Article
Biochemistry & Molecular Biology
Madhumalar Subramanian, Charlotte Kielar, Satoru Tsushima, Karim Fahmy, Jana Oertel
Summary: The use of engineered cysteines on membrane-scaffolding protein MSP1D1 allows the formation of multimers of nanodiscs, which is crucial for membrane protein research. Minimal interference with nanodisc formation and structure was demonstrated by various analytical techniques. Transmission electron microscopy showed the growth of submicron-sized tracts of stacked nanodiscs through oligonucleotide attachment to engineered cysteines.
Review
Biochemistry & Molecular Biology
James S. Davies, Michael J. Currie, Joshua D. Wright, Michael C. Newton-Vesty, Rachel A. North, Peter D. Mace, Jane R. Allison, Renwick C. J. Dobson
Summary: Multicomponent transporters in bacteria are crucial for the uptake of nutrients, with implications for colonization and pathogenicity in humans. Current research focuses on the membrane interactions and the roles of lipids and higher oligomers in these complex systems.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Sarah Dallo, Jeehae Shin, Shanwen Zhang, Qian Ren, Huan Bao
Summary: Signal transduction at the synapse relies on protein-lipid interactions for the regulation of synaptic vesicle biogenesis, neurotransmitter release, and postsynaptic receptor activation. Recent advances in nanodiscs have greatly enhanced our ability to study and manipulate these interactions, offering new opportunities for understanding synaptic transmission.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lauren E. Ball, Liam J. Riley, Waled Hadasha, Rueben Pfukwa, Corinne J. Smith, Timothy R. Dafforn, Bert Klumperman
Summary: Polymer-based lipid nanoparticles, such as DIBMA, have shown significant advancements in the study of membrane proteins. Research indicates that DIBMA exhibits excellent performance in lipid nanodisc formation and membrane protein extraction, with better solubilization efficiency and cleaner separation compared to SMA and commercially available DIBMA.
Review
Biochemistry & Molecular Biology
Stephen G. Sligar, Ilia G. Denisov
Summary: Membrane proteins play crucial roles in biological processes, but are often challenging to study. The NanoDisc platform offers a self-assembled system that solubilizes membrane proteins in water while maintaining their functional activity. NanoDiscs have utility in studying cellular signaling complexes and delivering drugs, showcasing their versatility in biochemistry and pharmacology.
Article
Biochemistry & Molecular Biology
Patricia Alvarez-Sieiro, Hendrik R. Sikkema, Bert Poolman
Summary: This study presents a novel in vivo method to transform homodimeric proteins into apparent heterodimers for purification. It emphasizes the importance of expression conditions and the order of purification steps for functional ABC-transporter complex formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Chancievan Thangaratnarajah, Jan Rheinberger, Cristina Paulino, Dirk J. Slotboom
Summary: Energy-coupling factor (ECF)-type transporters are small, asymmetric membrane protein complexes that import micronutrients into bacterial cells. Recent research suggests that during the transport process, protein-induced membrane deformations facilitate the toppling of the S component.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Elise Kaplan, Nicholas P. Greene, Abigail E. Jepson, Vassilis Koronakis
Summary: In gram-negative bacteria, the Lol system plays a vital role in transporting triacylated lipoproteins from the inner membrane to the outer membrane. LolA, the periplasmic chaperone protein, is crucial for this process. This study presents the crystal structure of liganded LolA, providing molecular details of lipoprotein association and demonstrating how LolA accommodates different lipoproteins by interacting with their acyl chains. Additionally, the comparison of LolA structures reveals that the insertion of lipoprotein acyl chains disrupts the interaction between LolA and LolC. These findings contribute to a better understanding of the trafficking pathway in gram-negative bacteria.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Andrew Wilson, Natividad Ruiz
Summary: LPS plays a critical role in the outer membrane of Gram-negative bacteria. The transmembrane helix of LptC is involved in maintaining LptC levels and coupling the activities of LptB and LptF/LptG.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
James I. Mitchell-White, Thomas Stockner, Nicholas Holliday, Stephen J. Briddon, Ian D. Kerr
Summary: Members of the mammalian G subfamily of ATP-binding cassette transporters exhibit significant differences in substrate specificity, with ABCG2 playing a crucial role in multidrug resistance due to its wide substrate specificity. Analysis of conservation differences between members in a multiple sequence alignment of ABCG sequences from mammals reveals possible explanations for functional differences. Mapping sets of residues onto the 3D structure of ABCG2 illustrates a network of residues that may confer additional conformational flexibility, allowing for transport of a wider array of substrates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Manuel Wagner, Daniel Blum, Stefanie L. Raschka, Lea-Marie Nentwig, Christoph G. W. Gertzen, Minghao Chen, Christos Gatsogiannis, Andrzej Harris, Sander H. J. Smits, Richard Wagner, Lutz Schmitt
Summary: This study demonstrates that Pdr5, as a multidrug resistance (MDR) efflux pump, not only actively transports substrates across the lipid bilayer, but also generates a proton motif force in the presence of Mg2+-ATP and substrates, thereby increasing its effectiveness.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Microbiology
N. Zohreh Pourhassan, Eymen Hachani, Olivia Spitz, Sander H. J. Smits, Lutz Schmitt
Summary: This study investigates the role of the ABC transporter hemolysin B (HlyB) in the HlyA secretion system. The results reveal that the HlyA T1SS is composed of multiple proteins, and the GG repeats and amphipathic helix are crucial for efficient secretion.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Irfan Prabudiansyah, Ramon van der Valk, Marie-Eve Aubin-Tam
Summary: FtsH is a membrane-bound protease that plays a crucial role in regulating cellular functions, and can maintain its activity when reconstituted into lipid nanodiscs. Research has shown that the lipid bilayer composition affects the proteolytic activity of FtsH.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Biochemistry & Molecular Biology
Justin Amengual, Luke Notaro-Roberts, Mu -Ping Nieh
Summary: Bicellar systems have gained popularity in the fields of biochemistry, physical chemistry, and drug delivery technology due to their diverse morphology. They have been used as model membranes for studying transmembrane protein behavior and interactions with the cell. Additionally, they have shown potential as theranostic nanocarriers in biopharmaceutical and diagnostic research.
BIOPHYSICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
E. Sabine M. Schleker, Sabine Buschmann, Hao Xie, Sonja Welsch, Hartmut Michel, Christoph Reinhart
Summary: Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are important transmembrane proteins that facilitate the transport of substances across cell membranes. In this study, the role and function of the ABC-B transporter STE6-2p in the methylotrophic yeast Pichia pastoris were investigated. The findings suggest that STE6-2p can transport rhodamines in vivo and remain active in the presence of verapamil and triazoles in vitro. Additionally, the high-resolution structures of an ABC transporter from P. pastoris in the apo conformation and in complex with verapamil and adenylyl imidodiphosphate (AMP-PNP) provide insights into a potential sterol-binding site of unknown function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Tomohiro Yamashita, Sawako Kamikaseda, Aya Tanaka, Hidetoshi Tozaki-Saitoh, Jose M. M. Caaveiro, Kazuhide Inoue, Makoto Tsuda
Summary: The study demonstrates the inhibitory effect of the calcium channel blocker cilnidipine on P2X7R, reducing inflammatory responses and neuropathic pain mediated by microglial cells. This suggests the therapeutic potential of cilnidipine in treating these conditions.
Article
Biochemistry & Molecular Biology
Kosuke Oyama, Takatoshi Ohkuri, Mao Inoue, Jose M. M. Caaveiro, Tadashi Ueda
Summary: The study established a procedure to highly express human CH2 domain and human Fc in yeast P. pastoris, resulting in glycosylated and non-glycosylated forms that can be easily separated with high purity. It was found that glycosylation increased the thermal stability of the CH2 domain, and the purified glycosylated CH2 domain elicited polyclonal antibodies in mice. These antibodies could be potential candidates for developing a novel affinity material to purify human antibodies using their CH2 domain.
JOURNAL OF BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Kosuke Oyama, Takatoshi Ohkuri, Jinta Ochi, Jose M. M. Caaveiro, Tadashi Ueda
Summary: The glycosylation and stabilization of the CH2 domain in IgG can decrease its aggregation and immunogenicity, and the combination of these two modifications can completely suppress its aggregation behavior.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Daisuke Takahashi, Eri Matsunaga, Tomohiro Yamashita, Jose M. M. Caaveiro, Yoshito Abe, Tadashi Ueda
Summary: In this study, an in-vitro screening system was established to identify inhibitors against AL amyloidosis. Two compounds, gossypetin and isoquercitrin, were found to directly interact with the target protein and enhance its kinetic stability, making them potential leads for developing drugs against AL amyloidosis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Takanori Yokoo, Aki Tanabe, Yoko Yoshida, Jose M. M. Caaveiro, Makoto Nakakido, Yoichiro Ikeda, Yoshihiro Fujimura, Masaneori Matsumoto, Kevin Entzminger, Toshiaki Maruyama, C. J. Okumura, Masaomi Nangaku, Kouhei Tsumoto
Summary: Atypical hemolytic uremic syndrome (aHUS) is a disease associated with dysregulation of the immune complement system. Mutations and the presence of anti-CFH autoantibodies (AAbs) are known to cause CFH dysfunction. This study revealed the mechanism of recognition of CFH by anti-CFH AAbs and VHH4 using biophysical data and X-ray crystallography.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sandra Valenciano-Bellido, Jose M. M. Caaveiro, Koldo Morante, Tatyana Sushko, Makoto Nakakido, Satoru Nagatoishi, Kouhei Tsumoto
Summary: This study characterizes the role of the linker region between NEAT2 and NEAT3 in the molecular mechanism of heme extraction by the IsdH protein. It demonstrates that the linker region contributes to the stability and proper positioning of NEAT3 for heme acquisition.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Daisuke Takahashi, Kento Yonezawa, Yuki Okizaki, Jose M. M. Caaveiro, Tadashi Ueda, Atsushi Shimada, Fumio Sakane, Nobutaka Shimizu
Summary: Diacylglycerol kinases (DGKs) are multi-domain lipid kinases that regulate the levels of lipid messengers. This study investigated the structural properties of DGK alpha N-terminal (RVH and EF) domains, revealing that Ca2+ binding induces conformational changes mainly in the EF domain and identified the RVH domain as a novel Ca2+-binding domain.
Article
Biochemistry & Molecular Biology
Sara Insausti, Miguel Garcia-Porras, Johana Torralba, Izaskun Morillo, Ander Ramos-Caballero, Igor de la Arada, Beatriz Apellaniz, Jose M. M. Caaveiro, Pablo Carravilla, Christian Eggeling, Edurne Rujas, Jose L. Nieva
Summary: Antibody engagement with the membrane-proximal external region (MPER) of the envelope glycoprotein (Env) of HIV-1 is crucial for understanding the broad neutralization of the virus. This study investigates the specific features developed by MPER-specific antibodies and their interactions with viral phospholipids. The findings reveal the position-dependent contribution of electrostatic interactions and the potential mechanism of action for neutralization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Seisho Kinoshita, Makoto Nakakido, Chinatsu Mori, Daisuke Kuroda, Jose M. M. Caaveiro, Kouhei Tsumoto
Summary: Research on VHH engineering for biotechnological and clinical applications is actively conducted to take advantage of their favorable biophysical properties. Humanization of camelid VHHs through CDR grafting with a humanized VHH in clinical trials resulted in changes to the affinity, thermal stability, and conformational structure. Mutational and back-mutational analyses on the framework regions revealed the significant contribution of bulky residues and intramolecular interactions to the properties of VHHs. Back-mutations restored intramolecular interactions, resulting in increased thermal stability and affinity, showing the potential for designing VHHs by modifying the framework region without altering the CDRs.
Article
Biology
Johana Torralba, Igor de la Arada, Angelica Partida-Hanon, Edurne Rujas, Madalen Arribas, Sara Insausti, Claire Valotteau, Javier Valle, David Andreu, Jose M. M. Caaveiro, Maria Angeles Jimenez, Beatriz Apellaniz, Lorena Redondo-Morata, Jose L. Nieva
Summary: This study investigates the molecular recognition of the carboxy-terminal section of the membrane-proximal external region (C-MPER) of the HIV-1 envelope glycoprotein in membrane mimetics. It found that transmembrane domain residues contribute to binding affinity and specificity, and anchoring the helical C-MPER epitope to the membrane enhances antibody binding affinity and relieves the effect on lipid bilayer stability exerted by the interfacial MPER helix.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Akinobu Senoo, Satoru Nagatoishi, Daisuke Kuroda, Sho Ito, Go Ueno, Jose M. M. Caaveiro, Kouhei Tsumoto
Summary: Small molecules that regulate protein-protein interactions have potential as valuable drugs. In this study, we propose that modulating the conformational ensemble of the proteins involved in an interaction can interfere with protein-protein interactions. We applied this concept to P-cadherin and found that a small molecule inhibitor modulates the conformational ensemble of P-cadherin, resulting in the inhibition of cell adhesion.
Meeting Abstract
Biochemistry & Molecular Biology
Seisho Kinoshita, Makoto Nakakido, Daisuke Kuroda, Jose M. M. Caaveiro, Kouhei Tsumoto
Article
Chemistry, Medicinal
Yuya Hirose, Naoya Shindo, Makiko Mori, Satsuki Onitsuka, Hikaru Isogai, Rui Hamada, Tadanari Hiramoto, Jinta Ochi, Daisuke Takahashi, Tadashi Ueda, Jose M. M. Caaveiro, Yuya Yoshida, Shigehiro Ohdo, Naoya Matsunaga, Shinsuke Toba, Michihito Sasaki, Yasuko Orba, Hirofumi Sawa, Akihiko Sato, Eiji Kawanishi, Akio Ojida
Summary: The study reports a new class of covalent inhibitors of 3CLpro with strong antiviral activity against SARS-CoV-2 replication, showing potential in terms of biochemical efficiency and pharmacokinetic properties.
JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Anna Yui, Jose Manuel Martinez Caaveiro, Daisuke Kuroda, Makoto Nakakido, Satoru Nagatoishi, Takahiro Maruno, Susumu Uchiyama, Kouhei Tsumoto
Article
Biochemistry & Molecular Biology
Misaki Ishii, Makoto Nakakido, Jose M. M. Caaveiro, Daisuke Kuroda, C. J. Okumura, Toshiaki Maruyama, Kevin Entzminger, Kouhei Tsumoto
Summary: This study successfully created antibodies recognizing specific methylated substrates using a unique method; through structural and biophysical analyses, molecular details of antigen recognition by the antibodies were revealed; computational simulations replicated biophysical data, capturing antibodies of varying affinity and specificity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
