasha I. Morgan, Taylor N. Ayers, Courtney E. Sparacino-Watkins, Anthony W. DeMartino, Kaitlin Bocian, Venkata Ragireddy, Qin Tong, Jests Tejero
Summary: Cytoglobin is a hemoprotein that can reduce nitrite to nitric oxide and bind lipids. Mutations of specific amino acids such as His81 (E7), Arg84, and Lys116 have implications on the reactivity towards nitrite, affinity for lipids, and lipid binding stability. These gain and loss-of-function mutations can be useful tools to study the physiological role of cytoglobin functions in vivo.
NITRIC OXIDE-BIOLOGY AND CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Qinzi Xu, Jason J. Rose, Xiukai Chen, Ling Wang, Anthony W. DeMartino, Matthew R. Dent, Sagarika Tiwari, Kaitlin Bocian, Xueyin N. Huang, Qin Tong, Charles F. McTiernan, Lanping Guo, Elmira Alipour, Trevor C. Jones, K. Burak Ucer, Daniel B. Kim-Shapiro, Jesus Tejero, Mark T. Gladwin
Summary: This study evaluates different hemoproteins and finds that 2,3-diphosphoglycerate stripped human hemoglobin (StHb) and N-ethylmaleimide modified hemoglobin (NEMHb) have high CO binding affinities and efficiently scavenge CO from erythrocytes, suggesting their potential therapeutic role in CO poisoning.
Article
Biochemistry & Molecular Biology
Anthony W. DeMartino, Laxman Poudel, Matthew R. Dent, Xiukai Chen, Qinzi Xu, Brendan S. Gladwin, Jesus Tejero, Swati Basu, Elmira Alipour, Yiyang Jiang, Jason J. Rose, Mark T. Gladwin, Daniel B. Kim-Shapiro
Summary: Nitric oxide (NO) is a signaling molecule that plays a role in regulating blood flow and platelet activation. However, the diffusion of NO is limited by reactions with hemoproteins. This study suggests that NO can be stabilized as NO-ferroheme and transported within the body to promote vasodilation.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anthony W. DeMartino, Matthew B. Amdahl, Kaitlin Bocian, Jason J. Rose, Jesus Tejero, Mark T. Gladwin
Summary: The research indicates that the His81 binding equilibrium of cytoglobin is modulated by the formation of a disulfide bridge between Cys38 and Cys83. Experimental results show the presence of at least two kinetically distinct subpopulations in cytoglobin, depending on the thiol oxidation states.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Anthony DeMartino, Jesus Tejero, Mark Gladwin
FREE RADICAL BIOLOGY AND MEDICINE
(2020)