Biology subjects

Yan, S.

Publications and source records attributed to Yan, S..

4 recordsLinked to original sources

bioRxiv2026

A Generic Numbering Scheme for TMEM16 Scramblases

The TMEM16 family of calcium-activated phospholipid scramblases (CaPLSs) and chloride channels (CaCCs) performs diverse physiological functions that include regulation of blood coagulation and apoptotic signaling, through a shared ten-transmembrane-helix (TM) architecture organized around a hydrophilic lipid-translocating groove. Mechanistic studies of TMEM16 family members have been hampered by the absence of a unified positional reference framework that would permit direct comparison of structurally equivalent residues across paralogs with different sequence numbering systems. Here we introduce a generic numbering scheme for TMEM16 scramblases (GNS-TMEM16), modeled on the Ballesteros & Weinstein system established for class A G protein-coupled receptors. A reference alignment (TMEM16-RA) was constructed from twelve human and mouse TMEM16 scramblases (TMEM16C/D/E/F/G/J) using structure-based ClustalW alignment of the ten TM helices. From this alignment, a TM-specific reference residue (TsRR) was identified for each helix by hierarchical application of three criteria: (1) 100% conservation in the core TMEM16-RA; (2) conservation in an augmented reference alignment (TMEM16-ARA) incorporating a group of phylogenetically more distant homologs composed of nhTMEM16, afTMEM16, TMEM16K, TMEM16A, and TMEM16B; and (3) structural and functional considerations, including helix-perturbing character, groove localization, conserved motif membership, and central TM position. The resulting ten TsRRs are Y1.50, W2.50, R3.50, E4.50, F5.50, P6.50, E7.50, D8.50, W9.50, and E10.50, and are illustrated in mTMEM16F. Each residue is assigned the identifier N.m(k), where N is the TM number, m is the position relative to the TsRR (for which m = 50), and k is the absolute sequence number. Loop residues receive dual identifiers referenced to the TsRRs of both flanking helices. Application of the GNS-TMEM16 is illustrated with the comparisons of the groove-opening measurements using pairwise distances between residues identified by their N.m indices to be corresponding across mTMEM16F, afTMEM16, and nhTMEM16. The results bring to light the advantages of corresponding residues identification in different TMEM16 proteins and show that the mammalian scramblase undergoes substantially larger separation at the extracellular groove entrance than either fungal homolog. Comparison of mutagenesis data guided by N.m correspondence shows at the conserved (E3.55,R6.26) salt-bridge locus, Ala substitution reduces activity more than 100-fold in nhTMEM16 but less than 2-fold in afTMEM16, illustrating that the GNS identifies structural equivalence of position without implying functional equivalence of the residue, which is a distinct advantage of GNS in providing mechanistic interpretation across paralogs. Also described is a protocol for extending the GNS-TMEM16 to uncharacterized protein sequences, including AlphaFold-predicted models, using structural superposition to mTMEM16F. Thus, the presented GNS-TMEM16 provides a stable positional reference for the integration and comparative analysis of structural, computational, and functional data across the TMEM16 family, utilizing a construction strategy applicable to yet other polytopic membrane protein families sharing a common transmembrane fold.

biophysics↗

bioRxiv2018

Stabilizing Obligatory Non-native Intermediates Along Co-transcriptional Folding Trajectories of SRP RNA Affects Cell Viability

Signal recognition particle (SRP) in Escherichia coli comprises protein Ffh and SRP RNA. Its essential functionality--co-translational protein-targeting/delivery to cellular membranes-- hinges on the RNA attaining a native long-hairpin fold that facilitates protein conformational rearrangements within the SRP complex. Since RNA folds co-transcriptionally on RNA polymerase, we use high-resolution optical tweezers to first characterize the mechanical unfolding/refolding of incrementally lengthened RNAs from stalled transcription complexes until reaching the full-length transcript. This analysis allows identification of folding intermediates adopted during the real-time co-transcriptional folding of SRP RNA. The co-transcriptional folding trajectories are surprisingly invariant to transcription rates, and involve formation of an obligatory non-native hairpin intermediate that eventually resolves into the native fold. SRP RNA variants designed to stabilize this non-native intermediate--likely sequestering the SRP ribonucleoprotein complex in an inactive form--greatly reduce cell viability, indicating that the same co-transcriptional folding mechanism operates in vivo and possible alternative antibiotic strategies.\n\nHighlightsO_LIFolding pathway of an essential functional RNA has been resolved co-transcriptionally.\nC_LIO_LIThe co-transcriptional folding pathway of SRP RNA is invariant to transcription rates.\nC_LIO_LINascent SRP RNA obligatorily forms a non-native intermediate before adopting the native fold.\nC_LIO_LIModulating transitions from the non-native to native SRP RNA hairpin fold alters cell viability.\nC_LI

biophysics↗

bioRxiv2018

ATP-dependent force generation and membrane scission by ESCRT-III and Vps4

The ESCRTs catalyze reverse-topology scission from the inner face of membrane necks in HIV budding, multivesicular endosome biogenesis, cytokinesis, and other pathways. We encapsulated a minimal ESCRT module consisting of ESCRT-III subunits Snf7, Vps24, and Vps2, and the AAA+ ATPase Vps4 such that membrane nanotubes reflecting the correct topology of scission could be pulled from giant vesicles. Upon ATP release by photo-uncaging, this system was capable of generating forces within the nanotubes in a manner dependent upon Vps4 catalytic activity, Vps4 coupling to the ESCRT-III proteins, and membrane insertion by Snf7. At physiological concentrations, single scission events were observed that correlated with forces of ~6 pN, verifying predictions that ESCRTs are capable of exerting forces on membranes. Imaging of scission with subsecond resolution revealed Snf7 puncta at the sites of membrane cutting, directly verifying longstanding predictions for the ESCRT scission mechanism.\n\nOne Sentence SummaryESCRT-III and Vps4 were reconstituted from within the interior of nanotubes pulled from giant vesicles, revealing that this machinery couples ATP-dependent force production for membrane scission.

biophysics↗

bioRxiv2017

Prediction (Or Not) During Language Processing. A Commentary On Nieuwland et al. (2017) And Delong et al. (2005)

The extent to which language processing involves prediction of upcoming inputs remains a question of ongoing debate. One important data point comes from DeLong et al. (2005) who reported that an N400-like event-related potential correlated with a probabilistic index of upcoming input. This result is often cited as evidence for gradient probabilistic prediction of form and/or semantics, prior to the bottom-up input becoming available. However, a recent multi-lab study reports a failure to find these effects (Nieuwland et al., 2017). We review the evidence from both studies, including differences in the design and analysis approach between them. Building on over a decade of research on prediction since DeLong et al. (2005)s original study, we also begin to spell out the computational nature of predictive processes that one might expect to correlate with ERPs that are evoked by a functional element whose form is dependent on an upcoming predicted word. For paradigms with this type of design, we propose an index of anticipatory processing, Bayesian surprise, and apply it to the updating of semantic predictions. We motivate this index both theoretically and empirically. We show that, for studies of the type discussed here, Bayesian surprise can be closely approximated by another, more easily estimated information theoretic index, the surprisal (or Shannon information) of the input. We re-analyze the data from Nieuwland and colleagues using surprisal rather than raw probabilities as an index of prediction. We find that surprisal is gradiently correlated with the amplitude of the N400, even in the data shared by Nieuwland and colleagues. Taken together, our review suggests that the evidence from both studies is compatible with anticipatory semantic processing. We do, however, emphasize the need for future studies to further clarify the nature and degree of form prediction, as well as its neural signatures, during language comprehension.

neuroscience↗