Journal Article10.1083/jcb.202410022
Making lipids very unhappy to discover how they bind to proteins
Christopher J. Stefan,Roberto Covino +1 more
TL;DR: Researchers developed a molecular dynamics simulations assay to accurately model lipid-binding poses in lipid transfer proteins, overcoming limitations in computational approaches to study lipid-binding mechanisms in membrane lipid composition maintenance.
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Abstract: Membrane lipid composition is maintained by conserved lipid transfer proteins, but computational approaches to study their lipid-binding mechanisms are limiting. Srinivasan et al. (https://doi.org/10.1083/jcb.202312055) develop a clever molecular dynamics simulations assay to accurately model lipid-binding poses in lipid transfer proteins.
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Highly accurate protein structure prediction with AlphaFold
John M. Jumper,Richard O. Evans,Alexander Pritzel,Tim Green,Michael Figurnov,Olaf Ronneberger,Kathryn Tunyasuvunakool,Russell Bates,Augustin Žídek,Anna Potapenko,Alex Bridgland,Clemens Meyer,Simon A. A. Kohl,Andrew J. Ballard,Andrew Cowie,Bernardino Romera-Paredes,Stanislav Nikolov,R. D. Jain,Jonas Adler,Trevor Back,Stig Petersen,David Reiman,Ellen Clancy,Michal Zielinski,Martin Steinegger,Michalina Pacholska,Tamas Berghammer,Sebastian Bodenstein,David L. Silver,Oriol Vinyals,Andrew W. Senior,Koray Kavukcuoglu,Pushmeet Kohli,Demis Hassabis +33 more
TL;DR: For example, AlphaFold as mentioned in this paper predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture. But the accuracy is limited by the fact that no homologous structure is available.
Improved protein structure prediction using predicted interresidue orientations
TL;DR: A deep residual network for predicting interresidue orientations, in addition to distances, and a Rosetta-constrained energy-minimization protocol for rapidly and accurately generating structure models guided by these restraints are developed.
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Lipid transfer proteins: the lipid commute via shuttles, bridges and tubes.
TL;DR: Understanding of how different lipids achieve their final destination at the molecular level allows a better explanation of the range of defects that occur in diseases associated with lipid transport and distribution, opening up the possibility of developing therapies that specifically target lipid transfer.
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TL;DR: The role of non-vesicular lipid transport has been discussed in this article, where a review describes what we know about non-veto lipid transfer mechanisms while also identifying many remaining unknowns: How do LTPs facilitate lipid movement from and into membranes, do LTLTPs require accessory proteins for efficient transfer in vivo, and how is directionality of transport determined?
Inter-organelle lipid transfer: a channel model for Vps13 and chorein-N motif proteins.
Joshua A. Lees,Karin M. Reinisch +1 more
TL;DR: This work highlights the recently identified chorein_N family of lipid transporters, including the Vps13 proteins and the autophagy protein Atg2, elongated proteins that, distinct from previously characterized transport proteins, bind tens of lipids at once.
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