Article
Multidisciplinary Sciences
Prasun Kumar, Neil G. Paterson, Jonathan Clayden, Derek N. Woolfson
Summary: The alpha-helix is important in structural biology and protein folding. This study shows that synthetic peptide assemblies can be built from 3(10)-helices, which are less common in natural proteins. The research provides principles and rules for designing in this unexplored region of protein structure.
Article
Multidisciplinary Sciences
Natsuki Mizutani, Akira Kawanabe, Yuka Jinno, Hirotaka Narita, Tomoko Yonezawa, Atsushi Nakagawa, Yasushi Okamura
Summary: This study investigated the electrochemical coupling in Ciona intestinalis VSP using electrophysiology, fluorometry, and structural modeling. It was found that two hydrophobic residues at the bottom of S4 play a crucial role in the VSD-CCR coupling, with the hydrophobic spine acting as a central hub for translating electrical signals into chemical signals in VSP.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Hohyung Kang, Heeeun Joo, Junghoon Choi, Yong-Jae Kim, Yullim Lee, Soo-Yeon Cho, Hee-Tae Jung
Summary: Metal oxide semiconductors (MOS) have shown high sensitivity and selectivity for detecting H2S. However, there is a lack of methods to extend this approach to the top-down fabrication of H2S sensors. In this study, a top-down lithographic process was developed to produce a 10 nm-scale SnO2 nanochannel for H2S sensing with high-resolution and high aspect ratio structures. The nanochannel exhibited highly sensitive H2S detection performances and could be efficiently sensitized with a p-n heterojunction. Introducing a NiO nanoheterojunction further enhanced the sensor performance, demonstrating the highest sensitivity range to date for state-of-the-art H2S sensors.
Article
Biology
Go Kasuya, Koichi Nakajo
Summary: In this study, the researchers investigated the interaction between KCNE3 and KCNQ1 voltage sensors in the KCNQ1-KCNE3-calmodulin complex. They found that the distance between the S1 segment and KCNE3 is optimized to achieve constitutive activity. In addition, they identified mutant pairs of KCNQ1 and KCNE3 that partially restored constitutive activity when expressed together.
Article
Computer Science, Information Systems
Luigi Fassio, Longyang Lin, Raffaele De Rose, Marco Lanuzza, Felice Crupi, Massimo Alioto
Summary: This paper introduces a voltage reference design that can operate over a wide supply voltage range and has low power consumption. By using process sensor-driven selection/merging of circuit replicas, it mitigates the effect of global variations and improves voltage accuracy in deep sub-threshold. Experimental results demonstrate the high performance of the design across different process corners.
Article
Engineering, Electrical & Electronic
Orazio Aiello, Paolo Crovetti, Pedro Toledo, Massimo Alioto
Summary: The ultra-low voltage, ultra-low power rail-to-rail dynamic voltage comparator is solely based on digital standard cells, allowing for operation at very low voltages down to deep sub-threshold. The circuit has demonstrated correct operation at a supply voltage ranging from 0.6V down to 0.15V, with a delay lower than 442 μs (10pW) at the latter voltage. Its input offset voltage is less than 30mV over the entire rail-to-rail common-mode input and supply range, making it suitable for direct powering from mm-scale harvesters.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS II-EXPRESS BRIEFS
(2021)
Proceedings Paper
Computer Science, Hardware & Architecture
Orazio Aiello, Pedro Toledo
Summary: This paper discusses the performance/temperature tradeoff in an ultra-low voltage, ultra-low power rail-to-rail dynamic voltage comparator made solely by digital standard cells. Measurements show correct operation under rail-to-rail common-mode input at a supply voltage ranging from 0.6V down to 0.15V, with performance trade-offs observed under temperature variations.
2021 19TH IEEE INTERNATIONAL NEW CIRCUITS AND SYSTEMS CONFERENCE (NEWCAS)
(2021)
Article
Multidisciplinary Sciences
Vasyl Bondarenko, Marta M. Wells, Qiang Chen, Tommy S. Tillman, Kevin Singewald, Matthew J. Lawless, Joel Caporoso, Nicole Brandon, Jonathan A. Coleman, Sunil Saxena, Erik Lindahl, Yan Xu, Pei Tang
Summary: In this study, using a combination of experiments and computational methods, the full-length intracellular domain (ICD) structure of the human alpha 7 nicotinic acetylcholine receptor in a resting state was determined. It was found that a significant portion of the ICD residues are located in highly flexible regions, with a large loop (loop L) contributing to its stability by anchoring onto the MA helix. Known motifs for cytoplasmic binding, regulation, and signaling were observed in both helices and disordered flexible regions, highlighting the important role of ICD conformational plasticity in orchestrating various biological processes.
NATURE COMMUNICATIONS
(2022)
Article
Mechanics
Ugis Lacis, Michele Pellegrino, Johan Sundin, Gustav Amberg, Stephane Zaleski, Berk Hess, Shervin Bagheri
Summary: The molecular processes of the motion of the contact line were characterized to assess the accuracy of two continuum two-phase models. The calibrated continuum models accurately captured droplet displacement and break-up, but differences were observed near dynamic wetting transitions when compared to atomistic simulations.
JOURNAL OF FLUID MECHANICS
(2022)
Article
Chemistry, Multidisciplinary
Milosz Wieczor, Vito Genna, Juan Aranda, Rosa M. Badia, Josep Lluis Gelpi, Vytautas Gapsys, Bert L. de Groot, Erik Lindahl, Marti Municoy, Adam Hospital, Modesto Orozco
Summary: Exascale computing will revolutionize molecular simulations, improving their quality and quantity. This article reviews how the biomolecular simulations field is preparing for this change and showcases the power of these simulation strategies through the work done by the HPC simulation community.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2023)
Article
Multidisciplinary Sciences
Shaotong Zhu, Akshay Sridhar, Jinfeng Teng, Rebecca J. Howard, Erik Lindahl, Ryan E. Hibbs
Summary: GABA(A) receptors are important drug targets in the central nervous system for treating anxiety, sleep disorders, and epilepsy. This study presents two high-resolution structures of GABA(A) receptors bound by the drugs zolpidem and DMCM, providing insights into receptor modulation.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Aujan Mehregan, Sergio Perez-Conesa, Yuxuan Zhuang, Ahmad Elbahnsi, Diletta Pasini, Erik Lindahl, Rebecca J. Howard, Chris Ulens, Lucie Delemotte
Summary: This article mainly introduces the characteristics and functions of the envelope (E) protein, one of the structural proteins of SARS-CoV-2. By combining experimental and computational methods, researchers have found that the E protein can multimerize independently and plays an important role in viral budding. The study also found that the E protein may promote viral replication by reducing intracellular Ca2+ levels.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2022)
Article
Biophysics
Magnus Lundborg, Christian Wennberg, Jack Lidmar, Berk Hess, Erik Lindahl, Lars Norlen
Summary: A molecular-level understanding of skin permeation can improve the prediction of skin permeability and the effects of chemical penetration enhancers. This approach can facilitate product development and safety assessment of cosmetics.
BIOPHYSICAL JOURNAL
(2022)
Article
Multidisciplinary Sciences
Marie Lycksell, Urska Rovsnik, Anton Hanke, Anne Martel, Rebecca J. Howard, Erik Lindahl
Summary: This study characterized the structure and dynamics of DeCLIC using cryo-EM, SANS, and MD simulations, revealing alternative conformations of the NTD and calcium-binding site and expanding the conformational landscape of the pLGIC family. Moreover, it demonstrated the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate highly conserved interfacial interactions in the pLGIC family.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Vasyl Bondarenko, Qiang Chen, Kevin Singewald, Nandan Haloi, Tommy S. Tillman, Rebecca J. Howard, Erik Lindahl, Yan Xu, Pei Tang
Summary: This study reveals the binding details and structural changes induced by Ivermectin in the alpha 7nAChR using nuclear magnetic resonance, comparative modeling, and molecular dynamics simulations. The binding of Ivermectin to the alpha 7nAChR is stabilized by hydrophobic interactions between adjacent subunits, resulting in an expanded inter-subunit gap. The ion-permeation pathway shows a profile similar to the desensitized alpha 7nAChR, providing insights into cytoplasmic signaling under different functional states.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Multidisciplinary Sciences
Dagimhiwat H. Legesse, Chen Fan, Jinfeng Teng, Yuxuan Zhuang, Rebecca J. Howard, Colleen M. Noviello, Erik Lindahl, Ryan E. Hibbs
Summary: Legesse et al. present structural studies of a human GABAA receptor in complex with positive and negative modulator neurosteroids, uncovering mechanisms of potentiation and inhibition. Allopregnanolone, a positive modulator, binds at the receptor-bilayer interface, while inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support the mechanism of allopregnanolone potentiating channel activity and suggest pore block as the dominant mechanism for sulfated neurosteroid inhibition.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
Summary: The high-resolution cryo-EM maps pose challenges in automatically fitting atoms to densities while maintaining a good fit and allowing protein secondary structure changes. This study presents a solution using a maximum likelihood approach to identify the most likely structure that produced the observed density map. The derived refinement potentials and adaptive force scaling algorithm demonstrate improved performance.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Meeting Abstract
Biophysics
Anton Jansen, Paul Bauer, Rebecca J. Howard, Erik Lindahl, Berk Hess
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Christian Blau, Linnea Yvonnesdotter, Erik Lindahl
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Akshay Sridhar, Sarah C. Lummis, Erik Lindahl, Rebecca J. Howard, Chris Ulens
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Sebastian Wingbermuhle, Erik Lindahl
BIOPHYSICAL JOURNAL
(2022)