Molecular basis for cis-urocanic acid as a 5-HT2A receptor agonist

The underlying mechanisms of urocanic acid (UA) to induce immune suppression remain elusive until the recent finding that cis-UA acts via the serotonin, 5-hydroxytryptamine (5-HT) receptor subtype 5-HT_2A. In the present study, the interactions of cis-UA to 5-HT_2A receptor were explored and compared with those of 5-HT to the same receptor using computational docking. Similar binding modes were observed for cis-UA and 5-HT with 5-HT_2A receptor and the former possessed relatively higher binding affinity, which may account for cis-UA being a serotonin receptor agonist. Moreover, the molecular basis for the distinct binding affinities between the trans- and cis-UA with 5-HT_2A receptor was also provided.     

Conformational changes in MetNI: steered molecular dynamic studies of the methionine ABC transporter with and without substrates

ATP-binding cassette (ABC) transporters are integral membrane proteins that utilised energy from ATP hydrolysis to translocate substrates across the membrane. In addition to the common nucleotide-binding domains (NBDs) and transmembrane domains (TMDs), the methionine ABC transporter has C-terminal regulatory domains (C2 domains) that belong to ACT protein family. When the amount of methionine in the cell is high, the transport stops. This phenomenon is called trans-inhibition. To understand how a trans-inhibited protein returns to an uninhibited, resting state, we performed steered molecular dynamic simulations with and without the substrates. From the simulations, we observed some important conformational changes in the whole ABC transporter, including the constriction in the translocation pathway in the TMDs and approach of the NBDs. However, the C2 domains behaved differently in two types of the simulations. These findings might help to explain the relationship of the conformational changes of the C2 domains with the rearrangements of the NBDs or TMDs, and provide a way to understand the trans-inhibition from an opposite direction.     

Molecular dynamic simulations analysis of ritonavir and lopinavir as SARS-CoV 3CL(pro) inhibitors

Since the emergence of the severe acute respiratory syndrome (SARS) to date, neither an effective antiviral drug nor a vaccine against SARS is available. However, it was found that a mixture of two HIV-1 proteinase inhibitors, lopinavir and ritonavir, exhibited some signs of effectiveness against the SARS virus. To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out for the SARS-CoV 3CL^pro free enzyme (free SARS) and its complexes with lopinavir (SARS-LPV) and ritonavir (SARS-RTV). The results show that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CL^pro. The binding affinities of LPV and RTV to SARS-CoV 3CL^pro do not show any significant difference. In addition, six hydrogen bonds were detected in the SARS-LPV system, while seven hydrogen bonds were found in SARS-RTV complex.     

Dose-response of Fricke- and PAGAT-dosimetry gels in kilovoltage and megavoltage photon beams: Impact of LET on sensitivity

Purpose: Dosimetry of ionizing radiation quantifies the energy deposited by an incident beam to the medium. This study presents the relative response of two types of gel dosimeters describing their differences by estimating radiation chemical yields produced in water radiolysis.Methods: Two types of gel dosimeter were used, namely an acid ferrous ion solution infused with xylenol orange known as Fricke gel and a polymer gel based on acrylamide and N,N’-methylenebis(acrylamide) known as PAGAT. Samples were irradiated using two photon beam energies, one from a conventional X-ray tube operated at 44 kV and the other one from a LINAC operated at 6 MV. The dosimeters were analyzed by optical absorbance and magnetic resonance imaging. Additionally, the linear energy transfer of each beam was calculated using Monte Carlo simulations for further estimation of the radiation chemical yields produced during water radiolysis.Results: Obtained results for both gel dosimeters indicate that their response at 44 kV and 6 MV are different, regardless of the read-out technique. On average, the sensitivity at 44 kV was found to be 65 % of the response at 6 MV. The calculated radiation chemical yields are in agreement with the observed experimental results.Conclusions: The main reason for the difference in the response of the dosimeters may be related to the linear energy transfer of each photon beam, which varies the production of primary chemical species during water radiolysis.     

Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: An alternative method for generating a high-resolution solution structure

Summary A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak intensities. As in the case of restrained molecular dynamics (rMD) refinement of structures, the experimental distance restraints and bounds are incorporated as a pseudo-energy term (or penalty function) into the mathematical expression for the molecular energy. However, the use of generalized helical parameters, rather than Cartesian coordinates, to define DNA conformation increases efficiency by decreasing by an order of magnitude the number of parameters needed to describe a conformation and by simplifying the potential energy profile. The Metropolis Monte Carlo method is employed to simulate an annealing process. The rMC method was applied to experimental 2D NOE data from the octamer duplex d(GTA-TAATG)·d(CATTATAC). Using starting structures from different locations in conformational space (e.g. A-DNA and B-DNA), the rMC calculations readily converged, with a root-mean-square deviation (RMSD) of <0.3 Å between structures generated using different protocols and starting structures. Theoretical 2D NOE peak intensities were calculated for the rMC-generated structures using the complete relaxation matrix program CORMA, enabling a comparison with experimental intensities via residual indices. Simulation of the vicinal proton coupling constants was carried out for the structures generated, enabling a comparison with the experimental deoxyribose ring coupling constants, which were not utilized in the structure determination in the case of the rMC simulations. Agreement with experimental 2D NOE and scalar coupling data was good in all cases. The rMC structures are quite similar to that refined by a traditional restrained MD approach (RMSD<0.5 Å) despite the different force fields used and despite the fact that MD refinement was conducted with additional restraints imposed on the endocyclic torsion angles of deoxyriboses. The computational time required for the rMC and rMD calculations is about the same. A comparison of structural parameters is made and some limitations of both methods are discussed with regard to the average nature of the experimental restraints used in the refinement.Abbreviations MC Monte Carlo - rMC restrained Monte Carlo - MD molecular dynamics - rMD restrained molecular dynamics - DG distance geometry - EM energy minimization - 2D NOE two-dimensional nuclear Overhauser effect - DQF-COSY double-quantum-filtered correlation spectroscopy - RMSD root-mean-square deviation To whom correspondence should be addressed.     

Implicit membrane treatment of buried charged groups: Application to peptide translocation across lipid bilayers

The energetic cost of burying charged groups in the hydrophobic core of lipid bilayers has been controversial, with simulations giving higher estimates than certain experiments. Implicit membrane approaches are usually deemed too simplistic for this problem. Here we challenge this view. The free energy of transfer of amino acid side chains from water to the membrane center predicted by IMM1 is reasonably close to all-atom free energy calculations. The shape of the free energy profile, however, for the charged side chains needs to be modified to reflect the all-atom simulation findings (IMM1-LF). Membrane thinning is treated by combining simulations at different membrane widths with an estimate of membrane deformation free energy from elasticity theory. This approach is first tested on the voltage sensor and the isolated S4 helix of potassium channels. The voltage sensor is stably inserted in a transmembrane orientation for both the original and the modified model. The transmembrane orientation of the isolated S4 helix is unstable in the original model, but a stable local minimum in IMM1-LF, slightly higher in energy than the interfacial orientation. Peptide translocation is addressed by mapping the effective energy of the peptide as a function of vertical position and tilt angle, which allows identification of minimum energy pathways and transition states. The barriers computed for the S4 helix and other experimentally studied peptides are low enough for an observable rate. Thus, computational results and experimental studies on the membrane burial of peptide charged groups appear to be consistent. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova.     

Identifying mismatches between conservation area networks and vulnerable populations using spatial randomization

Grassland birds are among the most globally threatened bird groups due to substantial degradation of native grassland habitats. However, the current network of grassland conservation areas may not be adequate for halting population declines and biodiversity loss. Here, we evaluate a network of grassland conservation areas within Wisconsin, U.S.A., that includes both large Focal Landscapes and smaller targeted conservation areas (e.g., Grassland Bird Conservation Areas, GBCAs) established within them. To date, this conservation network has lacked baseline information to assess whether the current placement of these conservation areas aligns with population hot spots of grassland‐dependent taxa. To do so, we fitted data from thousands of avian point‐count surveys collected by citizen scientists as part of Wisconsin''s Breeding Bird Atlas II with multinomial N‐mixture models to estimate habitat–abundance relationships, develop spatially explicit predictions of abundance, and establish ecological baselines within priority conservation areas for a suite of obligate grassland songbirds. Next, we developed spatial randomization tests to evaluate the placement of this conservation network relative to randomly placed conservation networks. Overall, less than 20% of species statewide populations were found within the current grassland conservation network. Spatial tests demonstrated a high representation of this bird assemblage within the entire conservation network, but with a bias toward birds associated with moderately tallgrasses relative to those associated with shortgrasses or tallgrasses. We also found that GBCAs had higher representation at Focal Landscape rather than statewide scales. Here, we demonstrated how combining citizen science data with hierarchical modeling is a powerful tool for estimating ecological baselines and conducting large‐scale evaluations of an existing conservation network for multiple grassland birds. Our flexible spatial randomization approach offers the potential to be applied to other protected area networks and serves as a complementary tool for conservation planning efforts globally.     

Probing subtle conformational changes induced by phosphorylation and point mutations in the TIR domains of TLR2 and TLR3

Extensive research performed on Toll‐like receptor (TLR) signaling has identified residues in the Toll/interleukin‐1 receptor (TIR) domains that are essential for its proper functioning. Among these residues, those in BB loop are particularly significant as single amino acid mutations in this region can cause drastic changes in downstream signaling. However, while the effect of these mutations on the function is well studied (like the P681H mutation in TLR2, the A795P mutation in TLR3, and the P714H mutation in TLR4), their influence on the dynamics and inter‐residue networks is not well understood. The effects of local perturbations induced by these mutations could propagate throughout the TIR domain, influencing interactions with other TIR domain‐containing proteins. The identification of these subtle changes in inter‐residue interactions can provide new insights and structural rationale for how single‐point mutations cause drastic changes in TIR–TIR interactions. We employed molecular dynamics simulations and protein structure network (PSN) analyses to investigate the structural transitions with special emphasis on TLR2 and TLR3. Our results reveal that phosphorylation of the Tyr 759 residue in the TIR domain of TLR3 introduces rigidity to its BB loop. Subtle differences in the intra BB loop hydrogen bonding network between TLR3 and TLR2 are also observed. The PSN analyses indicate that the TIR domain is highly connected and pinpoints key differences in the inter‐residue interactions between the wild‐type and mutant TIR domains, suggesting that TIR domain structure is prone to allosteric effects, consistent with the current view of the influence of allostery on TLR signaling.