Article
Biology
N. Dehghanbanadaki, H. Mehralitabar, R. Sotoudeh, H. Naderi-Manesh
Summary: In this study, the researchers investigated the role of the thumb palmitoleyl group and conserved disulfides in regulating the interaction and structural dynamics between Wnt and FZ receptors. Their results showed that the palmitoleyl group is important for stabilizing the Wnt-FZ interaction, and the disulfides modulate this contribution. Specifically, they identified the significant role of disulfide 183-190 in establishing a long-range salt-bridge interaction and positioning the palmitoleyl group appropriately for Wnt-FZ complex formation.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biotechnology & Applied Microbiology
Laura Navone, Thomas Vogl, Pawarisa Luangthongkam, Jo-Anne Blinco, Carlos H. Luna-Flores, Xiaojing Chen, Juhani von Hellens, Stephen Mahler, Robert Speight
Summary: This study presents a thermostable variant of the E. coli AppA phytase, ApV1, with an extra non-consecutive disulfide bond, which shows promising thermostability but leads to decreased production in Pichia pastoris. Co-expression of folding chaperones like protein disulfide bond isomerase (Pdi) significantly increased the production of ApV1 and restored yields to levels comparable with the wild-type enzyme. Engineering for enhanced enzymatic properties may result in folding complexity and reduced production in microbial systems, highlighting the importance of developing improved production strains in parallel to achieve desirable levels of recombinant protein for industrial processes.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Food Science & Technology
Lilang Li, Weikun Wu, Zixiao Deng, Shihai Zhang, Wutai Guan
Summary: By engineering the thermostability of Lipase Lip2 from Yarrowia lipolytica, its potential value in the enzymatic preparation of MLM-SLs has been enhanced, leading to increased reaction rate and recyclability.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nabarun Chandra Das, Parth Sarthi Sen Gupta, Satyaranjan Biswal, Ritwik Patra, Malay Kumar Rana, Suprabhat Mukherjee
Summary: Cystatin interacts strongly with TLR4 to regulate immune responses and potentially has anti-inflammatory properties. The study suggests targeting the cystatin-TLR4 interaction for the development of therapeutics or vaccines.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Pingyu Yan, Zhiyuan Zou, Shiyao Zhang, Rui Wang, Tingting Niu, Xia Zhang, Defu Liu, Xuejie Zhou, Alan K. Chang, Nathaniel G. N. Milton, Gary W. Jones, Jianwei He
Summary: The study investigated the binding between Pichia pastoris PDI and amyloidogenic proteins, revealing multiple binding modes between PDI and its substrates, suggesting different specificities and affinities. PDI may eliminate the need for misfolded proteins to be localized in ER-associated compartments by promoting protein folding.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Jingyi Zhao, Jing Chen, Huiyi Wang, Yan Guo, Kai Li, Jidong Liu
Summary: By computationally designing disulfide bridges, mutants of D-psicose 3-epimerase were successfully engineered to increase their optimum catalytic temperature, greatly enhance their thermal stability, and extend their half-lives, thereby significantly improving their potential for industrial application.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Polymer Science
Xiangrui Zheng, Hua Yang, Yaguang Sun, Yongqin Zhang, Yafang Guo
Summary: The paper investigates the self-healing mechanism based on disulfide bond exchange reactions at the atomic scale through molecular dynamics simulations. It explores the effects of crosslink density and healing time on self-healing efficiency and mechanical properties. The results show that high crosslink density improves mechanical properties but reduces molecular chain mobility, while shorter stress relaxation time leads to higher healing efficiency.
Article
Biology
Motonori Matsusaki, Rina Okada, Yuya Tanikawa, Shingo Kanemura, Dai Ito, Yuxi Lin, Mai Watabe, Hiroshi Yamaguchi, Tomohide Saio, Young-Ho Lee, Kenji Inaba, Masaki Okumura
Summary: The physiological functions of proteins are determined by their unique three-dimensional structures, with conserved disulfide-catalysts and chaperone networks playing a crucial role in correct protein folding and prevention of aggregation. Disruption of these networks is implicated in pathology. Complex formation among PDIs accelerates protein folding and prevents aggregation.
Article
Biochemistry & Molecular Biology
Yanyan Chu, Huanhuan Zhang, Mengke Yang, Rilei Yu
Summary: Transient receptor potential vanilloid 1 (TRPV1), a non-selective cation channel, can be activated by oxidants through cysteine modification. This study revealed that the formation of a disulfide bond between C387 and C391 leads to conformational changes in the channel, with several residues playing essential roles in the channel opening. These findings provide new insights into the activation mechanism of TRPV1 and have implications for the treatment of human diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Applied
Jamoliddin Razzokov, Sunnatullo Fazliev, Dinora Erkinova, Shavkat Mamatkulov, Zhitong Chen
Summary: This study investigated the effects of reactive oxygen and nitrogen species (RONS) on the human epidermal growth factor (hEGF) through molecular dynamics simulations. The results showed that nitrosylation induced conformational changes in hEGF and disruption of disulfide bonds, but the structural stability of hEGF remained mostly unaffected.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2022)
Article
Chemistry, Applied
Yuan Peng, Chuanyang Wang, Jian Yu, Jinhong Wu, Faxiang Wang, Yongle Liu, Xianghong Li
Summary: This study investigated the intermolecular interactions and self-assembly mechanism of rice glutelin amyloid fibril aggregates using experimental and computer simulation methods. The addition of NaCl and SDS promoted the aggregation of the fibrils, while the addition of urea caused degradation and depolymerization. Hydrogen bonding primarily drove the formation of the common cross 8-sheet structure, with hydrophobic and electrostatic interactions also involved. Molecular dynamics simulations confirmed the nucleation-elongation mechanism for the formation of the aggregates. Understanding the self-assembly pattern of amyloid fibril aggregates derived from food protein is crucial for their design and practical application.
FOOD HYDROCOLLOIDS
(2023)
Article
Biochemistry & Molecular Biology
Huitu Zhang, Jingcheng Sang, Li Li, Luying Jiang, Fuping Lu, Shan He, Wei Cui, Xiaoqing Zhang, Fufeng Liu
Summary: This study utilized molecular dynamics simulations to investigate the inhibitory effects of HCP on the conformational transformation of A beta. The results showed that HCP can prevent the conformational transition of A beta monomers in a concentration-dependent manner, suggesting its potential as an anti-A beta compound.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Francesco Tavanti, Alfonso Pedone, Maria Cristina Menziani
Summary: This study demonstrated through simulations how gold nanoparticles adsorb amyloid-beta monomers, reducing their tendency to form mature amyloid fibrils.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Yui Nakata, Yuuto Kitazaki, Hitomi Kanaoka, Erika Shingen, Rina Uehara, Kunihiro Hongo, Yasushi Kawata, Tomohiro Mizobata
Summary: The molecular chaperones HdeA and HdeB help protect client proteins from acid denaturation in E. coli. Both proteins can form fibrils at low pH, but the fibrils can be resolubilized at neutral pH. However, extended incubation at low pH can lead to the formation of irreversible fibrils. The secondary structure of HdeB fibrils remained alpha helical regardless of the conditions under which the fibrils were formed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Amit Srivastava, Jamal Hassan, Dirar Homouz
Summary: Water dynamics in nanochannels, especially in small carbon nanotubes, are influenced by confinement. Molecular dynamics simulations were performed to investigate the structure and dynamics of water in carbon nanotubes of various sizes and temperatures. The results showed that the radial density profile of water in small nanotubes had a single peak near the tube walls, while larger nanotubes exhibited coaxial tubular sheets of water molecules. Subdiffusive behavior was observed in ultra-narrow nanotubes, while Fickian diffusion was evident in larger nanotubes. The hydrogen bond correlation function of water in the nanotubes decayed slower than in bulk water, with the decay rate decreasing as the nanotube diameter increased.
Article
Biochemistry & Molecular Biology
You-Lin Xue, Hao Wang, Michael Riedy, Brittany-Lee Roberts, Yuna Sun, Yong-Bo Song, Gary W. Jones, Daniel C. Masison, Youtao Song
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2018)
Article
Mycology
Sean Doyle, Gary W. Jones, Stephen K. Dolan
Article
Biochemistry & Molecular Biology
Weibin Gong, Wanhui Hu, Linan Xu, Huiwen Wu, Si Wu, Hong Zhang, Jinfeng Wang, Gary W. Jones, Sarah Perrett
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Biochemistry & Molecular Biology
Linan Xu, Weibin Gong, Hong Zhang, Sarah Perrett, Gary W. Jones
Letter
Biochemistry & Molecular Biology
Xuejie Zhou, Xian Lu, Shuzhen Qin, Linan Xu, Xiaoying Chong, Junqing Liu, Pingyu Yan, Rui Sun, Ian P. Hurley, Gary W. Jones, Qiuyu Wang, Jianwei He
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2019)
Article
Multidisciplinary Sciences
Linan Xu, Nitika, Naushaba Hasin, Daragh D. Cuskelly, Donald Wolfgeher, Sean Doyle, Paul Moynagh, Sarah Perrett, Gary W. Jones, Andrew W. Truman
SCIENTIFIC REPORTS
(2019)
Article
Biochemistry & Molecular Biology
Linan Xu, Hong Zhang, Daragh D. Cuskelly, Sean Doyle, Sarah Perrett, Gary W. Jones
Summary: Hsp70 is a conserved chaperone that plays a critical role in maintaining protein homeostasis. Mutations in the SBD disrupt its hydrophobic core, leading to impairment of heat-shock response and prion propagation. The disruption of key residues in the SBD region results in instability and cleavage of Hsp70, impacting its ATPase function and overall stability. This ultimately compromises the stress response and prion propagation abilities of yeast cells.
MOLECULAR MICROBIOLOGY
(2021)
Article
Medicine, Research & Experimental
Linan Xu, Fiachra Humphries, Nezira Delagic, Bingwei Wang, Ashling Holland, Kevin S. Edgar, Jose R. Hombrebueno, Donna Beer Stolz, Ewa Oleszycka, Aoife M. Rodgers, Nadezhda Glezeva, Kenneth McDonald, Chris J. Watson, Mark T. Ledwidge, Rebecca J. Ingram, David J. Grieve, Paul N. Moynagh
Summary: The study demonstrated the instability of human ECSIT in a mouse model, with low levels of expression leading to impaired clearance of Salmonella and severe cardiac hypertrophy. Additionally, a reduction in mROS in macrophages was observed.
Article
Biochemistry & Molecular Biology
Linan Xu, Weibin Gong, Sarah A. Cusack, Huiwen Wu, Harriet M. Loovers, Hong Zhang, Sarah Perrett, Gary W. Jones
CELLULAR AND MOLECULAR LIFE SCIENCES
(2018)