Article
Multidisciplinary Sciences
Omar De Bei, Marialaura Marchetti, Luca Ronda, Eleonora Gianquinto, Loretta Lazzarato, Dimitri Y. Chirgadze, Steven W. Hardwick, Lee R. Cooper, Francesca Spyrakis, Ben F. Luisi, Barbara Campanini, Stefano Bettati
Summary: This study determines the structures of two IsdB:Hb complexes using single-particle cryo-electron microscopy, revealing the interaction mechanism between IsdB and Hb during heme extraction and the final step of heme transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Wenhao Cui, Yange Niu, Zejian Sun, Rui Liu, Lei Chen
Summary: In this study, the cryo-EM structures of human SGLT1 and SGLT2 in the substrate-bound state were determined, showing an occluded conformation with tightly sealed extracellular and intracellular gates. The sugar substrates were found to be caged inside a cavity surrounded by specific transmembrane helices. Structural analysis revealed the conformational changes associated with substrate binding and release. These structures provide important insights into the transport mechanisms of SGLT.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Mitchell A. Moseng, Meinan Lyu, Tanadet Pipatpolkai, Przemyslaw Glaza, Corey C. Emerson, Phoebe L. Stewart, Phillip J. Stansfeld, Edward W. Yu
Summary: The E. coli CusA membrane protein belongs to the HME subfamily of RND efflux pumps, recognizing and extruding Cu(I) and Ag(I) ions. It was found that different protomers of CusA within the trimer can simultaneously bind Cu(I) ions and function independently in ion transport. This discovery provides new insights into the mechanism of ion transport within the trimer.
Article
Biology
Xiaoxing Huang, Youwang Wang, Cong Yu, Hui Zhang, Qiang Ru, Xinxin Li, Kai Song, Min Zhou, Ping Zhu
Summary: This study reports the structures of human alpha-2-macroglobulin and reveals its dynamic transformation as a protease inhibitor and the molecular mechanism of substrate entrapment.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Biology
Hirohide Takahashi, Toshiki Yamada, Jerod S. Denton, Kevin Strange, Erkan Karakas
Summary: Volume-regulated anion channels (VRACs) mediate volume regulation and solute efflux from cells, but their composition and structure remain unclear. In this study, the authors developed novel homomeric LRRC8 chimeric channels that mimic native VRACs. They found that the LRRC8C-LRRC8A(IL1(25)) chimera has a seven-subunit structure, a large pore size, and normal pharmacology compared to non-functional homomeric channels. Lipid-like densities were also observed in the channel, suggesting a role in gating and regulation.
Article
Multidisciplinary Sciences
Anjie Xia, Xihao Yong, Changbin Zhang, Guifeng Lin, Guowen Jia, Chang Zhao, Xin Wang, Yize Hao, Yifei Wang, Pei Zhou, Xin Yang, Yue Deng, Chao Wu, Yujiao Chen, Jiawei Zhu, Xiaodi Tang, Jingming Liu, Shiyu Zhang, Jiahao Zhang, Zheng Xu, Qian Hu, Jinlong Zhao, Yuting Yue, Wei Yan, Zhaoming Su, Yuquan Wei, Rongbin Zhou, Haohao Dong, Zhenhua Shao, Shengyong Yang
Summary: This study presents the cryo-EM structures of GPR34 bound with LysoPS and its inhibition by the antagonist YL-365. The findings provide mechanistic insights into the endogenous agonist recognition and antagonist inhibition of GPR34, highlighting GPR34 as a promising target for disease treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Xi Zhang, Cang Wu, Zhihong Song, Dayong Sun, Liting Zhai, Chuang Liu
Summary: In this study, the structures of full-length SORLA were determined and two distinct conformations of apo-SORLA were identified using single-particle cryogenic electron microscopy. Unlike homologous proteins, SORLA existed in both monomer and dimer forms in a neutral solution. Only three hydrogen bonds near the dimer interface were involved in dimerization, and the orientation of residue R490 played a key role in ligand binding. These findings reveal a unique mechanism of SORLA dimerization for protein trafficking.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Le Thi My Le, James Robert Thompson, Sepehr Dehghani-Ghahnaviyeh, Shashank Pant, Phuoc Xuan Dang, Jarrod Bradley French, Takahisa Kanikeyo, Emad Tajkhorshid, Amer Alam
Summary: Phospholipid extrusion by ABC subfamily A (ABCA) exporters is essential for cellular physiology, but the molecular details of substrate interactions and transport mechanisms are still not well understood. In this study, cryo-EM structures of lipid-embedded human ABCA7 in different states were determined, revealing the structural framework for substrate entry and exit from ABCA7 and providing insights into the underlying conformational transitions. Combining functional analysis and molecular dynamics simulations, the study also shed light on lipid partitioning and localized membrane perturbations that contribute to ABCA7 function and may have implications for other ABCA family transporters.
Article
Biology
Jesse M. Hansen, Avital Horowitz, Eric M. Lynch, Daniel P. Farrell, Joel Quispe, Frank DiMaio, Justin M. Kollman
Summary: Many metabolic enzymes can self-assemble into filaments to organize and regulate metabolism, with this process often coinciding with significant metabolic changes. In yeast, cytoplasmic acidification upon starvation triggers the assembly of many metabolic enzymes into filaments, including CTPS. The assembly mechanism of CTPS is pH-sensitive and is conserved across different species.
Article
Multidisciplinary Sciences
Pu Qian, Cam T. Nguyen-Phan, Alastair T. Gardiner, Tristan I. Croll, Aleksander W. Roszak, June Southall, Philip J. Jackson, Cvetelin Vasilev, Pablo Castro-Hartmann, Kasim Sader, C. Neil Hunter, Richard J. Cogdell
Summary: The genomes of certain purple photosynthetic bacteria contain a multigene puc family that encodes a variety of alpha- and beta-polypeptides, forming a heterogeneous antenna of light-harvesting 2 (LH2) complexes. Through cryogenic electron microscopy (cryo-EM), the structures of four purified LH2 complexes, PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2, were determined. It was found that each complex contains a previously unknown polypeptide, gamma, and exhibits different absorption spectra.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Brent De Wijngaert, Shemaila Sultana, Anupam Singh, Chhaya Dharia, Hans Vanbuel, Jiayu Shen, Daniel Vasilchuk, Sergio E. Martinez, Eaazhisai Kandiah, Smita S. Patel, Kalyan Das
Summary: The study presents structures of two intermediate states of yeast mtRNAP during transcription initiation, elucidating molecular mechanisms of different steps and explaining key processes of transcription initiation.
Article
Multidisciplinary Sciences
Stefan G. Krimmer, Nicole Bertoletti, Yoshihisa Suzuki, Luka Katic, Jyotidarsini Mohanty, Sheng Shu, Sangwon Lee, Irit Lax, Wei Mi, Joseph Schlessinger
Summary: The development of various cells, including hematopoietic stem cells and germ cells, relies on the receptor tyrosine kinase KIT and its ligand stem cell factor (SCF). Somatic mutations in KIT lead to several types of human cancers. Cryo electron microscopy analysis reveals that oncogenic KIT mutants exhibit distinct structural arrangements compared to wild-type KIT. The D5 region of KIT is identified as a potential target for therapeutic intervention.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Amy K. Kendall, Mintu Chandra, Boyang Xie, William Wan, Lauren P. Jackson
Summary: This study improved the structure of retromer oligomer using single-particle cryo-electron microscopy (cryo-EM) and advanced data processing techniques. A new assembly interface formed by the N-termini of VPS26A and VPS35 was identified using a retromer mutant. The findings suggest that metazoan retromer may serve as an adaptable scaffold.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Shuman Peng, Yuting Zhan, Dongqi Zhang, Lu Ren, Anqi Chen, Zhou-Feng Chen, Haitao Zhang
Summary: This study reports the crystal structure of the inactive state of human GRPR in complex with the non-peptide antagonist PD176252, as well as the cryo-EM structures of GRPR bound to the endogenous peptide agonist gastrin-releasing peptide and the synthetic BBN analog [D-Phe6, beta-Ala11, Phe13, Nle14] Bn (6-14), in complex with Gq heterotrimers. These structures revealed the molecular mechanisms for the ligand binding, receptor activation, and Gq proteins signaling of GRPR, which could accelerate the design of GRPR antagonists and agonists for cancer and pruritus treatments.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Xiaoli Yang, Zhanyu Ding, Lisi Peng, Qiuyue Song, Deyu Zhang, Fang Cui, Chuanchao Xia, Keliang Li, Hua Yin, Shiyu Li, Zhaoshen Li, Haojie Huang
Summary: This study provides structural insights into the rearrangements of EP surface-loops and heavy chain dynamics in the EP catalytic cycle, advancing our understanding of EP-associated pancreatitis.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Multidisciplinary Sciences
Andrea Mattevi
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Friedrich Forster
Summary: Cryo-electron tomography is a powerful technique for studying molecular structures in cells and tissues. By using statistical methods, higher resolution insights can be obtained, making structural biology in native cells a reality.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2022)
Article
Biochemistry & Molecular Biology
Mario De Simone, Laura Alvigini, Lur Alonso-Cotchico, Vania Brissos, Jonatan Caroli, Maria Fatima Lucas, Emanuele Monza, Eduardo Pinho Melo, Andrea Mattevi, Ligia O. Martins
Summary: This study presents a new variant of the dioxygenase NOV1 that exhibits improved activity and stability compared to the wild type. The replacement of S283F in the variant leads to increased turnover rate and catalytic efficiency. The variant also demonstrates enhanced stabilization of the iron cofactor in the active site. Importantly, the variant is capable of catalyzing the conversion of isoeugenol to vanillin with high molar conversion yields within 24 hours.
Article
Biochemistry & Molecular Biology
Alessandro Boverio, Wahyu S. Widodo, Lars L. Santema, Henriette J. Rozeboom, Ruite Xiang, Victor Guallar, Andrea Mattevi, Marco W. Fraaije
Summary: In this study, the newly discovered carbohydrate oxidase NagOx from Ralstonia solanacearum was biochemically and structurally characterized. It showed high activity towards N-acetyl-D-galactosamine and N-acetyl-D-glucosamine, and could accept non-acetylated hexoses with lower efficiency. The crystal structure revealed a FAD-bound cavity and substrate docking highlighted a key residue involved in the accommodation of N-acetylated sugars. An enzyme variant with modified substrate acceptance profile was generated by replacing this residue. NagOx, being overexpressed in a bacterial host, has potential as a customizable biocatalyst for selective oxidation of monosaccharides and oligosaccharides.
Article
Cell Biology
Andrea Tirincsi, Sarah O'Keefe, Duy Nguyen, Mark Sicking, Johanna Dudek, Friedrich Forster, Martin Jung, Drazena Hadzibeganovic, Volkhard Helms, Stephen High, Richard Zimmermann, Sven Lang
Summary: Importing proteins into the endoplasmic reticulum is crucial for approximately 30% of the human proteome, involving precursor protein targeting and insertion or translocation across the ER membrane with the help of signals in precursor polypeptides. Little is known about the SRP-independent/SND pathway, and our study aimed to identify additional components and characterize the client spectrum of this pathway, finding that SND clients are predominantly membrane proteins.
Article
Multidisciplinary Sciences
Max Gemmer, Marten L. Chaillet, Joyce van Loenhout, Rodrigo Cuevas Arenas, Dimitrios Vismpas, Mariska Grollers-Mulderij, Fujiet A. Koh, Pascal Albanese, Richard A. Scheltema, Stuart C. Howes, Abhay Kotecha, Juliette Fedry, Friedrich Forster
Summary: This study uses cryo-electron tomography and molecular modeling to capture snapshots of mRNA translation and protein maturation at the ER membrane. They identify a high abundance pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) and observe distinct polysomes binding to different ER translocons specialized in protein synthesis. They also obtain near-complete atomic models of ER translocon variants, revealing specific interactions and stoichiometric cofactors associated with protein isomerases.
Article
Biochemistry & Molecular Biology
Susanne R. Bruekner, Wietske Pieters, Alexander Fish, A. Manuel Liaci, Serge Scheffers, Emily Rayner, Daphne Kaldenbach, Lisa Drost, Marleen Dekker, Sandrine van Hees-Stuivenberg, Elly Delzenne-Goette, Charlotte de Konink, Hellen Houlleberghs, Hendrikus Jan Dubbink, Abeer AlSaegh, Niels de Wind, Friedrich Forster, Hein te Riele, Titia K. Sixma
Summary: The homozygous V63E mutation in MSH2 disrupts a previously unappreciated interface between mismatch binding domains and leads to reduced DNA binding, which explains the pathogenic phenotype of this mutation and its association with increased cancer risk. Our research provides new insights into the mechanism of the V63E mutation and helps to understand the role of the MBD interface in replication fidelity.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yiming Guo, Laura Alvigini, Milos Trajkovic, Lur Alonso-Cotchico, Emanuele Monza, Simone Savino, Andrea Mattevi, Marco W. Fraaije
Summary: Various 4-alkylphenols can be obtained from lignocellulosic biomass through reductive catalytic fractionation. This study presents the engineering of a bacterial eugenol oxidase to catalyze the selective dehydrogenation of 4-n-propylguaiacol to isoeugenol. The engineered variant shows good activity, thermostability, and high chemoselectivity.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Gautier Bailleul, Guang Yang, Callum R. R. Nicoll, Andrea Mattevi, Marco W. W. Fraaije, Maria Laura Mascotti
Summary: Enzyme functional diversification is crucial for biological adaptation, allowing organisms to utilize or eliminate new substances and xenobiotics in new environments. This study uses a paleobiochemistry approach and enzymology techniques to uncover the historical substitutions that led to the functional diversification of the FMO family in tetrapods. Few amino acid replacements modulate the oxygenating flavin intermediate, transforming an ancestral multi-tasking FMO into a specialized monooxygenase. This finding highlights the importance of residues beyond the active site core in determining enzymatic function. Detoxification enzymes play a crucial role in the survival of animals in new environments.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Marika K. Kucinska, Juliette Fedry, Carmela Galli, Diego Morone, Andrea Raimondi, Tatiana Solda, Friedrich Forster, Maurizio Molinari
Summary: This study reveals that expansion of the mammalian ER leads to the disassembly of LINC complexes and swelling of ONM. Upon resolution of ER stress, the physiologic distance between ONM and INM is restored through a catabolic pathway called micro-ONM-phagy.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Callum R. Nicoll, Marta Massari, Marco W. Fraaije, Maria Laura Mascotti, Andrea Mattevi
Summary: Ancestral sequence reconstruction (ASR) is a powerful technique for understanding protein sequence changes across evolution and how they give rise to different phenotypes. It has been particularly useful in revealing common molecular factors governing enzyme function. This article highlights the strength of ASR in uncovering catalytic mechanisms and emerging phenotypes for various proteins, as well as its potential applications in biotechnology.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gwen Tjallinks, Alessandro Boverio, Ivana Maric, Henriette Rozeboom, Mark Arentshorst, Jaap Visser, Arthur F. J. Ram, Andrea Mattevi, Marco W. Fraaije
Summary: Patulin synthase (PatE) from Penicillium expansum was expressed in Aspergillus niger, allowing purification and characterization of PatE. The study confirmed that PatE is active not only on ascladiol, but also on several aromatic alcohols including 5-hydroxymethylfurfural.
Article
Biochemistry & Molecular Biology
Marten L. Chaillet, Gijs van der Schot, Ilja Gubins, Sander Roet, Remco C. Veltkamp, Friedrich Forster
Summary: Cryo-electron tomography is used to obtain 3D images of macromolecules in cells. Template matching (TM) is commonly used for macromolecule detection, but rotational searches have not been thoroughly investigated due to computational limitations. This study introduces a GPU implementation of TM in PyTOM software, enabling faster and more comprehensive rotation searches beyond the Crowther criterion. The improvements in sensitivity and false-discovery rate are demonstrated using ribosome detection as examples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Yiming Guo, Laura Alvigini, Mohammad Saifuddin, Ben Ashley, Milos Trajkovic, Lur Alonso-Cotchico, Andrea Mattevi, Marco W. Fraaije
Summary: This study presents a one-pot biocatalytic cascade reaction for the efficient synthesis of racemic syringaresinol, a valuable compound in nutraceutical and polymer chemistry. The process utilizes renewable lignocellulosic material and involves the engineering of enzymes to achieve high conversion and chemoselectivity. The study demonstrates the potential for the biocatalytic production of syringaresinol from renewable sources.
Review
Biochemistry & Molecular Biology
A. Manuel Liaci, Friedrich Forster
Summary: Cleavable and non-cleavable signal sequences target a quarter of the human proteome to the ER. Interaction between these signal sequences and ER targeting machinery determines protein location and translocation fidelity, as discussed in recent insights from structural biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)