Article
Biochemistry & Molecular Biology
Yoonji Bae, Sang Kwon Lee, Young Chan Chae, Chan Young Park, Sebyung Kang
Summary: Covalent protein-ligation methods were used to visualize the localization of proteins in cells and study the topology of membrane proteins. By selectively labeling membrane proteins in a topology-dependent manner, the method proved to be effective in both live and permeabilized cells.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Genetics & Heredity
Smrithi Salian, Hind Benkerroum, Thi Tuyet Mai Nguyen, Sheela Nampoothiri, Taroh Kinoshita, Temis Maria Felix, Fiona Stewart, Sanjay M. Sisodiya, Yoshiko Murakami, Philippe M. Campeau
Summary: DOORS syndrome is a rare disorder characterized by a range of symptoms, including deafness, intellectual disability, and others. This study identified two individuals with DOORS syndrome but without deafness, both carrying a homozygous missense variant in the PIGF gene. The study highlights the variability of clinical features in DOORS syndrome and the importance of considering inherited GPI deficiencies in diagnosis.
Article
Biochemistry & Molecular Biology
Geoffrey J. Taghon, Jacob B. Rowe, Nicholas J. Kapolka, Daniel G. Isom
Summary: Research has shown that cholesterol binds in a similar manner in cryo-EM and X-ray structures of GPCRs, with 92% of cholesterol molecules residing in predictable locations lacking discernable cholesterol-binding motifs.
Article
Biochemistry & Molecular Biology
Sung-jun Jung, Ji Eun Hani Kim, Tina Junne, Martin Spiess, Hyun Kim
Summary: This study investigated the targeting and topogenesis of the signal-anchored protein Spc3, finding that it reaches its final topology in two steps: partially dependent on SRP and then mediated by the Sec62/Sec63 complex.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Lei Wang, Haolin Zhong, Zhidong Xue, Yan Wang
Summary: DeepTMpred is a method for alpha-TMP topology prediction that utilizes pre-trained language model ESM, convolutional neural networks, attentive neural networks, and conditional random fields. It demonstrates superior predictive performance and rapid prediction speed.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Lei Wang, Haolin Zhong, Zhidong Xue, Yan Wang
Summary: Transmembrane proteins (TMPs) are crucial for cell recognition and communication. Determining the 3D structure of TMPs is challenging, and DeepTMpred model proposes a solution using pre-trained language models and neural networks for topology prediction. DeepTMpred demonstrates superior predictive performance, especially at the TMH level, and has significant implications for drug design and protein research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Cell Biology
Jingcheng Wang, Sungwon Han, Jin Ye
Summary: Ceramide regulates the topology of TM4SF20 by delaying the retrotranslocation of glycosylated N-linked glycans, causing protein accumulation. The results suggest that retrotranslocation plays a crucial role in the topological regulation of transmembrane proteins.
Article
Automation & Control Systems
Yanyan Ye, Siqin Liao, Yuanqing Wu, Mali Xing
Summary: This paper investigates the consensus problem of fractional-order multi-agent systems with the order alpha satisfying alpha is an element of (0, 1]. A novel distributed control protocol is constructed, which utilizes only past sampled position data of neighbors. Based on Laplace transform, Mittag-Leffler function, and matrix theory, necessary and sufficient criteria for consensus are established, depending on the order, coupling gains, sampling period, and communication topology. The intervals of coupling gains and sampling period for achieving consensus are presented. Numerical simulations validate the theoretical results.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2023)
Article
Microbiology
Mikhail Oliveira Leastro, Juliana Freitas-Astua, Elliot Watanabe Kitajima, Vicente Pallas, Jesus A. Sanchez-Navarro
Summary: The study revealed the association of citrus leprosis virus C2 movement protein and capsid protein with biological membranes, with both proteins exposing their N- and C-termini to the cell cytoplasmic compartment. These findings have important implications for the intracellular movement of the virus.
Article
Biochemical Research Methods
Camilo Fuentes-Beals, Alejandro Valdes-Jimenez, Gonzalo Riadi
Summary: This article introduces how to learn and create a Hidden Markov Model (HMM) without programming skills or a deep understanding of algorithms. It presents the structure and elements of HMM by addressing its original questions. The modeling process is illustrated with an example of modeling and predicting transmembrane segments. The article also introduces an educational webserver called HMMTeacher for guiding the input and solution of HMM algorithms.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Computer Science, Information Systems
Janghoon Yang, Yungho Choi
Summary: The study optimized the communication topology of a consensus network, proposed three different suboptimal topology algorithms to minimize the LQR cost, significantly reducing LQR cost by optimizing communication topology. The QTCMO algorithm showed significantly less complexity compared to the other two algorithms.
Article
Automation & Control Systems
Muhammad Ahsan Razaq, Muhammad Rehan, Choon Ki Ahn, Abdul Qayyum Khan, Muhammad Tufail
Summary: This paper focuses on leader-following consensus of multiagents with one-sided Lipschitz nonlinear dynamics under switching topologies and consensus control strategies. A new condition for consensus is established through dwell time constraints and communication restoration mechanisms. Simplified consensus controller design conditions are developed and consensus protocol gains can be obtained directly through convex routines. An algorithm using cone complementary linearization approach is also provided for solving nonlinear constraints in a numerical simulation demonstrating the efficiency of the proposed control schemes for multiagents.
IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS
(2021)
Article
Engineering, Multidisciplinary
Govind Saraswat, Vivek Khatana, Sourav Patel, Murti V. Salapaka
Summary: This article presents a finite-time stopping criterion for consensus algorithms in networks with dynamic communication topology. It proposes a maximum-minimum protocol to propagate global maximum and minimum values of agent states, allowing for a distributive determination of convergence in finite time. Experimental results illustrate the practical utility of the algorithm.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2023)
Article
Computer Science, Artificial Intelligence
N. Sakthivel, M. Mounika Devi
Summary: This paper addresses the consensus problem of nonlinear multiagent systems with uncertainties and switching network topology under truncated prediction feedback approach subjected to periodic scaling attacks. A state feedback controller is developed to ensure the stability of the closed loop systems, and a set of necessary conditions are derived in terms of linear matrix inequalities using the Lyapunov-Krasovskii functional.
Article
Multidisciplinary Sciences
Kyrie P. Grasekamp, Basile Beaud Benyahia, Najwa Taib, Bianca Audrain, Benjamin Bardiaux, Yannick Rossez, Nadia Izadi-Pruneyre, Maylis Lejeune, Xavier Trivelli, Zina Chouit, Yann Guerardel, Jean-Marc Ghigo, Simonetta Gribaldo, Christophe Beloin
Summary: E. coli and most diderm bacteria have unique lipid distribution, and we discovered a new MlaD type in Veillonella parvula that may be part of the ancestral core of the Mla system.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Jose Arcadio Farias-Rico, Frida Ruud Selin, Ioanna Myronidi, Marie Fruehauf, Gunnar von Heijne
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Biochemistry & Molecular Biology
Luigi Notari, Markel Martinez-Carranza, Jose Arcadio Farias-Rico, Pal Stenmark, Gunnar von Heijne
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Patricia Lara, Asa Tellgren-Roth, Hourinaz Behesti, Zachi Horn, Nina Schiller, Karl Enquist, Malin Cammenberg, Amanda Liljenstrom, Mary E. Hatten, Gunnar von Heijne, IngMarie Nilsson
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Biology
Vivekanandan Shanmuganathan, Nina Schiller, Anastasia Magoulopoulou, Jingdong Cheng, Katharina Braunger, Florian Cymer, Otto Berninghausen, Birgitta Beatrix, Kenji Kohno, Gunnar von Heijne, Roland Beckmann
Article
Biochemistry & Molecular Biology
Maximilian Seurig, Moira Ek, Gunnar von Heijne, Nir Fluman
NATURE CHEMICAL BIOLOGY
(2019)
Article
Cardiac & Cardiovascular Systems
Camilla Hage, Lars Lofgren, Filippos Michopoulos, Ralph Nilsson, Pia Davidsson, Chanchal Kumar, Mattias Ekstrom, Maria J. Eriksson, Patrik Lynga, Bengt Persson, Hakan Wallen, Li Ming Gan, Hans Persson, Cecilia Linde
JOURNAL OF CARDIAC FAILURE
(2020)
Article
Multidisciplinary Sciences
Grant Kemp, Ola B. Nilsson, Pengfei Tian, Robert B. Best, Gunnar von Heijne
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Rageia Elfageih, Alexandros Karyolaimos, Grant Kemp, Jan-Willem de Gier, Gunnar von Heijne, Renuka Kudva
Article
Biology
Felix Nicolaus, Ane Metola, Daphne Mermans, Amanda Liljenstrom, Ajda Krc, Salmo Mohammed Abdullahi, Matthew Zimmer, Thomas F. Miller, Gunnar von Heijne
Summary: The study investigates the cotranslational biosynthesis of E. coli inner membrane proteins and reveals the complexities in membrane integration process, including protein folding in the ribosome exit tunnel and interactions between charged residues and the membrane. The results also suggest residue-specific interactions between transmembrane helices during the integration process, supporting the 'sliding' model of translocon-mediated membrane protein integration.
Editorial Material
Multidisciplinary Sciences
Gunnar von Heijne
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Felix Nicolaus, Fatima Ibrahimi, Anne den Besten, Gunnar von Heijne
Summary: During the cotranslational insertion of membrane proteins mediated by SecYEG, both electrostatic and hydrophobic interactions involving sequence elements can impact the behavior of transmembrane helices, leading to delayed contact with the membrane.
Article
Biotechnology & Applied Microbiology
Felix Teufel, Jose Juan Almagro Armenteros, Alexander Rosenberg Johansen, Magnus Halldor Gislason, Silas Irby Pihl, Konstantinos D. Tsirigos, Ole Winther, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
Summary: Signal peptides are short amino acid sequences that regulate protein secretion and translocation. SignalP 6.0, a machine learning model, is introduced to detect all types of signal peptides, including those applicable to metagenomic data.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Daphne Mermans, Felix Nicolaus, Klara Fleisch, Gunnar von Heijne
Summary: In recent years, it has been discovered that many cytoplasmic proteins can dimerize while being translated. However, it was unclear whether this phenomenon also applies to integral membrane proteins. This study demonstrates that the inner membrane protein EmrE in Escherichia coli can indeed undergo cotranslational interactions, suggesting that membrane proteins can start to fold and dimerize during the membrane insertion process.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Daphne Mermans, Felix Nicolaus, Aysel Baygin, Gunnar von Heijne
Summary: Human growth hormone (hGH) is a protein with four helix bundles and has pharmacological interest. This study investigates the folding of hGH during expression in Escherichia coli, both in vitro translation with or without the chaperone trigger factor (TF) and in E. coli. The findings suggest that hGH begins folding before it is fully released from the ribosome and may interact with TF and other chaperones.
Article
Biology
Jose Juan Almagro Armenteros, Marco Salvatore, Olof Emanuelsson, Ole Winther, Gunnar von Heijne, Arne Elofsson, Henrik Nielsen
LIFE SCIENCE ALLIANCE
(2019)