Suggestions for new articles

From Proteopedia

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This page suggests molecules or topics for future articles in Proteopedia.

Nature, and perhaps other journals, allow comments from readers to be appended to scientific reports. Therefore, interactive 3D illustrations in Proteopedia, based on a report in Nature, can be linked to the online article in a comment.

Contents 1 Suggestions by Eric Martz 1.1 2015 1.1.1 October: B12 photoreceptor in bacteria regulates transcription 1.2 2012 1.2.1 April: Molecular Juggling of B12 in Methyltransferase 1.2.2 April: Ultraviolet-B Photoreceptor Dimer to Monomer 1.2.3 February: Muscarinic Acetylcholine Receptor 1.2.4 January: Neurotransmitter Sodium Symporter 1.3 2011 1.3.1 October: Catalytic Site Remodeling in an Enzyme 1.3.2 September: Active State Β2 Adrenergic Receptor Complex with G Protein Heterotrimer 1.3.3 September: Activation of the Classical Inward Rectifier Potassium Channel

Suggestions by Eric Martz

These suggestions are by User:Eric Martz, who invites anyone to start articles on these molecules. In cases where morphs can be done, Eric will be happy to provide technical help.

2015

October: B₁₂ photoreceptor in bacteria regulates transcription

• Jost M, Fernandez-Zapata J, Polanco MC, Ortiz-Guerrero JM, Chen PY, Kang G, Padmanabhan S, Elias-Arnanz M, Drennan CL. Structural basis for gene regulation by a B-dependent photoreceptor. Nature. 2015 Sep 28. doi: 10.1038/nature14950. PMID:26416754 doi:http://dx.doi.org/10.1038/nature14950

• CarH photoreceptors bind DNA on their N-terminal domains, and adenosylcobalamin (a vitamin B₁₂ derivitave) between their middle and C-terminal domains (5c8e). The DNA-binding conformation is a homo-tetramer.
• Light breaks a Co-C bond, releasing 5'-deoxyadenosine, causing a domain orientation shift of >8 Å. This disrupts the tetramer, releasing DNA, and activating transcription.
• Appears to be suitable for a morph (One of 5c8a, 5c8d, or 5c8e to the light-exposed form 5c8f).
• Extended data has static figures only (no movies).

2012

April: Molecular Juggling of B12 in Methyltransferase

• Kung Y, Ando N, Doukov TI, Blasiak LC, Bender G, Seravalli J, Ragsdale SW, Drennan CL. Visualizing molecular juggling within a B(12)-dependent methyltransferase complex. Nature. 2012 Mar 14. doi: 10.1038/nature10916. PMID:22419154 doi:10.1038/nature10916

• First crystal structures of a complete 220 kDa B₁₂-dependent methyltransferase complex (4djd, 4dje, 4djf, resolutions 2.4-3.5 Å).
• Dramatic rearrangements are seen, showing the trajectory of B₁₂ between resting and catalytic positions. These are the largest known conformational movements of proteins in a crystalline state.
• Probably suitable for a morph.
• Supplementary information contains no movies.
• Superposition of 4djd and 4djf:

• see also Methionine synthase

April: Ultraviolet-B Photoreceptor Dimer to Monomer

• Wu D, Hu Q, Yan Z, Chen W, Yan C, Huang X, Zhang J, Yang P, Deng H, Wang J, Deng X, Shi Y. Structural basis of ultraviolet-B perception by UVR8. Nature. 2012 Feb 29;484(7393):214-9. doi: 10.1038/nature10931. PMID:22388820 doi:10.1038/nature10931

• UVR8 is an ultraviolet-B photoreceptor in Arabidopsis. UVB irradiation converts it from a homodimer to a monomer, which interacts with partners leading to transcriptional activation of UV protective proteins. This 1.8 Å structure (wild type 4dnw, W285A 4dnu, and W285F 4dnv) reveals that no non-protein chromophore is involved. Trp 285 and 233 function as the chromophore. Arg 286 and Arg 338 are involved in an elaborate cation-pi interaction network with these and other tryptophans. UVB irradiation destabliizes these interactions and dissociates the dimer.
• In addition to numerous cation-pi interactions at the dimeric interface, there are numerous salt bridges.

February: Muscarinic Acetylcholine Receptor

• Haga K, Kruse AC, Asada H, Yurugi-Kobayashi T, Shiroishi M, Zhang C, Weis WI, Okada T, Kobilka BK, Haga T, Kobayashi T. Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Nature. 2012 Jan 25;482(7386):547-51. doi: 10.1038/nature10753. PMID:22278061 doi:10.1038/nature10753

• Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, Kobilka BK. Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature. 2012 Feb 22;482(7386):552-6. doi: 10.1038/nature10867. PMID:22358844 doi:10.1038/nature10867

• Kow RL, Nathanson NM. Structural biology: Muscarinic receptors become crystal clear. Nature. 2012 Feb 22;482(7386):480-1. doi: 10.1038/482480a. PMID:22358836 doi:10.1038/482480a

• Haga et al.: "the first human acetylcholine receptor to be characterized structurally ...." (3uon).

January: Neurotransmitter Sodium Symporter

• Krishnamurthy H, Gouaux E. X-ray structures of LeuT in substrate-free outward-open and apo inward-open states. Nature. 2012 Jan 9. doi: 10.1038/nature10737. PMID:22230955 doi:10.1038/nature10737

• LeuT is a bacterial homolog of neurotransmitter sodium symporters that remove neurotransmitters from the synapse and terminate neurotransmission. New structures presented in this paper "establish a structural framework for the mechanism of neurotransmitter sodium symporters and their modulation by therapeutic and illicit substances".
• A new substrate-free structure is outward-open, 3tt1. Comparison with a previous substrate-bound, outward occluded structure shows "how the binding of substrate closes the extracellular gate through local conformational changes".
• A new substrate-free inward-open structure, 3tt3, involves large scale conformational changes.
• The authors provide a supplementary true movie containing two morphs between three structures: substrate-free outward-open 3tt1 to leucine-bound, outward-occluded 2a65, and then to the inward-open 3tt3. Interactive morphs in Jmol could be advantageous.

2011

October: Catalytic Site Remodeling in an Enzyme

• Du J, Say RF, Lu W, Fuchs G, Einsle O. Active-site remodelling in the bifunctional fructose-1,6-bisphosphate aldolase/phosphatase. Nature. 2011 Oct 9. doi: 10.1038/nature10458. PMID:21983965 doi:10.1038/nature10458

• Fushinobu S, Nishimasu H, Hattori D, Song HJ, Wakagi T. Structural basis for the bifunctionality of fructose-1,6-bisphosphate aldolase/phosphatase. Nature. 2011 Oct 9;478(7370):538-41. doi: 10.1038/nature10457. PMID:21983966 doi:10.1038/nature10457

• Probably suitable for morphs illustrating details of catalysis. Du et al.: "Here we present a series of structural snapshots of the reaction that reveal a substantial remodeling of the active site ...." (e.g. their Fig. 2, unliganded 3t2b, DHAP liganded 3t2c, FBP liganded 3t2d, and the F6P product complex 3t2e). Fushinobu et al. describe "a dramatic conformational change in the active site" (e.g. their Fig. 1, DHAP complex 3r1m vs. FBP complex 1umg).
• Neither report includes a movie in their supplementary materials.

September: Active State Β2 Adrenergic Receptor Complex with G Protein Heterotrimer

• Rasmussen SG, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK. Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature. 2011 Jul 19;477(7366):549-55. doi: 10.1038/nature10361. PMID:21772288 doi:10.1038/nature10361

• Schwartz TW, Sakmar TP. Structural biology: snapshot of a signalling complex. Nature. 2011 Sep 28;477(7366):540-1. doi: 10.1038/477540a. PMID:21956322 doi:10.1038/477540a

• "... the first high resolution view of transmembrane signalling by a GPCR."
• Probably suitable for a morph comparing the agonist-occupied monomeric β2 adrenergic receptor and nucleotide-free G protein heterotrimer 3sn6 with the inactive carazolol-bound β2 adrenergic receptor from 2007, 2rh1, cf. Fig. 3. Transmembrane helix 6 moves 14 Å.
• Probably suitable for another morph comparing Gαs in the complex 3sn6 with GTPγs-bound Gαs 1azt, cf. Fig. 5.
• No movies are included in the supplementary materials for this publication.

September: Activation of the Classical Inward Rectifier Potassium Channel

• Hansen SB, Tao X, Mackinnon R. Structural basis of PIP(2) activation of the classical inward rectifier K(+) channel Kir2.2. Nature. 2011 Aug 28. doi: 10.1038/nature10370. PMID:21874019 doi:10.1038/nature10370

• "On PIP2 binding, a flexible expansion linker contracts to a compact helical structure, the cytoplasmic domain translates 6 Å and becomes tethered to the trans-membrane domain and the innner helix gate begins to open."
• Probably suitable for a morph. The apo structure is 3jyc, and the PIP2-bound structure, 3spi. Supplementary information does not include any movies.