James Michael Krieger

Dr. James Michael Krieger

The Francis Crick Institute, London, City of London, UK
orcid

Research Focus & Metrics

Academic Career Length

14Years (2013-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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5 April 2021 in Bioinformatics
Verified
Journal Article
Open access
PDF file
SZShe Zhang
She Zhang
JKJames Michael Krieger
James Michael Krieger
YZYan Zhang
Yan Zhang
CKCihan Kaya
Cihan Kaya
BKBurak Kaynak
Burak Kaynak
IBIvet Bahar
Ivet Bahar
ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We present major developments that led to ProDy 2.0: (i) improved interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of protein families, (iii) CryoDy for collective dynamics of supramolecular systems using cryo-EM density maps and (iv) essential site scanning analysis for identifying sites essential to modulating global dynamics. ProDy is open-source and freely available under MIT License from https://github.com/prody/ProDy. Supplementary data are available at Bioinformatics online.

10 September 2018 in Journal of Clinical Investigation
Verified
Journal Article
Open access
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HDHaider H. Dar
Haider H. Dar
YTYulia Y. Tyurina
Yulia Y. Tyurina
KMKarolina Mikulska-Ruminska
Karolina Mikulska-Ruminska
ISIndira Shrivastava
Indira Shrivastava
HTHsiu-Chi Ting
Hsiu-Chi Ting
VKValerian E. Kagan
Valerian E. Kagan
Ferroptosis is a death program executed via selective oxidation of arachidonic acid–phosphatidylethanolamines (AA-PE) by 15-lipoxygenases. In mammalian cells and tissues, ferroptosis has been pathogenically associated with brain, kidney, and liver injury/diseases. We discovered that a prokaryotic bacterium, Pseudomonas aeruginosa, that does not contain AA-PE can express lipoxygenase (pLoxA), oxidize host AA-PE to 15-hydroperoxy-AA-PE (15-HOO-AA-PE), and trigger ferroptosis in human bronchial epithelial cells. Induction of ferroptosis by clinical P. aeruginosa isolates from patients with persistent lower respiratory tract infections was dependent on the level and enzymatic activity of pLoxA. Redox phospholipidomics revealed elevated levels of oxidized AA-PE in airway tissues from patients with cystic fibrosis (CF) but not with emphysema or CF without P. aeruginosa. We believe that the evolutionarily conserved mechanism of pLoxA-driven ferroptosis may represent a potential therapeutic target against P. aeruginosa–associated diseases such as CF and persistent lower respiratory tract infections.

29 April 2016 in Science
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Journal Article
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BHBeatriz Herguedas
Beatriz Herguedas
JGJavier García-Nafría
Javier García-Nafría
OCOndrej Cais
Ondrej Cais
RFRafael Fernández-Leiro
Rafael Fernández-Leiro
JKJames Michael Krieger
James Michael Krieger
IGIngo H. Greger
Ingo H. Greger
Signaling at the synapse: Neurons signal to each other at synapses using neurotransmitters. Glutamate is a key neurotransmitter, and AMPA-type glutamate receptors (AMPARs) mediate rapid responses to glutamate release. These receptors mainly occur as heteromers comprising GluA1-4 subunits. Herguedas et al. used electron microscopy and x-ray crystallography to determine the structure of GluA2/3 and GluA2/4 heteromers. The structures differ from those determined previously for GluA2 homomers but emphasize how signals may be transmitted through these dynamic receptors. Science , this issue p. 10.1126/science.aad3873

27 November 2019 in Current Opinion in Structural Biology
Verified
Journal Article
Open access
YZYan Zhang
Yan Zhang
PDPemra Doruker
Pemra Doruker
BKBurak Kaynak
Burak Kaynak
SZShe Zhang
She Zhang
JKJames Michael Krieger
James Michael Krieger
IBIvet Bahar
Ivet Bahar
Allosteric behavior is central to the function of many proteins, enabling molecular machinery, metabolism, signaling and regulation. Recent years have shown that the intrinsic dynamics of allosteric proteins defined by their 3-dimensional architecture or by the topology of inter-residue contacts favors cooperative motions that bear close similarity to structural changes they undergo during their allosteric actions. These conformational motions are usually driven by energetically favorable or soft modes at the low frequency end of the mode spectrum, and they are evolutionarily conserved among orthologs. These observations brought into light evolutionary adaptation mechanisms that help maintain, optimize or regulate allosteric behavior as the evolution from bacterial to higher organisms introduces sequential heterogeneities and structural complexities.

1 September 2015 in Structure
Verified
Journal Article
Closed access
ADAnindita Dutta
Anindita Dutta
JKJames Michael Krieger
James Michael Krieger
JLJi Young Lee
Ji Young Lee
JGJavier Garcia-Nafria
Javier Garcia-Nafria
IGIngo H. Greger
Ingo H. Greger
IBIvet Bahar
Ivet Bahar

1 January 2019 in Acta Crystallographica Section F Structural Biology Communications
Verified
Journal Article
Closed access
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CSCarlos Óscar S. Sorzano
Carlos Óscar S. Sorzano
AJA. Jiménez
A. Jiménez
JMJ. Mota
J. Mota
JVJ. L. Vilas
J. L. Vilas
DNDavid Maluenda Niubó
David Maluenda Niubó
JCJM Carazo
JM Carazo