View source for Suggestions for new articles

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

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[http://www.nature.com/nature 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.
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==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.

===2025===
====April: Swinging lever mechanism of myosin directly shown by time-resolved cryo-EM====
<ref group="xtra">PMID: 40205053</ref><references group="xtra"/>
:*[[8r9v]] is before the power stroke. [[8rbf]] is afterwards.
:*Article has 6 stunning movies!

===2015===
====October:  B<sub>12</sub> photoreceptor in bacteria regulates transcription====
<ref group="xtra">PMID: 26416754</ref><references group="xtra"/>
:*CarH photoreceptors bind DNA on their N-terminal domains, and adenosylcobalamin (a vitamin B<sub>12</sub> 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 &gt;8 &Aring;. 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====
<ref group="xtra">PMID: 22419154</ref><references group="xtra"/>
:*First crystal structures of a complete 220 kDa B<sub>12</sub>-dependent methyltransferase complex ([[4djd]], [[4dje]], [[4djf]], [[resolution]]s 2.4-3.5 &Aring;).
:*Dramatic rearrangements are seen, showing the trajectory of  B<sub>12</sub> 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:
[[Image:Methylase.gif]]
:*see also [[Methionine synthase]]

====April: Ultraviolet-B Photoreceptor Dimer to Monomer====
<ref group="xtra">PMID: 22388820</ref><references group="xtra"/>
:*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 &Aring; 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====
<ref group="xtra">PMID: 22278061</ref><references group="xtra"/>
<ref group="xtra">PMID: 22358844</ref><references group="xtra"/>
<ref group="xtra">PMID: 22358836</ref><references group="xtra"/>
:*Haga ''et al.'': "the first human acetylcholine receptor to be characterized structurally ...." ([[3uon]]).

====January: Neurotransmitter Sodium Symporter====
<ref group="xtra">PMID: 22230955</ref><references group="xtra"/>
:*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 [[Morphs#True_Movies|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====
<ref group="xtra">PMID: 21983965</ref><references group="xtra"/>
<ref group="xtra">PMID: 21983966</ref><references group="xtra"/>
:*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 &Beta;2 Adrenergic Receptor Complex with G Protein Heterotrimer====
<ref group="xtra">PMID: 21772288</ref><references group="xtra"/>
<ref group="xtra">PMID: 21956322</ref><references group="xtra"/>
:* "... the first high resolution view of transmembrane signalling by a GPCR."
:*Probably suitable for a morph comparing the agonist-occupied monomeric &beta;2 adrenergic receptor and nucleotide-free G protein heterotrimer [[3sn6]] with the inactive carazolol-bound &beta;2 adrenergic receptor from 2007, [[2rh1]], cf. Fig. 3. Transmembrane helix 6 moves 14 &Aring;.
:*Probably suitable for another morph comparing G&alpha;s in the complex [[3sn6]] with GTP&gamma;s-bound G&alpha;s [[1azt]], cf. Fig. 5.
:*No movies are included in the supplementary materials for this publication.

====September: Activation of the Classical Inward Rectifier Potassium Channel====
<ref group="xtra">PMID: 21874019</ref><references group="xtra"/>
:* "On PIP2 binding, a flexible expansion linker contracts to a compact helical structure, the cytoplasmic domain translates 6 &Aring; 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.