Helix Motif Research Articles

Activation mechanism of the human Smoothened receptor

Smoothened (SMO) is a membrane protein of the class F subfamily of G protein-coupled receptors (GPCRs) and maintains homeostasis of cellular differentiation. SMO undergoes conformational change during activation, transmitting the signal across the membrane, making it amenable to bind to its intracellular signaling partner. Receptor activation has been studied at length for class A receptors, but the mechanism of class F receptor activation remains unknown. Agonists and antagonists bound to SMO at sites in the transmembrane domain (TMD) and the cysteine-rich domain have been characterized, giving a static view of the various conformations SMO adopts. Although the structures of the inactive and active SMO outline the residue-level transitions, a kinetic view of the overall activation process remains unexplored for class F receptors. We describe SMO’s activation process in atomistic detail by performing 300 μs of molecular dynamics simulations and combining it with Markov state model theory. A molecular switch, conserved across class F and analogous to the activation-mediating D-R-Y motif in class A receptors, is observed to break during activation. We also show that this transition occurs in a stage-wise movement of the transmembrane helices: TM6 first, followed by TM5. To see how modulators affect SMO activity, we simulated agonist and antagonist-bound SMO. We observed that agonist-bound SMO has an expanded hydrophobic tunnel in SMO’s core TMD, whereas antagonist-bound SMO shrinks this tunnel, further supporting the hypothesis that cholesterol travels through a tunnel inside Smoothened to activate it. In summary, this study elucidates the distinct activation mechanism of class F GPCRs and shows that SMO’s activation process rearranges the core TMD to open a hydrophobic conduit for cholesterol transport.

Structural and biochemical insights into PsEst3, a new GHSR-type esterase obtained from Paenibacillus sp. R4.

PsEst3, a psychrophilic esterase obtained from Paenibacillus sp. R4, which was isolated from the permafrost of Alaska, exhibits relatively high activity at low temperatures. Here, crystal structures of PsEst3 complexed with various ligands were generated and studied at atomic resolution, and biochemical studies were performed to analyze the structure-function relationship of PsEst3. Certain unique characteristics of PsEst3 distinct from those of other classes of lipases/esterases were identified. Firstly, PsEst3 contains a conserved GHSRA/G pentapeptide sequence in the GxSxG motif around the nucleophilic serine. Additionally, it contains a conserved HGFR/K consensus sequence in the oxyanion hole, which is distinct from that in other lipase/esterase families, as well as a specific domain composition (for example a helix-turn-helix motif) and a degenerative lid domain that exposes the active site to the solvent. Secondly, the electrostatic potential of the active site in PsEst3 is positive, which may cause unintended binding of negatively charged chemicals in the active site. Thirdly, the last residue of the oxyanion hole-forming sequence, Arg44, separates the active site from the solvent by sealing the acyl-binding pocket, suggesting that PsEst3 is an enzyme that is customized to sense an unidentified substrate that is distinct from those of classical lipases/esterases. Collectively, this evidence strongly suggests that PsEst3 belongs to a distinct family of esterases.

Molecular Dynamics Refinement of Open State Serotonin 5-HT3A Receptor Structures.

Pentameric ligand-gated ion channels play an important role in mediating fast neurotransmissions. As a member of this receptor family, cation-selective 5-HT3 receptors are a clinical target for treating nausea and vomiting associated with chemotherapy and radiation therapy (Thompson and Lummis, 2006). Multiple cryo-electron microscopy (cryo-EM) structures of 5-HT3 receptors have been determined in distinct functional states (e.g., open, closed, etc.) (Basak et al., 2018; Basak et al., 2018; Polovinkin et al., 2018; Zhang et al., 2015). However, recent work has shown that the transmembrane pores of the open 5-HT3 receptor structures rapidly collapse and become artificially asymmetric in molecular dynamics (MD) simulations. To avoid this hydrophobic collapse, Dämgen and Biggin developed an equilibration protocol that led to a stable open state structure of the glycine receptor in MD simulations (Dämgen and Biggin, 2020). However, the protocol failed to yield open-like structures of the 5-HT3 receptor in our simulations. Here, we present a refined equilibration protocol that involves the rearrangement of the transmembrane helices to achieve stable open state structures of the 5-HT3 receptor that allow both water and ion permeation through the channel. Notably, channel gating is mediated through collective movement of the transmembrane helices, involving not only pore lining M2 helices but also their cross-talk with the adjacent M1 and M3 helices. Thus, the successful application of our refined equilibration protocol underscores the importance of the conformational coupling between the transmembrane helices in stabilizing open-like structures of the 5-HT3 receptor.

Molecular mechanism underlying desensitization of the human proton-activated chloride (PAC) channel.

Opened by acidic pH, the Proton-Activated Chloride (PAC) channel has been recorded in a variety of cell types. Although its molecular identify has only recently been identified, the PAC channel has established important roles in acid-induced cell death, endosomal acidification, and macropinosome shrinkage. Previous cryo-EM studies of the PAC channel reported a proton-bound non-conducting structure at low pH, suggestive that PAC undergoes desensitization - a process common to ligand-gated ion channels. Comparison of the proposed open and desensitized structures demonstrated significant rotational movement of the transmembrane helix 1 (TM1), switching its interaction partner to a neighboring subunit. However, properties and underlying mechanisms underlying PAC channel desensitization remain to be largely unknown. In this study, we demonstrate that PAC undergoes pH-dependent desensitization upon prolonged acid exposure with patch-clamp electrophysiology. Additional studies with structure-guided mutagenesis identified several residues critical for PAC desensitization, including histidine (H) 98, glutamic acid (E) 94, and aspartic acid (D) 91 at the extracellular extension of the TM1, as well as E107, D109, and E250 at the interface of the extracellular domain (ECD) and transmembrane domain (TMD). Structural analysis and molecular dynamic simulations revealed extensive interactions between residues at the TM1 extension and those at the ECD-TMD interface. These interactions likely facilitate PAC desensitization by stabilizing the desensitized conformation of TM1. Our studies establish a new paradigm of channel desensitization in this ubiquitously expressed ion channel and pave the way for further investigation of its relevance in cellular physiology and disease.

Ionic interactions between gating charges and countercharges in voltage-sensing domain I independently regulate kinetics and voltage-dependence of Cav1.1 gating.

Voltage-gated calcium channels control a variety of processes in excitable cells. However, the exact mechanisms regulating kinetics and voltage-dependence of channel activation are not fully understood. Voltage-gated activation is determined by four distinct voltage-sensing domains (VSD I-IV) coupled to a common pore. Each VSD consists of four transmembrane helices (S1-S4) with S4 containing four to five gating charges. Upon membrane depolarization, consecutive interactions of these gating charges with negatively charged countercharges are believed to facilitate an upward movement of the S4 helices, leading to the opening of the pore and activation of the channel. Previous studies linked naturally occurring mutations of the innermost gating charge R4 (R174W) and its negative countercharge (E100) in CaV1.1 to muscle disease. To investigate the contribution of VSD I and the roles of its gating- and countercharges in channel gating, we combined structure-guided site-directed mutagenesis with patch-clamp analysis in dysgenic myotubes (CaV1.1-null). As E100 in helix S2 together with D126 in helix S3 form the highly conserved charge-transfer center of VSDs, we included this second negative countercharge (D126) in our analysis. While mutation of R174A resulted in a strong right-shift of voltage dependence, charge neutralizing mutations of the countercharges E100 and D126 both lead to a left-shift of voltage-dependence and to a slowing of channel activation. The double mutant of both countercharges resulted in an additive effect on activation kinetics, but left the voltage dependence of activation unaffected compared to the single mutants. Our findings indicate that VSD I substantially contributes to the regulation of both kinetics and voltage-dependence of activation; that the same ionic interactions are critical for both properties; but that the molecular mechanisms governing the two gating properties are functionally separate.

Investigating the interaction of TDP-43 with RNA using structural mass spectrometry.

Deposits of TDP-43, a disordered RNA-binding protein, in the brain is hallmark of amyotrophic lateral sclerosis (ALS). Binding of TDP-43 to RNA protects from aggregation. However, the structure(s) and conformational dynamics of monomeric TDP-43, its higher order assemblies, and the TDP-43-RNA complex remain elusive, despite their importance in understanding disease progression. Here we have used a combination of biophysical analyses and powerful mass spectrometry (MS) techniques to interrogate the conformational dynamics of monomeric full-length TDP-43 and its assemblies with RNA. Our results from HDX-MS show that, in the presence of RNA we observe allosteric protection from exchange in areas associated with amyloid formation suggesting a possible structural rearrangement that protects RNA bound TDP-43 from aggregation. We also identify allosteric changes within the short alpha helix motif located in the CTD upon RNA binding. These allosterically altered regions are known to influence the ability of TDP-43 to self-assemble and can fine-tune its RNA binding repertoire. Taken together, these data reveal new insights into the structure and dynamics of TDP-43, alongside the intra-protein and protein-RNA interactions which likely play a key role in fine tuning TDP-43 self-assembly into both condensates and amyloid fibrils. Understanding the molecular mechanism of these processes is key to elucidating the role of TDP-43 in the pathology of ALS and FTLD and may lead to new therapeutics to treat these diseases.

The homology of elevator and rocking bundle transporters.

Transporters act as cellular gatekeepers, shuttling vital substrates across cells’ semi-permeable membranes. They achieve this function through a handful of canonical mechanisms, two of which are the elevator and rocking bundle mechanisms. In the past, the transporter families that employ the elevator mechanism have been thought to be evolutionarily unrelated to each other, and the elevator mechanism has been seen as fundamentally distinct from the rocking bundle mechanism. Now, through detailed analysis of structure and sequence, we have found compelling quantitative evidence that the great majority of elevator transporters are homologous to each other and to all rocking bundle transporters. Key to this finding was the fact that structural architecture is conserved far longer during protein evolution than protein topology or amino acid sequence. In the full architectures of forty-four elevator and thirty-six rocking bundle transporters which have been structurally characterized, we observed comprehensive, complex, and quantitatively significant structural similarity that strongly suggested homology. We also observed that, in different elevator transporter families, connectivity between conserved helices is different, and rocking bundle transporters are missing a few of these helices. Correcting for these topological differences enabled us to perform meaningful sequence comparisons, which also quantitatively suggested homology. These results allowed us to construct a phylogenetic tree, which has enabled us to visualize the evolutionary relationships between transporter families and guide new investigation. Specifically, in closely related families with different topologies, we have observed conserved ion and substrate binding sites and functional helix motions, and we propose that mechanistic details from one transporter family can inform mechanistic hypotheses about other families. Overall, these results constitute a powerful new evolutionary context in which the fundamental similarities and differences between elevator and rocking bundle transporters and their mechanisms can be investigated and understood.

Structural insights into the elevator-type transport mechanism of a bacterial ZIP metal transporter

The Zrt-/Irt-like protein (ZIP) family consists of ubiquitously expressed divalent metal transporters critically involved in maintaining systemic and cellular homeostasis of zinc, iron, and manganese. Here, we present a study on a prokaryotic ZIP from Bordetella bronchiseptica (BbZIP) by combining structural biology, evolutionary covariance, computational modeling, and a variety of biochemical assays to tackle the issue of the transport mechanism which has not been established for the ZIP family. The apo state structure in an inward-facing conformation revealed a disassembled transport site, altered inter-helical interactions, and importantly, a rigid body movement of a 4-transmembrane helix (TM) bundle relative to the other TMs. The computationally generated and biochemically validated outward-facing conformation model revealed a slide of the 4-TM bundle, which carries the transport site(s), by approximately 8 Å toward the extracellular side against the static TMs which mediate dimerization. These findings allow us to conclude that BbZIP is an elevator-type transporter.

New simulation insights on the structural transition mechanism of bovine rhodopsin activation.

Inactive rhodopsin can absorb photons, which induces different structural transitions that finally activate rhodopsin. We have examined the change in spatial configurations and physicochemical factors that result during the transition mechanism from the inactive to the active rhodopsin state via intermediates. During the activation process, many existing atomic contacts are disrupted, and new ones are formed. This is related to the movement of Helix 5, which tilts away from Helix 3 in the intermediate state in lumirhodopsin and moves closer to Helix 3 again in the active state. Similar patterns of changing atomic contacts are observed between Helices 3 and 5 of the adenosine and neurotensin receptors. In addition, residues 220-238 of rhodopsin, which are disordered in the inactive state, fold in the active state before binding to the Gα, where it catalyzes GDP/GTP exchange on the Gα subunit. Finally, molecular dynamics simulations in the membrane environment revealed that the arrestin binding region adopts a more flexible extended conformation upon phosphorylation, likely promoting arrestin binding and inactivation. In summary, our results provide additional structural understanding of specific rhodopsin activation which might be relevant to other Class A G protein-coupled receptor proteins.

Understanding the Dynamics of the Structural States of Cannabinoid Receptors and the Role of Different Modulators.

The cannabinoid receptors CB1R and CB2R are members of the G protein-coupled receptor (GPCR) family. These receptors have recently come to light as possible therapeutic targets for conditions affecting the central nervous system. However, because CB1R is known to have psychoactive side effects, its potential as a drug target is constrained. Therefore, targeting CB2R has become the primary focus of recent research. Using various molecular modeling studies, we analyzed the active, inactive, and intermediate states of both CBRs in this study. We conducted in-depth research on the binding properties of various groups of cannabinoid modulators, including agonists, antagonists, and inverse agonists, with all of the different conformational states of the CBRs. The binding effects of these modulators were studied on various CB structural features, including the movement of the transmembrane helices, the volume of the binding cavity, the internal fluids, and the important GPCR properties. Then, using in vitro experiments and computational modeling, we investigated how vitamin E functions as a lipid modulator to influence THC binding. This comparative examination of modulator binding to CBRs provides significant insight into the mechanisms of structural alterations and ligand affinity, which can directly help in the rational design of selective modulators that target either CB1R or CB2R.

Strand 1A variant in neuroserpin shows increased aggregation and no loss of inhibition: implication in ameliorating polymerization to retain activity.

Neuroserpin (NS) is predominantly expressed in the brain and is the primary inhibitor of tissue plasminogen activator (tPA). NS variants are associated with the neurogenerative disease termed familial encephalopathy with neuroserpin inclusion bodies (FENIB). The disease is characterized by variable age of onset and severity. The reactive center loop (RCL) insertion-based inhibitory mechanism of NS requires a coordinated conformational change leading to a shift in the strands of the β-sheet A and movement of helix F. Strand 1A is connected to the helix F at its C terminal end and with the strand 2A at its N terminal, both these domain move for accommodating the inserting loop; therefore, a variant that influences their movement may alter the inhibition rates. A molecular dynamic simulation analysis of a H138C NS variant from strand 1A showed a large decrease in conformational fluctuations as compared with wild-type NS. H138 was mutated, expressed, purified and a native-PAGE and transmission electron microscopy (TEM) analysis showed that this variant forms large molecular weight aggregates on a slight increase in temperature. However, a circular dichroism analysis showed its secondary structure to be largely conserved. Surprisingly, its tPA inhibition activity and complex formation remain unhindered even after the site-specific labeling of H138C with Alexa fluor C5 maleimide. Further, a helix F-strand 1A (W154C-H138C) double variant still shows appreciable inhibitory activity. Increasingly, it appears that aggregation and not loss of inhibition is the more likely cause of shutter region-based variants phenotypes, indicating that hindering polymer formation using small molecules may retain inhibitory activity in pathological variants of NS.

ATP hydrolytic activity of purified Spf1p correlate with micellar lipid fluidity and is dependent on conserved residues in transmembrane helix M1.

P5A ATPases are expressed in the endoplasmic reticulum (ER) of all eukaryotic cells, and their disruption results in pleiotropic phenotypes related to severe ER stress. They were recently proposed to function in peptide translocation although their specificity have yet to be confirmed in reconstituted assays using the purified enzyme. A general theme for P-type ATPases is that binding and transport of substrates is coupled to hydrolysis of ATP in a conserved allosteric mechanism, however several independent reports have shown purified Spf1p to display intrinsic spontaneous ATP hydrolytic activity after purification. It has never been determined to what extend this spontaneous activity is caused by uncoupling of the enzyme. In this work we have purified a functional tagged version of the Saccharomyces cerevisiae P5A ATPase Spf1p and have observed that the intrinsic ATP hydrolytic activity of the purified and re-lipidated protein can be stimulated by specific detergents (C12E8, C12E10 and Tween20) in mixed lipid/detergent micelles in the absence of any apparent substrate. We further show that this increase in activity correlate with the reaction temperature and the anisotropic state of the mixed lipid/detergent micelles and further that this correlation relies on three highly conserved phenylalanine residues in M1. This suggests that at least part of the intrinsic ATP hydrolytic activity is allosterically coupled to movements in the TM domain in the purified preparations. It is suggested that free movement of the M1 helix represent an energetic constraint on catalysis and that this constraint likely is lost in the purified preparations resulting in protein with intrinsic spontaneous ATP hydrolytic activity. Removal of the N-terminal part of the protein apparently removes this activity.

Mechanism of enhanced sensitivity of mutated β-adrenergic-like octopamine receptor to amitraz in honeybee Apis mellifera: An insight from MD simulations.

Amitraz is one of the critical acaricides/insecticides for effective control of pest infestation of Varroa destructor mite, a devastating parasite of Apis mellifera, because of its low toxicity to honeybees. Previous assays verified that a typical G protein-coupled receptor, β-adrenergic-like octopamine receptor (Octβ2R), is the unique target of amitraz, but the honeybee Octβ2R resists to amitraz. However, the underlying molecular mechanism of the enhanced sensitivity or toxicity of amitraz to mutated honeybee Octβ2RE208V/I335T/I350V is not fully understood. Here, molecular dynamics simulations are employed to explore the implied mechanism of the enhanced sensitivity to amitraz in mutant honeybee Octβ2R. We found that amitraz binding stabilized the structure of Octβ2R, particularly the intracellular loop 3 associated with the Octβ2R signaling. Then, it was further demonstrated that both mutations and ligand binding resulted in a more rigid and compact amitraz binding site, as well as the outward movement of the transmembrane helix 6, which was a prerequisite for G protein coupling and activation. Moreover, mutations were found to promote the binding between Octβ2R and amitraz. Finally, community analysis illuminated that mutations and amitraz strengthened the residue-residue communication within the transmembrane domain, which might facilitate the allosteric signal propagation and activation of Octβ2R. Our results unveiled structural determinants of improved sensitivity in the Octβ2R-amitraz complex and may contribute to further structure-based drug design for safer and less toxic selective insecticides. © 2022 Society of Chemical Industry.

Allosteric activation of CRISPR-Cas12a requires the concerted movement of the bridge helix and helix 1 of the RuvC II domain.

Nucleases derived from the prokaryotic defense system CRISPR-Cas are frequently re-purposed for gene editing and molecular diagnostics. Hence, an in-depth understanding of the molecular mechanisms of these enzymes is of crucial importance. We focused on Cas12a from Francisella novicida (FnCas12a) and investigated the functional role of helix 1, a structural element that together with the bridge helix (BH) connects the recognition and the nuclease lobes of FnCas12a. Helix 1 is structurally connected to the lid domain that opens upon DNA target loading thereby activating the active site of FnCas12a. We probed the structural states of FnCas12a variants altered in helix 1 and/or the bridge helix using single-molecule FRET measurements and assayed the pre-crRNA processing, cis- and trans-DNA cleavage activity. We show that helix 1 and not the bridge helix is the predominant structural element that confers conformational stability of FnCas12a. Even small perturbations in helix 1 lead to a decrease in DNA cleavage activity while the structural integrity is not affected. Our data, therefore, implicate that the concerted remodeling of helix 1 and the bridge helix upon DNA binding is structurally linked to the opening of the lid and therefore involved in the allosteric activation of the active site.

Multistimuli-Responsive Hydroplaning Superhydrophobic Microrobots with Programmable Motion and Multifunctional Applications.

Superhydrophobic microrobots that can swim efficiently and rapidly on water under the action of external stimuli have attracted significant research attention for various applications. However, most studies on superhydrophobic microrobots have focused on single-stimulus driving modes, which limit the motion and functional applications of microrobots in complex aquatic environments. Therefore, multistimuli-responsive superhydrophobic microrobots that are capable of drifting rapidly on water through light, magnetic, and chemical control were developed in this study. The stability and environmental adaptability of the microrobots were systematically investigated. The microrobots achieved programmable trajectory motion on water, particularly complex motions such as circular, spiral, and helical movements under the coupled influence of chemical and magnetic fields. Importantly, the motion and control of multimicrorobots can be realized by combining control methods. Under the action of light and magnetic field, multimicrorobots could realize cooperative movement and completed the transportation of cargo. Additionally, broad multifunctional applications of the microrobots were explored in terms of oil spill recovery and solution mix. This study provides a method for the preparation and development of superhydrophobic microrobots with multistimuli-responsive characteristics.

Lysine 101 in the CRAC Motif in Transmembrane Helix 2 Confers Cholesterol-Induced Thermal Stability to the Serotonin1A Receptor.

G protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins that transduce signals across the plasma membrane and orchestrate a multitude of physiological processes within cells. The serotonin1A receptor is a crucial neurotransmitter receptor in the GPCR family involved in a multitude of neurological, behavioral and cognitive functions. We have previously shown, using a combination of experimental and simulation approaches, that membrane cholesterol acts as a key regulator of organization, dynamics, signaling and endocytosis of the serotonin1A receptor. In addition, we showed that membrane cholesterol stabilizes the serotonin1A receptor against thermal deactivation. In the present work, we explored the molecular basis of cholesterol-induced thermal stability of the serotonin1A receptor. For this, we explored the possible role of the K101 residue in a cholesterol recognition/interaction amino acid consensus (CRAC) motif in transmembrane helix 2 in conferring the thermal stability of the serotonin1A receptor. Our results show that a mutation in the K101 residue leads to loss in thermal stability of the serotonin1A receptor imparted by cholesterol, independent of membrane cholesterol content. We envision that our results could have potential implications in structural biological advancements of GPCRs and design of thermally stabilized receptors for drug development.

Elucidation of partial activation of cannabinoid receptor type 2 and identification of potential partial agonists: Molecular dynamics simulation and structure-based virtual screening

Cannabinoid receptor type 2 (CB2R) is a member of the class A G protein-coupled receptor (GPCRs) family and a component of the endocannabinoid system that is modulated by the psychoactive chemical from Cannabis sativa, partial agonist Δ9-tetrahydrocannabinol (Δ9-THC). Selective activation of CB2R allows for the treatment of inflammatory and immune-related conditions without the psychotropic effects of CB1R. While CB2R-selective agonists are available, CB2R partial agonists are scarce. Hence, the pharmacological difference between CB2R full agonists and partial agonists remains to be deciphered, prompting the search for novel partial agonists. Here, using an induced-fit docking approach, we built a partial agonist Δ9-THC bound CB2R system from the inactive CB2R structure (PDB ID: 5ZTY) and performed microsecond molecular dynamics (MD) simulations. The simulations reveal an upward shift of the “toggle switch” W6.48(258) and minor outward movement of the transmembrane helix 6 (TM6). Dynamic network model identifies a possible communication path between the ligand and the toggle switch” W6.48(258). Furthermore, to identify potential CB2R partial agonists, we conducted structure-based virtual screening of ZINC15 “Druglike” library containing 17,900742 compounds against 3 conformations derived from MD simulation of CB2R complexed with partial agonist Δ9-THC using Glide virtual screening protocol comprising various filters with increasing accuracy. Nine diverse compounds predicted to have high MM-GBSA binding energy scores and good ADMET properties (including high gastrointestinal absorption and low toxicity) are proposed as potential CB2R partial agonists.

Enhanced radiation of nonlinear Thomson backscattering by a tightly focused Gaussian laser pulse and an external magnetic field

The electron dynamics and the Thomson backscattering of an electron moving in a combined field of a tightly focused Gaussian laser pulse and an external uniform magnetic field are investigated in detail. It is found that by considering the tightly focused Gaussian laser pulse, the electron can be pushed out from the laser pulse by the ponderomotive force, resulting in the symmetry breaking of the electron dynamics from the Gaussian envelope, which can dramatically enhance the radiation intensity. It is also found that by introducing an external magnetic field, the emergence of the cyclotron motion of the electron under the external magnetic field also breaks the symmetry of the electron dynamics and enhances the radiation. Especially in the resonance case, i.e., the cyclotron frequency of the electron is close to the laser frequency, the emission spectrum is further enhanced due to the great extension of the interaction time and the symmetry breaking by the beat wave between the helix motion and the cyclotron motion of the electron in the combined field, and a platform with high radiation intensity containing the THz band has also appeared.

Opposite motion of the Central Helices of efflux pump KmrA is important for its export efficiency

Efflux pump of Major Facilitator Superfamily (MFS) is widely distributed in bacteria, while its role in regulating antibiotic resistance of nosocomial pathogen Klebsiella pneumoniae remains unclear. Herein we analyzed the effect of amino acid substitution of MFS efflux pump KmrA on its export efficiency via molecular biology and molecular dynamics (MD). After searching across the 804 sequenced K. pneumoniae isolates, we identified four major variants of KmrA, while one of them KmrA-A was demonstrated an inactive one in MIC and ethidium bromide efflux assays. Subsequently, MD simulations of KmrA and its variants were conducted and the opposite motion of the central helices were observed for the active variants, while it was not found for KmrA-A. To further identify the importance of the opposite motion to the conformational transition, we calculated their differences in volume of binding pocket, salt bridge and hydrophilic interaction with water based on the rocker-switch model. Our results indicated that the opposite motion of KmrA conferred a larger binding pocket and stronger hydrogen bond with water at inward-facing conformation. An unusual substitution S374A of KmrA-A disrupted the normal motion of central helices by enhancing hydrophobic interactions between them, resulting into the altered positions and strengths of salt bridge, which was deduced to affect the conformational transition. Overall our data provided detailed information on the regular of KmrA's moving trajectory, demonstrating the importance of opposite motion of central helices to KmrA's export efficiency.

MYCN Directly Targets NeuroD1 to Promote Cellular Proliferation in Neuroblastoma.

NeuroD1 is a neuronal differentiation factor that contains a basic helix–loop–helix (bHLH) motif. Recently, NeuroD1 was found to be associated with tumorigenesis in neuroblastoma (NB) and is known to promote cell proliferation and migration in these cells. Here we found that MYCN regulates the expression of NeuroD1 in NB cells and that the downregulation of MYCN using short hairpin RNAs (shRNA) results in the inhibition of cellular proliferation in NB cells. Moreover, the phenotype induced by MYCN shRNA was rescued by the exogenous expression of NeuroD1. Chromatin immunoprecipitation (ChIP) assay showed that MYCN directly binds to the E-box element in the NeuroD1 promoter region. In addition, our evaluation of two clinical databases showed that there was a positive correlation between the expression of MYCN and NeuroD1 in NB patients, which supports our in vitro data. In conclusion, this study demonstrates that MYCN-regulated NeuroD1 expression is one of the important mechanisms underlying enhanced cellular proliferation induced by the increase in MYCN expression in NB, and our results provide an important therapeutic target for NB in the future.