Article
Biochemistry & Molecular Biology
Nikolai N. Sluchanko, Eugene G. Maksimov, Yury B. Slonimskiy, Larisa A. Varfolomeeva, Antonina Y. Bukhanko, Nikita A. Egorkin, Georgy Tsoraev, Maria G. Khrenova, Baosheng Ge, Song Qin, Konstantin M. Boyko, Vladimir O. Popov
Summary: This study presents the first crystal structures of OCP2 from cyanobacteria with different morphoecophysiological characteristics and provides a comprehensive comparison of their structure, spectroscopy, and function with OCP1, OCP3, and all-OCP ancestor. The structures enable the correlation of spectroscopic signatures with the effective number of hydrogen and the discovery of chalcogen bonds anchoring the ketocarotenoid in OCP, as well as the rotation of the echinenone's beta-ionone ring in the CTD. The structural data also helped rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2024)
Article
Biochemistry & Molecular Biology
Haijun Liu
Summary: This study investigates intrinsically disordered proteins/regions (IDPRs) in the interface of photosynthetic pigment protein complexes using a joint platform that combines in silico models and structural mass spectrometry data. The research reveals the structure of the PB domain and its associations with other proteins in the complex.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shijia Yuan, Lisha Xia, Chenxi Wang, Fan Wu, Bingjie Zhang, Chen Pan, Zhiran Fan, Xiaoguang Lei, Raymond C. Stevens, Andrej Sali, Liping Sun, Wenqing Shui
Summary: In this study, the conformational ensemble of an activated GPCR-G protein complex is mapped at near-atomic resolution using cross-linking mass spectrometry (CLMS) and integrative structure modeling. The integrative structures reveal heterogeneous conformations for potential alternative active states of the GLP-1 receptor-Gs complex, showing marked differences from the cryo-EM structure. The functional significance of interface residue contacts observed only in the integrative structures is validated through alanine scanning mutagenesis coupled with pharmacological assays.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Analytical
Azadeh Mohammadi, Aline Tschanz, Alexander Leitner
Summary: Carboxyl-group specific chemical cross-linking, using a combination of dihydrazide linkers and DMTMM as coupling reagent, can be adjusted to favor one reaction product over the other by varying the ratios of the two reagents. This strategy significantly increases the number of identified cross-linked peptides in model proteins and demonstrates complementarity and increased cross-link coverage in larger protein complexes like the bovine 20S proteasome and the Escherichia coli 70S ribosome.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kianoush Jeiran, Scott M. Gordon, Denis O. Sviridov, Angel M. Aponte, Amanda Haymond, Grzegorz Piszczek, Diego Lucero, Edward B. Neufeld, Iosif I. Vaisman, Lance Liotta, Ancha Baranova, Alan T. Remaley
Summary: This study developed a novel method to divide apoB-100 into subunits and domains, and validated the models using mass spectrometry cross-linking and known disulfide bond positions. The continuous structure of apoB-100 was generated, and the dynamics during particle size transitions were examined. Additionally, the proposed model of receptor ligand binding provides new insights into the functions of apoB-100.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Mengze Sun, Feng Yuan, Yuliang Tang, Peng Zou, Xiaoguang Lei
Summary: In this study, we developed an APEX-CXMS method for profiling subcellular protein-protein interactions (PPIs), providing a powerful tool for understanding cellular signaling events and disease pathogenesis.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Andrew Wheat, Clinton Yu, Xiaorong Wang, Anthony M. Burke, Ilan E. Chemmama, Robyn M. Kaake, Peter Baker, Scott D. Rychnovsky, Jing Yang, Lan Huang
Summary: A robust in vivo XL-MS platform has been developed to map protein-protein interactions at a systems level, enabling the construction of the largest in vivo PPI network to date from HEK 293 cells. This advanced strategy provides a highly detailed panoramic portrait of human interactomes associated with diverse cellular pathways and can be generalized for charting protein interaction landscapes in any organisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Environmental
Estefania Alvarez-Castillo, Maria Jesus Pelagio, Carlos Bengoechea, Antonio Guerrero
Summary: This study aims to improve the mechanical properties of superabsorbent bioplastics based on porcine plasma protein by adding different amounts of glutaraldehyde as a cross-linking agent. The results showed that adding glutaraldehyde through immersion can significantly reduce soluble material loss.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Polymer Science
Alexis Wolfel, Huiyi Wang, Ernesto Rafael Osorio-Blanco, Julian Bergueiro, Marcelo Ricardo Romero, Cecilia Ines Alvarez Igarzabal, Marcelo Calderon
Summary: Advancements in nanogel applications require precise control over their size, structure, and functionalization. In this work, a post-synthesis reaction strategy was developed to modify the structure and functionalization of thermoresponsive nanogels. The incorporation of a cleavable crosslinker allows control over the crosslinking degree and architecture of the nanogels, and introduces alpha-oxoaldehydes for subsequent bio-conjugation. This strategy provides a valuable tool for fine-tuning drug delivery nanodevices in a post-synthetic step.
Article
Multidisciplinary Sciences
Lin Mei, Matthew J. Reynolds, Damien Garbett, Rui Gong, Tobias Meyer, Gregory M. Alushin
Summary: This study focuses on the role of T-plastin in constructing actin networks. By using a machine-learning-enabled cryo-electron microscopy technique, the researchers uncover a sequential bundling mechanism that allows T-plastin to bridge and link parallel and antiparallel actin filaments. This bridging mechanism is essential for adapting to different actin network structures and functions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Takahiro Masuya, Shinpei Uno, Masatoshi Murai, Hideto Miyoshi
Summary: The study provides direct evidence that the quinone reaction cavity is accessible from the proposed matrix-side region covered by the ND3 TMH1-2 loop, despite initial doubts regarding the accessibility of the cavity from this region.
Article
Biochemistry & Molecular Biology
Cornelia G. Spruijt, Cathrin Grawe, Simone C. Kleinendorst, Marijke P. A. Baltissen, Michiel Vermeulen
Summary: The study investigates the relative orientation of different subunits within the NuRD complex using multiple cross-link IP mass spectrometry experiments, confirming that the core of the complex consists of MTA, RBBP, and HDAC proteins. It also reveals interactions between CDK2AP1 and CDK2AP2 with the NuRD complex, shedding light on the topology of peripheral NuRD subunits relative to the core complex. The data provide a more detailed understanding of the assembly and structure of the NuRD complex.
Article
Chemistry, Applied
Xiu-Er Luo, Ruo-Yong Wang, Jin-Hua Wang, Ying Li, Huai-Nan Luo, Xin-An Zeng, Meng-Wai Woo, Zhong Han
Summary: In this study, corn porous starch (CPS) was prepared using enzymatic hydrolysis and further enhanced by the treatment of a pulsed electric field (PEF). The PEF treated porous starch (CPS-PEF) was cross-linked with sodium trimetaphosphate (STMP). The results showed that PEF treatment improved the oil absorption and surface properties of CPS, and the cross-linking further enhanced the adsorption properties and thermal stability of the porous starch. Double modification with PEF and cross-linking proved to be an effective method for the preparation of porous starch.
Article
Plant Sciences
Konstantinos Kotsaridis, Vassiliki A. Michalopoulou, Dimitra Tsakiri, Dina Kotsifaki, Aikaterini Kefala, Nikos Kountourakis, Patrick H. N. Celie, Michael Kokkinidis, Panagiotis F. Sarris
Summary: In this study, it was found that the fusion of Exo70B1 protein in Arabidopsis with XopP is stable at high temperatures. XopP is able to phosphorylate Exo70B1 and protect it from AtCPK5 phosphorylation, thereby evading the host's immune response.
Article
Biochemical Research Methods
Johannes F. Hevler, Albert J. R. Heck
Summary: Mitochondria, packed with proteins, play important roles in various cellular processes. While many mitochondrial protein complexes have been identified, some protein-protein interactions remain elusive. Cross-linking mass spectrometry (XL-MS) has proven to be a valuable tool for the in-depth characterization of these interactions. In this article, experimental strategies for the analysis of proteome-wide protein-protein interactions in mitochondria using XL-MS are highlighted, along with recent technological advances that can further enhance the in situ characterization of these interactions.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Review
Biochemical Research Methods
Deng Liu, Michelle Liberton, John Hendry, Javad Aminian-Dehkordi, Costas D. Maranas, Himadri B. Pakrasi
Summary: Cyanobacteria, as photoautotrophic organisms, capture and store solar energy in the form of biomass, which has been traditionally used for food and nutrition. Synthetic biology strategies are currently being employed to increase cyanobacterial biomass yield and productivity, as well as to engineer them as cellular factories for sustainable food and nutrient production.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Kristen E. Wendt, Patricia Walker, Annesha Sengupta, Justin Ungerer, Himadri B. Pakrasi
Summary: Natural transformation, a process by which bacteria uptake and incorporate extracellular DNA, plays a significant role in bacterial evolution. Cyanobacteria, serving as important model systems for studying photosynthesis, have not been extensively characterized for natural transformation. By introducing polymorphic alleles, a naturally transformable and fast-growing cyanobacterial strain was created.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Virginia M. Johnson, Sandeep Biswas, Johnna L. Roose, Himadri B. Pakrasi, Haijun Liu
Summary: Photosystem II (PSII) undergoes a complex lifecycle involving multiple assembly proteins, including Psb27, which transiently binds and departs from PSII assembly intermediates. In this study, Psb27 mutant strains were compared to explore its impact on PSII function and assembly. Over-expression of Psb27 resulted in minimal impact on PSII quantum yield but showed increased tolerance to fluctuating light conditions. These findings suggest that Psb27 plays a role in PSII repair and assembly.
PHOTOSYNTHESIS RESEARCH
(2022)
Article
Microbiology
Nancy Y. Kiang, Wesley D. Swingley, Dikshyant Gautam, Jared T. Broddrick, Daniel J. Repeta, John F. Stolz, Robert E. Blankenship, Benjamin M. Wolf, Angela M. Detweiler, Kathy Ann Miller, Jacob J. Schladweiler, Ron Lindeman, Mary N. Parenteau
Summary: In this study, we isolated a cyanobacterium containing chlorophyll-d from the intertidal field site at Moss Beach, California. The strain, designated as Acaryochloris sp. (marina) strain Moss Beach, has a unique pigment composition and genome sequence. It is closely related to strain S15, an epiphyte of red algae, and could potentially be the closest known relative to the original source of chlorophyll-d discovered by Manning and Strain in 1943.
Review
Microbiology
Virginia M. Johnson, Himadri B. Pakrasi
Summary: Photosystem II is a light-driven water-plastoquinone oxidoreductase that plays a crucial role in maintaining high photosynthetic activity at the cellular level. Studying its lifecycle in cyanobacteria, especially through new structural findings enabled by cryo-electron microscopy, provides valuable insights into Photosystem II assembly and repair.
Article
Microbiology
Patricia L. Walker, Himadri B. Pakrasia
Summary: We identified a protein called HltA that plays a key role in the high light tolerance of Synechococcus elongatus UTEX 2973. HltA contains a functional PP2C-type protein phosphatase domain and a regulatory N-terminal GAF domain. It is widely found in cyanobacteria and is important for the photosynthetic lifestyle of these organisms.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemistry & Molecular Biology
Haijun Liu
Summary: This study investigates intrinsically disordered proteins/regions (IDPRs) in the interface of photosynthetic pigment protein complexes using a joint platform that combines in silico models and structural mass spectrometry data. The research reveals the structure of the PB domain and its associations with other proteins in the complex.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Plant Sciences
Dariusz M. Niedzwiedzki, Nikki Cecil M. Magdaong, Xinyang Su, Haijun Liu
Summary: This study reports the existence of a nonameric acpPC in a dinoflagellate. Compared to the well-characterized trimeric acpPC, the nonameric acpPC exhibits a longer emission wavelength and substantially altered excited state lifetimes of Chl a. The presence of this nonameric acpPC may enable efficient downhill excitation energy transfer and utilize a protective self-relaxation strategy. Therefore, the highly-oligomerized acpPC nonamer is considered as a functional unit in the Symbiodiniaceae thylakoid membrane.
PHOTOSYNTHESIS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Ryan Puskar, Chloe Du Truong, Kyle Swain, Saborni Chowdhury, Ka-Yi Chan, Shan Li, Kai-Wen Cheng, Ting Yu Wang, Yu-Ping Poh, Yuval Mazor, Haijun Liu, Tsui-Fen Chou, Brent L. Nannenga, Po-Lin Chiu
Summary: The study utilizing cryo-EM reveals the structure of an asymmetric bacterial photosynthetic supercomplex, providing insights into light excitation energy transfer routes and a possible evolutionary transition intermediate of the bacterial photosynthetic supercomplex.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Michelle Liberton, Sandeep Biswas, Himadri B. Pakrasi
Summary: Cyanobacteria are the only oxygenic photosynthetic organisms capable of nitrogen fixation, with regulation of photosynthesis during the diurnal cycle hypothesized to be linked with nitrogen fixation. The availability of nitrogen has a significant impact on productivity in aquatic environments. The study found that increased nitrogen availability led to higher levels of PSII protein and promoted cell growth.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Annesha Sengupta, Anindita Bandyopadhyay, Max G. Schubert, George M. Church, Himadri B. Pakrasi
Summary: In this study, we investigated the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe, with the goal of improving its productivity. Our findings demonstrate that partial truncation of the antenna leads to a growth advantage and increased sucrose production. However, targeted deletion of the linker protein proved detrimental, highlighting the importance of maintaining a minimal rod-core structure for efficient light harvesting.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Sandeep Biswas, Dariusz M. Niedzwiedzki, Himadri B. Pakrasi
Summary: Photosystem II in oxygenic organisms is a large membrane-bound pigment protein complex that undergoes rapid turnover. The assembly of Photosystem II involves the formation of multiple intermediates, including the CP43-preassembly complex (pCP43). In this study, the energy transfer dynamics in pCP43 were investigated through spectroscopic analysis and fluorescence decay kinetics. The results revealed the efficiency of energy transfer from beta-carotene to chlorophyll a and demonstrated the pathways of singlet excitation relaxation/decay and triplet state sensitization.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2023)
Article
Plant Sciences
Sandeep Biswas, Dariusz M. Niedzwiedzki, Michelle Liberton, Himadri B. Pakrasi
Summary: In photosynthesis, cyanobacteria use pigments and chlorophyll-binding proteins (such as CP43, CP47, IsiA, and PcbC) to harvest and transfer light energy for energy trapping and dissipation. Research shows that these proteins have similar spectral properties, suggesting a common ancestor, and a closer evolutionary relationship between CP47 and IsiA.
PHOTOSYNTHESIS RESEARCH
(2023)