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Xiaoying Cai

University of California, Los Angeles

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Yao He

Guangdong University of Technology

Changlin Tian

University of Science and Technology of China

Longhua Zhang

University of Science and Technology of China

Z. Hong Zhou

University of California, Los Angeles

Jingtian Zheng

University of Illinois Chicago

Iris Yu

University of California, Los Angeles

Jeff F. Miller

University of California, Los Angeles

Weimin Gong

University of Science and Technology of China

Anthony Imani

California NanoSystems Institute

Dean Scholl

University of California, Los Angeles

Cooperative Institutions

University of Science and Technology of China

Chinese Academy of Sciences

Hefei National Center for Physical Sciences at Nanoscale

National Institutes of Health

University of California, Los Angeles

California NanoSystems Institute

National Eye Institute

University College London

University of Exeter

Royal Devon & Exeter NHS Foundation Trust

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CCDC 189768: Experimental Crystal Structure Determination

The Cambridge Structural Database (2002)

Xiaoying Cai B. Gehrhus P.B. Hitchcock M.F. Lappert J. Chris Slootweg

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

10.5517/cc6cgkk

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Combined approaches of EPR and NMR illustrate only one transmembrane helix in the human IFITM3

Scientific Reports (2016)

Shenglong Ling Chengwei Zhang Wei Wang Xiaoying Cai Lu Yu

Abstract Interferon-inducible transmembrane protein IFITM3 was known to restrict the entry of a wide spectrum of viruses to the cytosol of the host. The mechanism used by the protein to restrict viral entry is unclear given the unavailability of the membrane topology and structures of the IFITM family proteins. Systematic site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) studies of IFITM3 in detergent micelles identified a single, long transmembrane helix in the C-terminus and an intramembrane segment in the N-terminal hydrophobic region. Solution NMR studies of the same sample verified the secondary structure distribution and demonstrated two rigid regions interacting with the micellar surface. The resulting membrane topology of IFITM3 supports the mechanism of an enhanced restricted membrane hemi-fusion.

Site-directed spin labeling

Helix (gastropod)

Membrane topology

Unavailability

10.1038/srep24029

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Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy

bioRxiv (Cold Spring Harbor Laboratory) (2024)

Jingtian Zheng Yi-Chien Wu Xiaoying Cai Philana Phan Ekrem Emrah Er

Three-dimensional (3D) optical microscopy, combined with advanced tissue clearing, permits

Correlative

Fluorescence-lifetime imaging microscopy

10.1101/2024.05.14.594162

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A Novel Bi-Directional Channel for Nutrient Uptake across Mycobacterial Outer Envelope

Microorganisms (2024)

Lei Liu Chongzheng Wen Xiaoying Cai Weimin Gong

Nutrients are absorbed by special transport proteins on the cell membrane; however, there is less information regarding transporters across the mycobacterial outer envelope, which comprises dense and intricate structures. In this study, we focus on the model organism

Envelope (radar)

10.3390/microorganisms12091827

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Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials

The International Journal of High Performance Computing Applications (2004)

Yuefan Deng James Glimm J. W. Davenport Xiaoying Cai Eugene Santos

We estimate that a novel architecture massively parallel computer, the QCDOC, can integrate molecular dynamics equations for 10 5 particles interacting via long-range forces (including Coulomb) for 1–10 s of simulated time using several weeks of computing time using 8000 or 10,000 processors. This number of atoms is typical for biological molecules. The two main conclusions we reach are as follows. (1) This is an increase of more than one order of magnitude in simulated time over current simulations. (2) The novel architecture, with 24 parallel channels of low latency communication per processor, allows improved long-range communication and an unusual degree of fine-scale parallelism, compared to conventional switch-based architectures. The technical heart of the paper is a detailed analysis of the computing time used in the Ewald method as a function of the required accuracy, the size of the molecular dynamics cell, and the hardware design parameters.

Molecular Communication

10.1177/1094342004044010

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A single NaK channel conformation is not enough for non-selective ion conduction

Nature Communications (2018)

Chaowei Shi Yao He Kitty Hendriks Bert L. de Groot Xiaoying Cai

Abstract NaK and other non-selective channels are able to conduct both sodium (Na + ) and potassium (K + ) with equally high efficiency. In contrast to previous crystallographic results, we show that the selectivity filter (SF) of NaK in native-like lipid membranes adopts two distinct conformations that are stabilized by either Na + or K + ions. The atomic differences of these conformations are resolved by solid-state NMR (ssNMR) spectroscopy and molecular dynamics (MD) simulations. Besides the canonical K + permeation pathway, we identify a side entry ion-conduction pathway for Na + permeation unique to NaK. Moreover, under otherwise identical conditions ssNMR spectra of the K + selective NaK mutant (NaK2K) reveal only a single conformational state. Therefore, we propose that structural plasticity within the SF and the selection of these conformations by different ions are key molecular determinants for highly efficient conduction of different ions in non-selective cation channels.

NAK

10.1038/s41467-018-03179-y

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Species identification of Trichinella isolates from China

Veterinary Parasitology (2008)

Bao‐Quan Fu Minyao Liu Changyu Yao Wen‐Hsiung Li Y.G. Li

Trichinella

Trichinella spiralis

Trichinosis

genomic DNA

10.1016/j.vetpar.2008.10.033

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Citations (17)

Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy

iScience (2025)

Jingtian Zheng Yi-Chien Wu Xiaoying Cai Philana Phan M. Gill

Correlative

10.1016/j.isci.2025.111934

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Crystal structure of the soluble domain of TiME protein from Mycobacterium tuberculosis

Weimin Gong Xiaoying Cai L. Liu Wen Chen

10.2210/pdb7cu8/pdb

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Identification and architecture of a putative secretion tube across mycobacterial outer envelope

Science Advances (2021)

Xiaoying Cai Lei Liu Chunhong Qiu Chongzheng Wen Yao He

Structural and in vivo functional analyses reveal a possible protein secretion tube across the mycobacterial outer envelope.

Envelope (radar)

Identification

10.1126/sciadv.abg5656

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Citations (4)