Article
Chemistry, Applied
Xiao Jiang, Yaru Wang, Yuan Wang, Huoqing Huang, Yingguo Bai, Xiaoyun Su, Jie Zhang, Bin Yao, Tao Tu, Huiying Luo
Summary: The study successfully improved the thermostability of GoxM4 from Aspergillus niger by combining enzyme activity and structure stability, obtaining a more stable mutant, GoxM8. The mutant showed a significant increase in melting temperature (Tm) compared to GoxM4, while maintaining a similar catalytic efficiency, effectively addressing the activity-stability trade-off in enzymes. The research provided a typical example for investigating the balance between enzyme activity and stability.
Article
Chemistry, Applied
Jie Luo, Chenshuo Song, Wenjing Cui, Laichuang Han, Zhemin Zhou
Summary: A combinatorial mutant M4 with improved stability and activity was obtained through multi-strategy engineering, showing a 20.7-fold increase in half-life and doubled catalytic efficiency. Molecular dynamics simulation revealed an obvious flexible region shifting in the structure of mutant M4, which was considered as a key factor in counteracting the stability-activity trade-off. Further analysis showed that the flexible region shifting was driven by region dynamical networks reshaping. This work provides insights into the counteraction mechanism and offers a potential strategy for enzyme evolution through computational protein engineering.
Article
Biochemistry & Molecular Biology
Jhenifer Yonara de Lima, Emanuella de Castro Andreassa, Isis Venturi Biembengut, Tatiana de Arruda Campos Brasil de Souza
Summary: This study investigates the role of T12, Y25, and T89 in the activities of asparaginase and glutaminase. Through structural analysis and enzymatic assays, the study provides insights into the enzymatic behavior of EcA and paves the way for the design of improved EcA enzymes, which is important in the treatment of ALL.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Till El Harrar, Benedikt Frieg, Mehdi D. Davari, Karl-Erich Jaeger, Ulrich Schwaneberg, Holger Gohlke
Summary: This study investigates the impact of aqueous ionic liquids on a model enzyme through molecular dynamics simulations and finds that they can affect enzyme activity by modifying local structural stability, eventually leading to perturbations in the catalytic site and protein core. The identification of perturbation pathways and specific interactions with IL ions helps predict variant libraries with improved tolerance to aqueous ionic liquids.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Fangying Dong, Meng Zhang, Rui Ma, Cheng Lu, Fei Xu
Summary: By studying the conformational dynamics of mutants, essential sites affecting enzyme catalytic activity in multipoint combinatorial mutants can be predicted and provide a strategy for guiding protein design.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Cheng Zhang, Nuria Codina, Jiazhi Tang, Haoran Yu, Nesrine Chakroun, Frank Kozielski, Paul A. Dalby
Summary: The research findings highlighted the different destabilizing pathways of protein structure under low pH and high temperature stress conditions, revealing the potential for stabilizing mutations in the CL domain and C-L-C(H)1 interface. The analysis also identified key salt bridge losses as a cause of conformational changes under different stresses, with implications for future engineering efforts to enhance stability.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Psychology, Biological
Lei Qiao, Lijie Zhang, Antao Chen
Summary: This study examined the inverse relationship between cognitive flexibility and stability using a novel version of the flexibility-stability paradigm and the classic cued task switching paradigm. The results showed that cognitive flexibility was negatively correlated with stability, as increased distractor proportions led to decreased flexibility and increased stability. Additionally, cognitive flexibility and stability were regulated by a single control system instead of two independent mechanisms.
INTERNATIONAL JOURNAL OF PSYCHOPHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bethany Kolbaba-Kartchner, I. Can Kazan, Jeremy H. Mills, S. Banu Ozkan
Summary: The study explores the relationship between protein dynamics and enzymatic function in beta-lactamases, revealing that allosteric coupling of rigid residues to the active site has profound effects on enzyme function. By altering the dynamic profile of TEM-1 using computational protein design methods, it was found that changing residues surrounding highly coupled rigid residues significantly affected enzymatic activity and stability. This integration of computational protein design methods with analyses of protein dynamics represents a general approach to extend understanding of the relationship between dynamics and function in other enzyme classes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Chang Ren, Xin Wen, Jun Mencius, Shu Quan
Summary: The study presents an in vivo stability biosensor for monitoring protein stability and coupling it with fluorescent readouts. The biosensor was shown to be useful in directed evolution to obtain improved variants of proteins, and in deep mutational scanning to reveal informative stability landscapes in proteins.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biotechnology & Applied Microbiology
Joan Planas-Iglesias, Sergio M. Marques, Gaspar P. Pinto, Milos Musil, Jan Stourac, Jiri Damborsky, David Bednar
Summary: Enzymes are natural catalysts that execute biochemical reactions, and their effectiveness has been optimized through evolution. Biocatalysts from various sources are used in industrial production, environmental protection, and biomedical applications. Protein engineering and computational techniques can improve enzyme function for diverse applications.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Medicine, Research & Experimental
Victoria E. Wood, Kate Groves, Lok Man Wong, Luyan Kong, Christopher Bird, Meenu Wadhwa, Milena Quaglia, Paul Matejtschuk, Paul A. Dalby
Summary: Protein engineering and formulation for therapeutic proteins present a major challenge in the biopharmaceutical industry due to the need for prolonged shelf-life. Understanding the impact of mutations and formulations on protein structure and dynamics can lead to more predictive approaches for improvement. Studies using intrinsic fluorescence analysis and hydrogen deuterium exchange mass spectrometry have revealed insights into the reorganization and stabilization of specific protein loops, providing valuable information for enhancing protein stability and reducing aggregation rates.
MOLECULAR PHARMACEUTICS
(2022)
Article
Agronomy
Walter D. Carciochi, Patricio Grassini, Seth Naeve, James E. Specht, Mitiku Mamo, Ron Seymour, Aaron Nygren, Nathan Mueller, Sarah Sivits, Christopher Proctor, Jenny Rees, Todd Whitney, Nicolas Cafaro La Menza
Summary: This study aims to determine if the trade-off between seed yield and SPC persists when irrigation is applied and how management, soil, and weather factors influence the trade-off. The study found that irrigation-induced higher soybean yields are possible without a concurrent reduction in SPC, which is contrary to the general expectation.
FIELD CROPS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Merve Arslan, Tugce Ulucay, Seyit Kale, Sibel Kalyoncu
Summary: Based on a mutagenesis study of conserved residues near HCDR3, it was found that key residues positioned around the salt bridge between VH-K94 and VH-D101 have an extensive impact on the conformation of HCDR3, thus providing insights for simultaneously improving both affinity and stability of antibodies.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Physics, Multidisciplinary
Karel Proesmans
Summary: Stochastic thermodynamics has become a framework to study the thermodynamics of small-scaled systems. The relation between entropy production and precision is one of the most important research topics in this field. In this paper, the author investigates the amount of dissipation needed to follow a pre-determined trajectory and derives the trade-off relation between precision and dissipation. The optimal protocol for maximizing precision with a given amount of dissipation is also derived.
COMMUNICATIONS PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Adrian van Kan, Alexandros Alexakis, Marc-Etienne Brachet
Summary: In this study, Levy on-off intermittency arising from multiplicative alpha-stable white noise close to an instability threshold was investigated in linear and nonlinear regimes for a pitchfork bifurcation with fluctuating growth rate. Different parameter regimes were identified, with critical exponents computed from the stationary distribution. The properties of the system, influenced by nonequilibrium, power-law-distributed fluctuations, were found to be substantially different from Gaussian thermal fluctuations in terms of statistics and critical behavior.
Article
Biochemistry & Molecular Biology
Henry C. Wilkinson, Paul A. Dalby
Summary: This study explores the effects of site-specific saturation mutagenesis within enzyme active sites and the potential benefits of incorporating noncanonical amino acids (ncAA) on improving enzyme activity and stability simultaneously. By fine-tuning residue 385 with different aromatic ring substituents, the researchers were able to significantly enhance specific activity, catalytic performance, and stability of the enzyme, showcasing the advantages of expanding designer libraries to include ncAAs.
Article
Biophysics
Valentina A. Spiteri, James Doutch, Robert P. Rambo, Jayesh Gor, Paul A. Dalby, Stephen J. Perkins
Summary: A comparative structural study of glycosylated and deglycosylated monoclonal human IgG1 revealed perturbations in the Fab-Fc separation after deglycosylation, with a broader conformational spectrum observed in the Fc region of deglycosylated IgG1 compared to glycosylated IgG1. This variability in Fc conformations was found to account for the loss of binding to the Fc gamma receptor in deglycosylated IgG1.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
John E. Hales, Samir Aoudjane, Gabriel Aeppli, Paul A. Dalby
Summary: The adoption of process analytical technologies in the biopharmaceutical industry can reduce the cost of therapeutic drugs and facilitate investigation of new bioprocesses. Control of critical process parameters is crucial for ensuring product quality, but developing the necessary sophisticated analytical technologies has proven to be a challenge.
JOURNAL OF CHROMATOGRAPHY A
(2021)
Article
Chemistry, Physical
Wenlong Zheng, Haoran Yu, Sai Fang, Kaitong Chen, Zhe Wang, Xiuli Cheng, Gang Xu, Lirong Yang, Jianping Wu
Summary: The study utilized a CAST/ISM strategy to accelerate the directed evolution of LTA by focusing on amino acid residues within the substrate pocket. Significant progress was made in the synthesis of products, showing promise for industrial applications.
Article
Biochemistry & Molecular Biology
Ke Liu, Haoran Yu, Guoyun Sun, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, Long Liu
Summary: This study focused on enhancing the production of pyruvate and d-alanine through improving the catalytic efficiency of Pm1 enzyme and integrating new metabolic pathways. The newly developed high-throughput screening method successfully identified mutants with higher catalytic efficiency, leading to increased production of pyruvate. Ultimately, by utilizing CRISPR/Cas9 technology, the engineered strain achieved high pyruvic acid titer, showcasing the potential for industrial production using biocatalysis.
Article
Medicine, Research & Experimental
Victoria E. Wood, Kate Groves, Lok Man Wong, Luyan Kong, Christopher Bird, Meenu Wadhwa, Milena Quaglia, Paul Matejtschuk, Paul A. Dalby
Summary: Protein engineering and formulation for therapeutic proteins present a major challenge in the biopharmaceutical industry due to the need for prolonged shelf-life. Understanding the impact of mutations and formulations on protein structure and dynamics can lead to more predictive approaches for improvement. Studies using intrinsic fluorescence analysis and hydrogen deuterium exchange mass spectrometry have revealed insights into the reorganization and stabilization of specific protein loops, providing valuable information for enhancing protein stability and reducing aggregation rates.
MOLECULAR PHARMACEUTICS
(2022)
Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Agriculture, Multidisciplinary
Xiumiao Yao, Tingting Kang, Zhongji Pu, Tao Zhang, Jianping Lin, Lirong Yang, Haoran Yu, Mianbin Wu
Summary: This study utilized multiple strategies to enhance the amidase from Agrobacterium tumefaciens d3, resulting in improved variants with better performance, and the mechanism of enhancement was revealed through molecular dynamics simulations.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Medicine, Research & Experimental
Mark-Adam W. Kellerman, Teresa Almeida, Timothy R. Rudd, Paul Matejtschuk, Paul A. Dalby
Summary: Structure-function relationships in proteins are influenced by the trade-off between stability and bioactivity. This study uses NMR spectroscopy to identify key amino acid residues in granulocyte colony-stimulating factor (G-CSF) that affect global stability and undergo conformational changes. It is found that certain residues are important for both stability and function, suggesting a possible link between the two. These findings provide insights into the crucial role of specific residues in the structure-function trade-off of proteins.
MOLECULAR PHARMACEUTICS
(2022)
Article
Biotechnology & Applied Microbiology
Yun Feng, Zhongji Pu, Li Zhu, Mianbin Wu, Lirong Yang, Haoran Yu, Jianping Lin
Summary: A dual-enzyme screening method was developed to obtain several variants of D-allulose 3-epimerase, among which the triple mutant showed significant improvement, aiding the development of industrial biocatalysts for D-allulose production.
ENZYME AND MICROBIAL TECHNOLOGY
(2022)
Article
Medicine, Research & Experimental
Hongyu Zhang, Paul A. Dalby
Summary: Combined administration of antibody therapeutics is beneficial, but the stability of the antibodies may be affected when combined into a single product.
MOLECULAR PHARMACEUTICS
(2022)
Article
Chemistry, Physical
Ziyuan Wang, Haisheng Zhou, Haoran Yu, Zhongji Pu, Jinling Xu, Hongyu Zhang, Jianping Wu, Lirong Yang
Summary: This study investigates the substrate recognition mechanism of glutamate dehydrogenase (GluDH) and develops a computational engineering strategy to redesign the binding pocket, leading to the synthesis of noncanonical amino acids. Tailor-made variants were created to improve the specific activities for producing high-value products. The computational enzyme redesign strategy shows promise in enhancing the production of noncanonical amino acids.
Article
Biochemical Research Methods
Qunfeng Zhang, Wenlong Zheng, Zhongdi Song, Qiang Zhang, Lirong Yang, Jianping Wu, Jianping Lin, Gang Xu, Haoran Yu
Summary: This study developed machine learning models to predict the substrate specificity of PylRS for novel NCAAs. The models showed high accuracy and provided a framework for expanding the substrate scope of PylRS variants and developing machine learning models for other PylRS variants.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Nanoscience & Nanotechnology
Pengcheng Li, Mengting Zhang, Shulin Wang, Haoran Yu, Jianping Wu, Lirong Yang, Gang Xu
Summary: Multimetallic catalysis can enhance catalytic performance through synergistic effects, and the loading of Pd-Ni-Fe catalysts onto UiO-66 can significantly improve selective hydrogenation reactions. The addition of Fe was found to enhance the selectivity of the desired product, and the optimal Pd1Ni2Fe6/UiO-66 catalyst exhibited high conversion and selectivity. The catalyst also demonstrated versatility, stability, and the advantage of easy separation and reusability. The reaction mechanism and pathway were proposed based on product distribution and catalyst properties.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Wenlong Zheng, Zhongji Pu, Lanxin Xiao, Gang Xu, Lirong Yang, Haoran Yu, Jianping Wu
Summary: The l-threonine aldolase from Leishmania major was engineered to improve its diastereoselectivity by considering the physico-chemical properties of the substrate access path, leading to significant enhancement in diastereomeric excess (de) value.
CHEMICAL COMMUNICATIONS
(2022)