Taste receptor T1R1-T1R3 can be activated by binding to several natural ligands, e.g., l-glutamate and 5′-ribonucleotides etc., thereby stimulating the umami taste. The molecular mechanism of umami ...recognition at atomic details, however, remains elusive. Here, using homology modeling, molecular docking and molecular dynamics (MD) simulations, we investigate the effects of five natural umami ligands on the structural dynamics of T1R1-T1R3. Our work identifies the key residues that are directly involved in recognizing the binding ligands. In addition, two adjacent binding sites in T1R1 are determined for substrate binding, and depending on the molecular size and chemical properties of the incoming ligand, one or both binding sites can be occupied. More interestingly, the ligand binding can modulate the pocket size, which is likely correlated with the closing and opening motions of T1R1. We then classify these five ligands into two groups according to their different binding effects on T1R1, which likely associate with the distinct umami signals stimulated by various ligands. This work warrants new experimental assays to further validate the theoretical model and provides guidance to design more effective umami ligands.
•Revealing the binding effects of five umami ligands on the structural dynamics of T1R1-T1R3 at atomic resolution.•Molecular size and carried charges of the umami ligands determine their specific binding sites.•This work provides further guidance to design more effective and structurally diversified umami substances.
Soluble
-glycosyltransferase from
(ApNGT) catalyzes the glycosylation of asparagine residues, and represents one of the most encouraging biocatalysts for
-glycoprotein production. Since the sugar ...tolerance of ApNGT is restricted to limited monosaccharides (
, Glc, GlcN, Gal, Xyl, and Man), tremendous efforts are devoted to expanding the substrate scope of ApNGT
enzyme engineering. However, rational design of novel NGT variants suffers from an elusive understanding of the substrate-binding process from a dynamic point of view. Here, by employing extensive all-atom molecular dynamics (MD) simulations integrated with a kinetic model, we reveal, at the atomic level, the complete donor-substrate binding process from the bulk solvent to the ApNGT active-site, and the key intermediate states of UDP-Glc during its loading dynamics. We are able to determine the critical transition event that limits the overall binding rate, which guides us to pinpoint the key ApNGT residues dictating the donor-substrate entry. The functional roles of several identified gating residues were evaluated through site-directed mutagenesis and enzymatic assays. Two single-point mutations, N471A and S496A, could profoundly enhance the catalytic activity of ApNGT. Our work provides deep mechanistic insights into the structural dynamics of the donor-substrate loading process for ApNGT, which sets a rational basis for design of novel NGT variants with desired substrate specificity.
Major histocompatibility complex class I (MHC-I) molecules display antigenic peptides on the cell surface for T cell receptor scanning, thereby activating the immune response. Peptide loading into ...MHC-I molecules is thus a critical step during the antigen presentation process. Chaperone TAP-binding protein related (TAPBPR) plays a critical role in promoting high-affinity peptide loading into MHC-I, by discriminating against the low-affinity ones. However, the complete peptide loading dynamics into TAPBPR-bound MHC-I is still elusive. Here, we constructed kinetic network models based on hundreds of short-time MD simulations with an aggregated simulation time of ∼21.7 μs, and revealed, at atomic level, four key intermediate states of one antigenic peptide derived from melanoma-associated MART-1/Melan-A protein during its loading process into TAPBPR-bound MHC-I. We find that the TAPBPR binding at the MHC-I pocket-F can substantially reshape the distant pocket-B
via
allosteric regulations, which in turn promotes the following peptide N-terminal loading. Intriguingly, the partially loaded peptide could profoundly weaken the TAPBPR-MHC stability, promoting the dissociation of the TAPBPR scoop-loop (SL) region from the pocket-F to a more solvent-exposed conformation. Structural inspections further indicate that the peptide loading could remotely affect the SL binding site through both allosteric perturbations and direct contacts. In addition, another structural motif of TAPBPR, the jack hairpin region, was also found to participate in mediating the peptide editing. Our study sheds light on the detailed molecular mechanisms underlying the peptide loading process into TAPBPR-bound MHC-I and pinpoints the key structural factors responsible for dictating the peptide-loading dynamics.
Computational simulations reveal strong interplay between TAPBPR and the incoming peptide during peptide loading into MHC-I.
Abstract
Thymine DNA glycosylase (TDG), as a repair enzyme, plays essential roles in maintaining the genome integrity by correcting several mismatched/damaged nucleobases. TDG acquires an efficient ...strategy to search for the lesions among a vast number of cognate base pairs. Currently, atomic-level details of how TDG translocates along DNA as it approaches the lesion site and the molecular mechanisms of the interplay between TDG and DNA are still elusive. Here, by constructing the Markov state model based on hundreds of molecular dynamics simulations with an integrated simulation time of ∼25 μs, we reveal the rotation-coupled sliding dynamics of TDG along a 9 bp DNA segment containing one G·T mispair. We find that TDG translocates along DNA at a relatively faster rate when distant from the lesion site, but slows down as it approaches the target, accompanied by deeply penetrating into the minor-groove, opening up the mismatched base pair and significantly sculpturing the DNA shape. Moreover, the electrostatic interactions between TDG and DNA are found to be critical for mediating the TDG translocation. Notably, several uncharacterized TDG residues are identified to take part in regulating the conformational switches of TDG occurred in the site-transfer process, which warrants further experimental validations.
Major histocompatibility complex class II (MHC-II) plays an indispensable role in activating CD4+ T cell immune responses by presenting antigenic peptides on the cell surface for recognition by ...T cell receptors. The assembly of MHC-II and antigenic peptide is therefore a prerequisite for the antigen presentation. To date, however, the atomic-level mechanism underlying the peptide-loading dynamics for MHC-II is still elusive. Here, by constructing Markov state models based on extensive all-atom molecular dynamics simulations, we reveal the complete peptide-loading dynamics into MHC-II for one SARS-CoV-2 S-protein-derived antigenic peptide (235ITRFQTLLALHRSYL249). Our Markov state model identifies six metastable states (S1–S6) during the peptide-loading process and determines two dominant loading pathways. The peptide could potentially approach the antigen-binding groove via either its N- or C-terminus. Then, the consecutive insertion of several anchor residues into the binding pockets profoundly dictates the peptide-loading dynamics. Notably, the MHC-II αA52-E55 motif could guide the peptide loading into the antigen-binding groove via forming β-sheets conformation with the incoming peptide. The rate-limiting step, namely S5→S6, is mainly attributed to a considerable desolvation penalty triggered by the binding of the peptide C-terminus. Moreover, we further examined the conformational changes associated with the peptide exchange process catalyzed by the chaperon protein HLA-DM. A flipped-out conformation of MHC-II αW43 captured in S1–S3 is considered a critical anchor point for HLA-DM to modulate the structural dynamics. Our work provides deep structural insights into the key regulatory factors in MHC-II responsible for peptide recognition and guides future design for peptide vaccines against SARS-CoV-2.
Abstract
Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in ...maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesions, TDG employs a base-flipping strategy to recognize the damaged nucleobases, whereby the interrogated nt is extruded from the DNA helical stack and binds into the TDG active site. The dynamic mechanism of the base-flipping process at an atomistic resolution, however, remains elusive. Here, we employ the Markov State Model (MSM) constructed from extensive all-atom molecular dynamics (MD) simulations to reveal the complete base-flipping process for a G.T mispair at a tens of microsecond timescale. Our studies identify critical intermediates of the mispaired dT during its extrusion process and reveal the key TDG residues involved in the inter-state transitions. Notably, we find an active role of TDG in promoting the intrahelical nt eversion, sculpturing the DNA backbone, and penetrating into the DNA minor groove. Three additional TDG substrates, namely dU, 5fC, and 5caC, are further tested to evaluate the substituent effects of various chemical modifications of the pyrimidine ring on base-flipping dynamics.
Developing on-site earthquake early warning systems has been a challenging problem because of time limitations and the amount of information that can be collected before the warning needs to be ...issued. A potential solution that could prevent severe disasters is to predict the potential strong motion using the initial P-wave signal and provide warnings before serious ground shaking starts. In practice, the accuracy of prediction is the most critical issue for earthquake early warning systems. Traditional methods use certain criteria, selected through intuition or experience, to make the prediction. However, the criteria thresholds are difficult to select and may significantly affect the prediction accuracy. This paper investigates methods based on artificial intelligence for predicting the greatest earthquake ground motion early, when the P-wave arrives at seismograph stations. A neural network model is built to make the predictions using a small window of the initial P-wave acceleration signal. The model is trained by seismic waves collected from 1991 to 2019 in Taiwan and is evaluated by events in 2020 and 2021. From these evaluations, the proposed scheme significantly outperforms the threshold-based method in terms of its accuracy and average leading time.
Taiwan that is located at the junction of the Eurasian Plate and the Philippine Sea Plate is one of the most active seismic zones in the world. Devastating earthquakes have occurred around the island ...and have caused severe damages from time to time. To avoid the severe loss, earthquake early warning (EEW) is of great importance, and one of the most critical issues of EEW is fast and reliable detection for the presence of earthquakes. Traditional methods for earthquake detection usually use criterion-based algorithms to detect the onset of the earthquake waves. Currently, the thresholds for those criteria are usually decided empirically and may result in excessive false alarms. Obviously, false alarms can cause undue panics and diminish the credibility of the system. In this article, the recurrent neural network (RNN) models are adopted to develop a real-time EEW system. The developed system is designed to identify the occurrence of an earthquake event, and the duration of the P-wave and the S-wave. It was trained and tested using the seismograms recorded in Taiwan from 2016 to 2017. From the simulation results, the proposed scheme outperforms the traditional criterion-based schemes in terms of detection accuracy and processing time.
Pyrophosphate ion (PPi) release after nucleotide incorporation is a necessary step for RNA polymerase II (pol II) to enter the next nucleotide addition cycle during transcription elongation. However, ...the role of pol II residues in PPi release and the mechanistic relationship between PPi release and the conformational change of the trigger loop remain unclear. In this study, we constructed a Markov state model (MSM) from extensive all-atom molecular dynamics (MD) simulations in the explicit solvent to simulate the PPi release process along the pol II secondary channel. Our results show that the trigger loop has significantly larger intrinsic motion after catalysis and formation of PPi, which in turn aids PPi release mainly through the hydrogen bonding between the trigger loop residue H1085 and the (Mg–PPi)2– group. Once PPi leaves the active site, it adopts a hopping model through several highly conserved positively charged residues such as K752 and K619 to release from the pol II pore region of the secondary channel. These positive hopping sites form favorable interactions with PPi and generate four kinetically metastable states as identified by our MSM. Furthermore, our single-mutant simulations suggest that H1085 and K752 aid PPi exit from the active site after catalysis, whereas K619 facilitates its passage through the secondary channel. Finally, we suggest that PPi release could help the opening motion of the trigger loop, even though PPi release precedes full opening of the trigger loop due to faster PPi dynamics. Our simulations provide predictions to guide future experimental tests.
HIV-1 entry is mediated firstly by the molecular recognition between the viral glycoprotein gp120 and its receptor CD4 on host T-cells. As a key antigen that can be targeted by neutralizing ...antibodies, gp120 has been a focus for extensive studies with efforts to understand its structural properties and conformational dynamics upon receptor binding. An atomistic-level revelation of gp120 opening dynamics activated by CD4, however, is still unknown. Here, by constructing a Markov State Model (MSM) based on hundreds of Molecular Dynamics (MD) simulations with an aggregated simulation time of ∼20 microseconds (μs), we identify the key metastable states of gp120 during its opening dynamics upon CD4 binding. The MSM provides a clear dynamic model whereby the identified metastable states coexist and can reach an equilibrium. More importantly, a hydrophobic core flanked by variable loops (V1V2 and V3) and the β20/21 region plays an essential role in triggering the gp120 opening. Any destabilizing effects introduced into the hydrophobic core, therefore, can be expected to promote transition of gp120 to an open state. Moreover, the variable loops demonstrate high flexibilities in fully open gp120. In particular, the V3 region is capable of exploring both closed and open conformations, even with the V1/V2 loops largely adopting an open form. In addition, the bridging sheet formation in gp120 is likely induced by the incoming co-receptor/antibody recognitions, since the V1/V2 structure is highly heterogeneous so that the bridging-sheet formed conformation is not the most populated state. Our studies provide deep insights into the dynamic features of gp120 and its molecular recognitions to the broadly neutralizing antibodies, which guides future attempts to design more effective gp120 immunogens.
One hydrophobic core flanked by V1V2, V3 and β20 of HIV-1 gp120 is responsible for mediating the opening dynamics of gp120 upon receptor binding.
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