Anti-correlated Motion Research Articles

Sucrose and Gibberellic Acid Binding Stabilize the Inward-Open Conformation of AtSWEET13: A Molecular Dynamics Study.

In plants, sugar will eventually be exported transporters (SWEETs) facilitate the translocation of mono- and disaccharides across membranes and play a critical role in modulating responses to gibberellin (GA3), a key growth hormone. However, the dynamic mechanisms underlying sucrose and GA3 binding and transport remain elusive. Here, we employed microsecond-scale molecular dynamics (MD) simulations to investigate the influence of sucrose and GA3 binding on SWEET13 transporter motions. While sucrose exhibits high flexibility within the binding pocket, GA3 remains firmly anchored in the central cavity. Binding of both ligands increases the average channel radius along the transporter's principal axis. In contrast to the apo form, which retains its initial conformation throughout the simulation, ligand-bound complexes undergo a significant conformational transition characterized by further opening of the intracellular gate relative to the inward-open crystal structure (5XPD). This opening is driven by ligand-induced bending of helix V, stabilizing the inward-open state. Sucrose binding notably enhances the flexibility of the intracellular gate and amplifies anticorrelated motions between the N- and C-terminal domains at the intracellular side, suggesting an opening-closing motion of these domains. Principal component analysis revealed that this gating motion is most pronounced in the sucrose complex and minimal in the apo form, highlighting sucrose's ability to induce high-amplitude gating. Our binding free energy calculations indicate that SWEET13 has lower binding affinity for sucrose compared to GA3, consistent with its role in sugar transport. These results provide insight into key residues involved in sucrose and GA3 binding and transport, advancing our understanding of SWEET13 dynamics.

Phosphorylation at the D56 residue of MtrA in Mycobacterium tuberculosis enhances its DNA binding affinity by modulating inter-domain interaction

The response regulator, MtrA, plays a major role in adaptation to the host environment, cell division, replication, and dormancy activation of Mycobacterium tuberculosis (Mtb). The phosphorylation of the response regulator MtrA alters the downstream activity, typically involving changes in DNA binding activity. However, there is a substantial knowledge gap in understanding the phosphorylation-mediated structural changes in MtrA. Additionally, the active conformation of the protein has yet to be determined. Therefore, in this study, we have investigated the phosphorylation-induced conformational changes of MtrA using all-atom molecular dynamics simulations under various phosphorylation conditions. The results from this study demonstrate that the phosphorylation at D56 (pD56-MtrA) increases the compactness of the MtrA protein by stabilizing the inter-domain interaction between the regulatory domain and DNA binding domain. Notably, the higher occupancy H-bond (over 95 %) between Arg200-Asn100 in case of the pD56-MtrA condition, which is otherwise absent in the non-phosphorylated (uMtrA) condition, suggests the importance of this interaction in the active conformation of the protein. The dynamic cross-correlation analysis reveals that phosphorylation (especially pD56-MtrA) reduces the anti-correlated motions and increases correlated motions between different domains. Moreover, the higher DNA binding affinity of pD56-MtrA compared to uMtrA supported by molecular docking and MD simulation followed by MMPBSA analysis suggests that pD56-MtrA is the possible active conformation of the MtrA protein. Overall, this investigation elucidates the key structural changes in MtrA under different phosphorylated conditions, which might help in designing novel therapeutics against tuberculosis.

Weak Pinning and Long-Range Anticorrelated Motion of Phase Boundaries in Driven Diffusive Systems.

We show that domain walls separating coexisting extremal current phases in driven diffusive systems exhibit complex stochastic dynamics with a subdiffusive temporal growth of position fluctuations due to long-range anticorrelated current fluctuations and a weak pinning at long times. This weak pinning manifests itself in a saturated width of the domain wall position fluctuations that increases sublinearly with the system size. As a function of time t and system size L, the width w(t,L) has a scaling behavior w(t,L)=L^{3/4}f(t/L^{9/4}), with f(u) constant for u≫1 and f(u)∼u^{1/3} for u≪1. An Orstein-Uhlenbeck process with long-range anticorrelated noise is shown to capture this scaling behavior. The exponent 9/4 is a new dynamical exponent for relaxation processes in driven diffusive systems.

Structural dynamics of the RNA dependent RNA polymerase of H1N1 strain affecting humans: a bioinformatics approach

The Influenza flu is a pandemic disease that renders the highest risk factor to the society due to its efficient ability of airborne transmission. Studies on the H1N1 strain gained significant focus, since its pandemic outbreak in 2009 and particularly the computational studies on its structural elements significantly aided in revealing their functional uniqueness. Among the 10 structural proteins of H1N1, the RNA-dependent RNA polymerase (RdRp) heterotrimeric protein complex, which is responsible for the synthesis of viral RNA (vRNA) from the negative-sense RNA genome of the virus, is the focus of the present study. This study aimed to investigate the structural dynamics of the RdRp complex with particular emphasis on the reported 17 mutations. The mutant strain is more stabilized by strong concerted residue-residue interactions at both intra- and inter- monomeric levels. In comparison, the mutant strain is structurally flexible with enhanced stabilizing interactions. The structural dynamics of RdRp are significantly governed by the dynamics of the (i) endonuclease domain of PA, (ii) RNA-entry region of PB1 and (iii) cap-binding region of PB2. Explicitly, the cap binding region of PB2 expresses (i) a concerted motion with the RNA-entry region, along with (ii) an anti-correlated motion with the endonuclease domain of the PA subunit, which further supports the stable dynamics of cap-binding towards RNA binding. These findings contribute to the understanding of the structural dynamics associated with the pandemic and mutant structures of RdRp and render a basic knowledge for further development of novel inhibitors towards influenza flu affected humans. Communicated by Ramaswamy H. Sarma

Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase

The Fibroblast Growth Factor Receptor1 (FGFR1) kinase wields exquisite control on cell fate, proliferation, differentiation, and homeostasis. An imbalance of FGFR1 signaling leads to several pathogeneses of diseases ranging from multiple cancers to allergic and neurodegenerative disorders. In this study, we investigated the phosphorylation-induced conformational dynamics of FGFR1 in apo and ATP-bound states via all-atom molecular dynamics simulations. All simulations were performed for 2 × 2 µs. We have also investigated the energetics of the binding of ATP to FGFR1 using the molecular mechanics Poisson-Boltzmann scheme. Our study reveals that the FGFR1 kinase can reach a fully active configuration through phosphorylation and ATP binding. A 3–10 helix formation in the activation loop signifies its rearrangement leading to stability upon ATP binding. The interaction of phosphorylated tyrosine (pTyr654) with positively charged residues forms strong salt-bridge interactions, driving the compactness of the structure. The dynamic cross-correlation map reveals phosphorylation enhances correlated motions and reduces anti-correlated motions between different domains. We believe that the mechanistic understanding of large-conformational changes upon the activation of the FGFR1 kinase will aid the development of novel targeted therapeutics. Communicated by Ramaswamy H. Sarma

Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase.

Calcium (Ca2+) signaling plays an important role in the regulation of many cellular functions. Ca2+-binding protein calmodulin (CaM) serves as a primary effector of calcium function. Ca2+/CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. However, the mechanism underlying the influence of Ca2+ on the conformational dynamics of the DAPK1-CaM interactions is still unclear. Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1-CaM complex in the Ca2+-bound and-unbound states to reveal the importance of Ca2+. MD simulations revealed that removal of Ca2+ increased the anti-correlated inter-domain motions between DAPK1 and CaM, which weakened the DAPK1-CaM interactions. Binding free energy calculations validated the decreased DAPK1-CaM interactions in the Ca2+-unbound state. Structural analysis further revealed that Ca2+ removal caused the significant conformational changes at the DAPK1-CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. These results may be useful to understand the biological role of Ca2+ in physiological processes.

Computational Dissection of the Role of Trp305 in the Regulation of the Death-Associated Protein Kinase-Calmodulin Interaction.

Death-associated protein kinase 1 (DAPK1), as a calcium/calmodulin (CaM) regulated serine/threonine kinase, functions in apoptotic and autophagy pathways and represents an interesting drug target for inflammatory bowel disease and Alzheimer’s disease. The crystal structure of the DAPK1 catalytic domain and the autoregulatory domain (ARD) in complex with CaM provides an understanding of CaM-dependent regulation of DAPK1 activity. However, the molecular basis of how distinct Trp305 (W305Y and W305D) mutations in the ARD modulate different DAPK1 activities remains unknown. Here, we performed multiple, μs-length molecular dynamics (MD) simulations of the DAPK1–CaM complex in three different (wild-type, W305Y, and W305D) states. MD simulations showed that the overall structural complex did not change significantly in the wild-type and W305Y systems, but underwent obvious conformational alteration in the W305D system. Dynamical cross-correlation and principal component analyses revealed that the W305D mutation enhanced the anti-correlated motions between the DAPK1 and CaM and sampled a broader distribution of conformational space relative to the wild-type and W305Y systems. Structural and energetical analyses further exhibited that CaM binding was unfavored in response to the W305D mutation, resulting in the decreased binding of CaM to the W305D mutant. Furthermore, the hydrogen bonds and salt bridges responsible for the loss of CaM binding on the interface of the DAPK1–CaM complex were identified in the W305D mutant. This result may provide insights into the key role of Trp305 in the regulation of CaM-mediated DAPK1 activity.

Li+ transference number and dynamic ion correlations in glyme-Li salt solvate ionic liquids diluted with molecular solvents.

Highly concentrated electrolytes (HCEs) have attracted significant interest as promising liquid electrolytes for next-generation Li secondary batteries, owing to various beneficial properties both in the bulk and at the electrode/electrolyte interface. One particular class of HCEs consists of binary mixtures of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and oligoethers that behave like ionic liquids. [Li(G4)][TFSA], which comprises an equimolar mixture of LiTFSA and tetraglyme (G4), is an example. In our previous works, the addition of low-polarity molecular solvents to [Li(G4)][TFSA] was found to effectively enhance the conductivity while retaining the unique Li-ion solvation structure. However, it remains unclear how the diluents affect another key electrolyte parameter-the Li+ transference number-despite its critical importance for achieving the fast charging/discharging of Li secondary batteries. Thus, in this study, the effects of diluents on the extremely low Li+ transference number under anion-blocking conditions in [Li(G4)][TFSA] were elucidated, with a special focus on the polarity of the additional solvents. The concentration dependence of the dynamic ion correlations was further studied in the framework of the concentrated electrolyte theory. The results revealed that a non-coordinating diluent is not involved in the modification of the ion transport mechanism, and therefore the low Li+ transference number is inherited by the diluted electrolytes. In contrast, a coordinating diluent effectively reduces the anti-correlated ion motions of [Li(G4)][TFSA], thereby improving the Li+ transference number. This is the first time that the significant effects of the coordination properties of the diluting solvents on the dynamic ion correlations and Li+ transference numbers have been reported for diluted solvate ionic liquids.

Cooperation between Excitation Energy Transfer and Antisynchronously Coupled Vibrations.

The effects of the environment in energy transfer systems have been continuously studied for decades. Here, we investigate how the energy transfer and the emergence of vibrational correlations cooperate with each other based on simulations with a few numerically approximate mixed quantum classical (MQC) methods. By adopting a two-state system with locally coupled underdamped vibrations that are resonant with the electronic energy gap, we observe prominent energy dissipations from the electronic system to the vibrations, rehighlighting the role of underdamped vibrations as a temporal electronic energy buffer. More importantly, this energy dissipation generates specific phase relations between the two vibrations. Namely, the vibrations become anticorrelated right after the initiation of the energy transfer but then synchronized as the transfer completes. These phase relations are interpreted as a selective activation of an anticorrelated motion of the vibrations and a subsequent deactivation by thermal energy redistribution. Furthermore, we show that a single vibration simultaneously coupled to the two electronic states with opposite phases induces a completely equivalent energy transfer dynamics as the two localized vibrations. Finally, we discuss how the vibrational energy dissipation dynamics is affected by the adopted MQC approaches and warn about the increased subtlety toward properly treating dissipation effects over having reliable population dynamics.

Study of the dynamics of Ceritinib in complex with common variants of anaplastic lymphoma kinase

ABSTRACT Anaplastic lymphoma kinase, a transmembrane receptor tyrosine kinase belongs to the insulin receptor superfamily. Genetic aberrations including mutation, amplification, and gene fusion have led to its involvement in the development of cancer in patients and have also been approved for targeted therapy by Food and Drug Administration. Mutations in its kinase domain have resulted in resistance to targeted therapy. In the present study, using molecular dynamics simulations we explore the mechanism of resistance of the ALK inhibitor-Ceritinib with Phenylalanine variant at position 1174 while comparing it with the wild type and other reported mutants. We observed that binding of Ceritinib to the Phenylalanine 1174 mutant results in elevated fluctuations in residues which are component of the adenosine triphosphate binding pocket. Residues of P loop, β3 strand and αC Helix undergo anti correlated motions with respect to the αD, αE helix, component amino acids of β6-β7 strands and their interconnecting loop. This anti-correlated motion of the residues around the binding pocket results in the elevated deviations of the bound Ceritinib. Molecular mechanics-generalized born surface area free energy of binding analysis reveals comparatively weak binding of the Ceritinib to this variant compared to other forms of ALK kinase studied.

Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations

The nucleocapsid (N) protein from Peste des petits ruminants virus enwraps the nascent genomic RNA primarily to protect it from cellular enzymatic degradation. Here, we have combined molecular modeling and 1 μs long Gaussian accelerated molecular dynamics simulations to study the structural and conformational properties of the apo N-protein and three protein-RNA complexes, namely wild type (WT), MT1 (I46T/E297D/G342E), and MT2 (I46T/E297D/G342E/W333G). The root-mean-squared deviation (RMSD) analysis reveals that although MT2 deviates most significantly from the initial structure, the RNA binding region is more stable compared to WT or MT1. Further, the flexible nature of the N protein is revealed from the principal component analysis. Our study shows that the solvent accessible surface area of the binding region increases drastically for both mutant complexes compared to WT. The dynamic cross-correlation analysis suggests that the overall anticorrelated motion weakens after the RNA binding. MT2 displays a relatively larger positive correlation than WT or MT1. The binding free energy is estimated for all three complexes via the molecular mechanics/generalized Born surface (MM/GBSA) scheme, and it decreases in the order WT > MT1 > MT2. In all cases, the protein-RNA binding is mainly driven by the van der Waals interactions since the intermolecular electrostatic interaction is overcompensated by desolvation energy. All hotspot residues are identified from the per-residue decomposition of the total binding free energy. In MT2, RNA contributes most favorably compared to WT or MT1. We believe our study will help in understanding the mechanism of RNA recognition by N proteins. Communicated by Ramaswamy H. Sarma

A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations

The with-no-lysine (WNK) kinase causes pseudohypoaldosteronism type II, a genetic form of hypertension. Due to ∼80% similarity among four isoforms (WNK1/2/3/4) of the WNK protein family, the discovery of an ATP-competitive inhibitor renders a significant challenge. Here, we combined molecular modeling and molecular dynamics simulations to study the structural and conformational properties of the WNK kinase isoforms bound to an ATP competitive inhibitor (WNK463). We have also investigated the effect of phosphorylation on the conformational properties of each isoform. The largest deviation of Cα atoms is observed for the unphosphorylated uWNK4 complex, while the least deviation is obtained for uWNK3. The G-loop and αC-helix regions are also more flexible in uWNK4 compared to the other three unphosphorylated isoforms. However, in uWNK1, the A-loop region is the most flexible compared to other complexes. In all cases, phosphorylation stabilizes different regions of the protein–inhibitor complexes. In the case of uWNK4, relatively higher anti-correlated motions are observed compared to the other three unphosphorylated complexes. Furthermore, in the case of uWNK4, the distance between N- and C-lobes is found to be slightly higher than other complexes. This distance is reduced in all four complexes after the phosphorylation. Principal component analyses suggest that the phosphorylation leads to structural stabilization in WNK1 and WNK4, while it causes more flexibility in WNK2 and WNK3. Overall, our study provides comprehensive and comparative information on the structural dynamics of the WNK isoform family with the known competitive inhibitor that would aid in the development of a new inhibitor. Communicated by Ramaswamy H. Sarma

Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations

Non-B strains cause nearly 90% of the worldwide human immunodeficiency virus (HIV) infections. At the same time, the protease inhibitors (PIs) were designed for subtype B. Therefore, the use of PIs in the non-B subtype context requires further investigation. Herein, we have investigated the effectiveness of currently used four PIs, namely atazanavir, darunavir, lopinavir, and tipranavir against subtype CRF01_AE (PRCRF) by employing the MD/MMPBSA (molecular dynamics/molecular mechanics Poisson-Boltzmann surface area) scheme. Our investigation reveals that tipranavir is the most potent inhibitor against PRCRF while the other three PIs display a similar binding affinity. The energetic penalty arises due to the desolvation of polar groups always disfavor the association between PRCRF and PI, and this contribution is the least in the case of tipranavir/PRCRF compared to the other three PI-PRCRF complexes resulting in a better binding affinity for tipranavir. Further, it is revealed that the primary interaction controlling the binding of inhibitors with PRCRF is the van der Waals forces. The dynamic cross-correlation map and principal component analysis show that the anti-correlated motion at the flap region of PRCRF is diminished after the ligand binding. Further, our studies indicate that D25' forms a stable H-bond with darunavir, lopinavir, and tipranavir, while D25 forms a stable H-bond with atazanavir. The per-residue based decomposition of free energy reveals the actual residual origin of the binding free energy and identify the hotspot residues. Overall, the data presented in this study can guide the computer-aided rational design of more potent drugs targetting HIV-1 PRCRF. Communicated by Ramaswamy H. Sarma

Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation

Phosphodiesterase 4B (PDE4B) is a potential therapeutic target for the inflammatory respiratory diseases such as congestive obstructive pulmonary disease (COPD) and asthma. The sequence identity of ∼88% with its isoform PDE4D is the key barrier in developing selective PDE4B inhibitors which may help to overcome associated side effects. Despite high sequence identity, both isoforms differ in few residues present in N-terminal (UCR2) and C-terminal (CR3) involved in catalytic site formation. Previously, we designed and tested specific PDE4B inhibitors considering N-terminal residues as a part of the catalytic cavity. In continuation, current work thoroughly presents an MD simulation-based analysis of N-terminal residues and their role in ligand binding. The various parameters viz. root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA), dynamical cross-correlation matrix (DCCM) analysis, secondary structure analysis and residue interaction mapping were investigated to establish rational. Results showed that UCR2 reduced RMSF values for the metal binding pocket (31.5 ± 11 to 13.12 ± 6 Å2) and the substrate-binding pocket (38.8 ± 32 to 17.3 ± 11 Å2). UCR2 enhanced anti-correlated motion at the active site region that led to the improved ligand-binding affinity of PDE4B from −24.57 ± 3 to −35.54 ± 2 kcal/mol. Further, the atomic-level analysis indicated that T-π and π-π interactions between inhibitors and residues are vital forces that regulate inhibitor association to PDE4B with high affinity. In conclusion, UCR2, the N-terminal domain, embraces the dynamics of PDE4B active site and stabilizes PDE4B inhibitor interactions. Therefore the N-terminal domain needs to be considered while designing next-generation, selective PDE4B-inhibitors as potential anti-inflammatory drugs. Communicated by Ramaswamy H. Sarma

A beginner's guide to molecular dynamics simulations and the identification of cross-correlation networks for enzyme engineering.

The functional properties of proteins are decided not only by their relatively rigid overall structures, but even more importantly, by their dynamic properties. In a protein, some regions of structure exhibit highly correlated or anti-correlated motions with others, some are highly dynamic but uncorrelated, while other regions are relatively static. The residues with correlated or anti-correlated motions can form a so-called dynamic cross-correlation network, through which information can be transmitted. Such networks have been shown to be critical to allosteric transitions, and ligand binding, and have also been shown to be able to mediate epistatic interactions between mutations. As a result, they are likely to play a significant role in the development of new enzyme engineering strategies. In this chapter, protocols are provided for the assessment of dynamic cross-correlation networks, and for their application in protein engineering. Transketolase from E. coli is used as a model and the software GROMACS is applied for carrying out MD simulations to generate trajectories containing structural ensembles. The trajectory is then used for a dynamic cross correlation analysis using the R package, Bio3D. A matrix of all atom-wise cross-correlation coefficients is finally obtained, which can be displayed in a graphical representation termed a dynamical cross-correlation matrix.

Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations.

The With-No-Lysine (WNK) kinase is considered to be a master regulator for various cation-chloride cotransporters involved in maintaining cell-volume and ion homeostasis. Here, we have investigated the phosphorylation-induced structural dynamics of the WNK1 kinase bound to an inhibitor via atomistic molecular dynamics simulations. Results from our simulations show that the phosphorylation at Ser382 could stabilize the otherwise flexible activation loop (A-loop). The intrahelix salt-bridge formed between Arg264 and Glu268 in the unphosphorylated system is disengaged after the phosphorylation, and Glu268 reorients itself and forms a stable salt-bridge with Arg348. The dynamic cross-correlation analysis shows that phosphorylation diminishes anticorrelated motions and increases correlated motions between different domains. Structural network analysis reveals that the phosphorylation causes structural rearrangements and shortens the communication path between the αC-helix and catalytic loop, making the binding pocket more suitable for accommodating the ligand. Overall, we have characterized the structural changes in the WNK kinase because of phosphorylation in the A-loop, which might help in designing rational drugs.

Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance

Pyrazinamide (PZA) is an important component of first-line anti-tuberculosis (anti-TB) drugs. The anti-TB agent is activated into an active form, pyrazinoic acid (POA), by Mycobacterium tuberculosis (MTB) pncA gene encoding pyrazinamidase (PZase). The major cause of PZA-resistance has been associated with mutations in the pncA gene. We have detected several novel mutations including V131F, Q141P, R154T, A170P, and V180F (GeneBank Accession No. MH461111) in the pncA gene of PZA-resistant isolates during PZA drug susceptibility testing followed by pncA gene sequencing. Here, we investigated molecular mechanism of PZA-resistance by comparing the results of experimental and molecular dynamics. The mutants (MTs) and wild type (WT) PZase structures in apo and complex with PZA were subjected to molecular dynamic simulations (MD) at the 40 ns. Multiple factors, including root mean square deviations (RMSD), binding pocket, total energy, dynamic cross correlation, and root mean square fluctuations (RMSF) of MTs and WT were compared. The MTs attained a high deviation and fluctuation compared to WT. Binding pocket volumes of the MTs, were found, lower than the WT, and the docking scores were high than WT while shape complementarity scores were lower than that of the WT. Residual motion in MTs are seemed to be dominant in anti-correlated motion. Mutations at locations, V131F, Q141P, R154T, A170P, and V180F, might be involved in the structural changes, possibly affecting the catalytic property of PZase to convert PZA into POA. Our study provides useful information that will enhance the understanding for better management of TB. Abbreviations DST drug susceptibility testing Δelec electrostatic energy LJ Lowenstein–Jensen medium MGIT mycobacterium growth indicator tubes MTs mutants MD molecular dynamic simulations MTB Mycobacterium tuberculosis NALC–NaOH N-acetyl-l-cysteine–sodium hydroxide NIH National Institutes of Health NPT amount of substance (N), pressure (P) temperature (T) NVT moles (N), volume (V) temperature (T) PZase pyrazinamidase Δps polar solvation energy PTRL Provincial Tuberculosis Reference Laboratory RMSD root mean square deviations RMSF root mean square fluctuations ΔSASA solvent accessible surface area energy TB tuberculosis GTotal total binding free energy ΔvdW Van der Waals energy WT wild type Communicated by Ramaswamy H. Sarma

Dynamics and binding interactions of peptide inhibitors of dengue virus entry.

In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potentially modified further to be active against all dengue strains. Molecular docking was performed using AutoDock Vina and the best-ranked peptide-domain III complex was further explored using molecular dynamics simulations. Molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) was used to calculate the relative binding free energies and to locate the key residues of peptide-protein interactions. The predicted binding affinity correlated well with the previous experimental studies. DET4 outperformed DET2 and is oriented within the binding site through favorable vdW and electrostatic interactions. Pairwise residue decomposition analysis has revealed several key residues that contribute to the binding of these peptides. Residues in DET2 interact relatively lesser with the domain III compared to DET4. Dynamic cross-correlation analysis showed that both the DET2 and DET4 trigger different dynamic patterns on the domain III. Correlated motions were seen between the residue pairs of DET4 and the binding site while binding of DET2 results in anti-correlated motion on the binding site. This work showcases the use of computational study in elucidating and explaining the experiment observation on an atomic level.

Modeling the structural and dynamical changes of the epithelial calcium channel TRPV5 caused by the A563T variation based on the structure of TRPV6

TRPV5, transient receptor potential cation channel vanilloid subfamily member 5, is an epithelial Ca2+ channel that plays a key role in the active Ca2+ reabsorption process in the kidney. A single nucleotide polymorphism (SNP) rs4252499 in the TRPV5 gene results in an A563T variation in the sixth transmembrane (TM) domain of TRPV5. Our previous study indicated that this variation increases the Ca2+ transport function of TRPV5. To understand the molecular mechanism, a model of TRPV5 was established based on the newly deposited structure of TRPV6 that has 83.1% amino acid identity with TRPV5 in the modeled region. Computational simulations were performed to study the structural and dynamical differences between the TRPV5 variants with A563 and T563. Consistent with the TRPV1-based simulation, the results indicate that the A563T variation increases the contacts between residues 563 and V540, which is one residue away from the key residue D542 in the Ca2+-selective filter. The variation enhanced the stability of the secondary structure of the pore region, decreased the fluctuation of residues around residue 563, and reduced correlated and anti-correlated motion between monomers. Furthermore, the variation increases the pore radius at the selective filter. These findings were confirmed using simulations based on the recently determined structure of rabbit TRPV5. The simulation results provide an explanation for the observation of enhanced Ca2+ influx in TRPV5 caused by the A563T variation. The A563T variation is an interesting example of how a residue distant from the Ca2+-selective filter influences the Ca2+ transport function of the TRPV5 channel.Communicated by Ramaswamy H. Sarma

Investigating Human Visual Sensitivity to Binocular Motion-in-Depth for Anti- and De-Correlated Random-Dot Stimuli.

Motion-in-depth can be detected by using two different types of binocular cues: change of disparity (CD) and inter-ocular velocity differences (IOVD). To investigate the underlying detection mechanisms, stimuli can be constructed that isolate these cues or contain both (FULL cue). Two different methods to isolate the IOVD cue can be employed: anti-correlated (aIOVD) and de-correlated (dIOVD) motion signals. While both types of stimuli have been used in studies investigating the perception of motion-in-depth, for the first time, we explore whether both stimuli isolate the same mechanism and how they differ in their relative efficacy. Here, we set out to directly compare aIOVD and dIOVD sensitivity by measuring motion coherence thresholds. In accordance with previous results by Czuba et al. (2010), we found that motion coherence thresholds were similar for aIOVD and FULL cue stimuli for most participants. Thresholds for dIOVD stimuli, however, differed consistently from thresholds for the two other cues, suggesting that aIOVD and dIOVD stimuli could be driving different visual mechanisms.