Chiral proofreading during protein biosynthesis and its evolutionary implications.

Homochirality of biomacromolecules is a prerequisite for their proper functioning and hence essential for all life forms. This underscores the role of cellular chiral checkpoints in enforcing homochirality during protein biosynthesis. d-Aminoacyl-tRNA deacylase (DTD) is an enzyme that performs 'chirality-based proofreading' to remove d-amino acids mistakenly attached to tRNAs, thus recycling them for further rounds of translation. Paradoxically, owing to its l-chiral rejection mode of action, DTD can remove glycine as well, which is an achiral amino acid. However, this activity is modulated by discriminator base (N73) in tRNA, a unique element that protects the cognate Gly-tRNAGly . Here, we review our recent work showing various aspects of DTD and tRNAGly coevolution and its key role in maintaining proper translation surveillance in both bacteria and eukaryotes. Moreover, we also discuss two major optimization events on DTD and tRNA that resolved compatibility issues among the archaeal and the bacterial translation apparatuses. Importantly, such optimizations are necessary for the emergence of mitochondria and successful eukaryogenesis.

Rate of formation of caustics in heavy particles advected by turbulence.

The rate of collision and the relative velocities of the colliding particles in turbulent flows are a crucial part of several natural phenomena, e.g. rain formation in warm clouds and planetesimal formation in protoplanetary discs. The particles are often modelled as passive, but heavy and inertial. Within this model, large relative velocities emerge due to formation of singularities (caustics) of the gradient matrix of the velocities of the particles. Using extensive direct numerical simulations of heavy particles in both two (direct and inverse cascade) and three-dimensional turbulent flows, we calculate the rate of formation of caustics, [Formula: see text] as a function of the Stokes number ([Formula: see text]). The best approximation to our data is [Formula: see text], in the limit [Formula: see text] where [Formula: see text] is a non-universal constant. This article is part of the theme issue 'Scaling the turbulence edifice (part 2)'.

Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria.

Mitochondria emerged through an endosymbiotic event involving a proteobacterium and an archaeal host. However, the process of optimization of cellular processes required for the successful evolution and survival of mitochondria, which integrates components from two evolutionarily distinct ancestors as well as novel eukaryotic elements, is not well understood. We identify two key switches in the translational machinery­one in the discriminator recognition code of a chiral proofreader DTD [d-aminoacyl­transfer RNA (tRNA) deacylase] and the other in mitochondrial tRNAGly­that enable the compatibility between disparate elements essential for survival. Notably, the mito-tRNAGly discriminator element is the only one to switch from pyrimidine to purine during the bacteria-to-mitochondria transition. We capture this code transition in the Jakobida, an early diverging eukaryotic clade bearing the most bacterial-like mito-genome, wherein both discriminator elements are present. This study underscores the need to explore the fundamental integration strategies critical for mitochondrial and eukaryotic evolution.

Contemporary Pharmacotherapeutic Approach in Pulmonary Arterial Hypertension.

Since the 1973 World Symposium on Pulmonary Hypertension, advancements in the understanding of pathophysiology and pathobiology have led to a myriad of pharmacotherapies for the disease. This article journeys through the development of therapeutic approaches for pulmonary arterial hypertension.

Selective Stabilization of Aspartic Acid Protonation State within a Given Protein Conformation Occurs via Specific "Molecular Association".

Proteins involved in proton-/electron-transfer processes often possess "functional" aspartates/aspartic acids (Asp) with variable protonation states. The mechanism of Asp protonation-deprotonation within proteins is unclear. Two questions were asked-the possible types of determinants responsible for Asp protonation-deprotonation and the spatial arrangements of the determinants leading to selective stabilization. The questions were analyzed using nine different solvent models, which scanned the complete protein dielectric range, and four protein models, which illustrated the spatial arrangements around Asp, termed as "molecular association". The methods employed were quantum chemical calculations and constant pH simulations. The types of the determinants identified were charge-charge interaction, H bonding, dipole-π interaction, extended electronic conjugation, dielectric effect, and solvent accessibility. All solvent-exposed Asp [buried fraction (BF) less than 0.5] were aspartates, and buried Asp were either aspartic acids or aspartates, each having a different "molecular association". The exposed aspartates were stabilized via a H-bonding network with bulk water, buried aspartates via salt bridge or, minimum, two intramolecular H bonds, and buried aspartic acids via, minimum, one intramolecular H bond. An "acid-alcohol pair" (involving Ser/Thr/Tyr) was a common determinant to any "functional" buried aspartate/aspartic acid. Higher energy "molecular associations" observed within proteins compared to those within water, presumably, indicated easy molecular restructuring and alteration of the Asp protonation states during a protein-mediated proton/electron transfer.

Statistics of relative velocity for particles settling under gravity in a turbulent flow.

We study the joint probability distributions of separation R and radial component of the relative velocity V_{R} of particles settling under gravity in a turbulent flow. We also obtain the moments of these distributions and analyze their anisotropy using spherical harmonics. We find that the qualitative nature of the joint distributions remains the same as no-gravity case. Distributions of V_{R} for fixed values of R show a power-law dependence on V_{R} for a range of V_{R}; the exponent of the power law depends on the gravity. Effects of gravity are also manifested in the following ways: (a) Moments of the distributions are anisotropic; degree of anisotropy depends on particle's Stokes number, but does not depend on R for small values of R. (b) Mean velocity of collision between two particles is decreased for particles having equal Stokes numbers but increased for particles having different Stokes numbers. For the later, collision velocity is set by the difference in their settling velocities.

Evaluating suspected pulmonary hypertension: A structured approach.

Pulmonary arterial hypertension (PAH) is a common consideration when patients have unexplained signs of cardiopulmonary disease. Guidelines have been issued regarding diagnosis and management of this condition. Since multiple conditions can mimic components of PAH, the clinician should think about the patient's total clinical condition before diagnosing and categorizing it. Proper evaluation and etiologic definition are crucial to providing the appropriate therapy. This review offers a case-based guide to the evaluation of patients with suspected PAH.

Heavy inertial particles in turbulent flows gain energy slowly but lose it rapidly.

We present an extensive numerical study of the time irreversibility of the dynamics of heavy inertial particles in three-dimensional, statistically homogeneous, and isotropic turbulent flows. We show that the probability density function (PDF) of the increment, W(τ), of a particle's energy over a time scale τ is non-Gaussian, and skewed toward negative values. This implies that, on average, particles gain energy over a period of time that is longer than the duration over which they lose energy. We call this slow gain and fast loss. We find that the third moment of W(τ) scales as τ^{3} for small values of τ. We show that the PDF of power-input p is negatively skewed too; we use this skewness Ir as a measure of the time irreversibility and we demonstrate that it increases sharply with the Stokes number St for small St; this increase slows down at St≃1. Furthermore, we obtain the PDFs of t^{+} and t^{-}, the times over which p has, respectively, positive or negative signs, i.e., the particle gains or loses energy. We obtain from these PDFs a direct and natural quantification of the slow gain and fast loss of the energy of the particles, because these PDFs possess exponential tails from which we infer the characteristic loss and gain times t_{loss} and t_{gain}, respectively, and we obtain t_{loss}

Statistics of the relative velocity of particles in turbulent flows: Monodisperse particles.

We use direct numerical simulations to calculate the joint probability density function of the relative distance R and relative radial velocity component V_{R} for a pair of heavy inertial particles suspended in homogeneous and isotropic turbulent flows. At small scales the distribution is scale invariant, with a scaling exponent that is related to the particle-particle correlation dimension in phase space, D_{2}. It was argued [K. Gustavsson and B. Mehlig, Phys. Rev. E 84, 045304 (2011)PLEEE81539-375510.1103/PhysRevE.84.045304; J. Turbul. 15, 34 (2014)1468-524810.1080/14685248.2013.875188] that the scale invariant part of the distribution has two asymptotic regimes: (1) |V_{R}|≪R, where the distribution depends solely on R, and (2) |V_{R}|≫R, where the distribution is a function of |V_{R}| alone. The probability distributions in these two regimes are matched along a straight line: |V_{R}|=z^{*}R. Our simulations confirm that this is indeed correct. We further obtain D_{2} and z^{*} as a function of the Stokes number, St. The former depends nonmonotonically on St with a minimum at about St≈0.7 and the latter has only a weak dependence on St.

Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures.

We have demonstrated earlier that protein microenvironments were conserved around disulfide-bridged cystine motifs with similar functions, irrespective of diversity in protein sequences. Here, cysteine thiol modifications were characterized based on protein microenvironments, secondary structures and specific protein functions. Protein microenvironment around an amino acid was defined as the summation of hydrophobic contributions from the surrounding protein fragments and the solvent molecules present within its first contact shell. Cysteine functions (modifications) were grouped into enzymatic and non-enzymatic classes. Modifications studied were-disulfide formation, thio-ether formation, metal-binding, nitrosylation, acylation, selenylation, glutathionylation, sulfenylation, and ribosylation. 1079 enzymatic proteins were reported from high-resolution crystal structures. Protein microenvironments around cysteine thiol, derived from above crystal structures, were clustered into 3 groups-buried-hydrophobic, intermediate and exposed-hydrophilic clusters. Characterization of cysteine functions were statistically meaningful for 4 modifications (disulfide formation, thioether formation, sulfenylation, and iron/zinc binding) those have sufficient amount of data in the current dataset. Results showed that protein microenvironment, secondary structure and protein functions were conserved for enzymatic cysteine functions, in contrast to the same function from non-enzymatic cysteines. Disulfide forming enzymatic cysteines were tightly packed within intermediate protein microenvironment cluster, have alpha-helical conformation and mostly belonged to CxxC motif of electron transport proteins. Disulfide forming non-enzymatic cysteines did not belong to conserved motif and have variable secondary structures. Similarly, enzymatic thioether forming cysteines have conserved microenvironment compared to non-enzymatic cystienes. Based on the compatibility between protein microenvironment and cysteine modifications, more efficient drug molecules could be designed against cysteine-related diseases.

How long do particles spend in vortical regions in turbulent flows?

We obtain the probability distribution functions (PDFs) of the time that a Lagrangian tracer or a heavy inertial particle spends in vortical or strain-dominated regions of a turbulent flow, by carrying out direct numerical simulations of such particles advected by statistically steady, homogeneous, and isotropic turbulence in the forced, three-dimensional, incompressible Navier-Stokes equation. We use the two invariants, Q and R, of the velocity-gradient tensor to distinguish between vortical and strain-dominated regions of the flow and partition the Q-R plane into four different regions depending on the topology of the flow; out of these four regions two correspond to vorticity-dominated regions of the flow and two correspond to strain-dominated ones. We obtain Q and R along the trajectories of tracers and heavy inertial particles and find out the time t_{pers} for which they remain in one of the four regions of the Q-R plane. We find that the PDFs of t_{pers} display exponentially decaying tails for all four regions for tracers and heavy inertial particles. From these PDFs we extract characteristic time scales, which help us to quantify the time that such particles spend in vortical or strain-dominated regions of the flow.

Amino acid function relates to its embedded protein microenvironment: A study on disulfide-bridged cystine.

In our previous study, we have shown that the microenvironments around conserved amino acids are also conserved in protein families (Bandyopadhyay and Mehler, Proteins 2008; 72:646-659). In this study, we have hypothesized that amino acids perform similar functions when embedded in a certain type of protein microenvironment. We have tested this hypothesis on the microenvironments around disulfide-bridged cysteines from high-resolution protein crystal structures. Although such cystines mainly play structural role in proteins, in certain enzymes they participate in catalysis and redox reactions. We have performed and report a functional annotation of enzymatically active cystines to their respective microenvironments. Three protein microenvironment clusters were identified: (i) buried-hydrophobic, (ii) exposed-hydrophilic, and (iii) buried-hydrophilic. The buried-hydrophobic cluster encompasses a small group of 22 redox-active cystines, mostly in alpha-helical conformations in a -C-x-x-C- motif from the Oxido-reductase enzyme class. All these cystines have high strain energy and near identical microenvironments. Most of the active cystines in hydrolase enzyme class belong to buried hydrophilic microenvironment cluster. In total there are 34 half-cystines detected in buried hydrophilic cluster from hydrolases, as a part of enzyme active site. Even within the buried hydrophilic cluster, there is clear separation of active half-cystines between surface exposed part of the protein and protein interior. Half-cystines toward the surface exposed region are higher in number compared to those in protein interior. Apart from cystines at the active sites of the enzymes, many more half-cystines were detected in buried hydrophilic cluster those are part of the microenvironment of enzyme active sites. However, no active half-cystines were detected in extremely hydrophilic microenvironment cluster, that is, exposed hydrophilic cluster, indicating that total exposure of cystine toward the solvent is not favored for enzymatic reactions. Although half-cystines in exposed-hydrophilic clusters occasionally stabilize enzyme active sites, as a part of their microenvironments. Analysis performed in this work revealed that cystines as a part of active sites in specific enzyme families or folds share very similar protein microenvironment regions, despite of their dissimilarity in protein sequences and position specific sequence conservations. Proteins 2016; 84:1576-1589. © 2016 Wiley Periodicals, Inc.

Deviation-angle and trajectory statistics for inertial particles in turbulence.

Small particles in suspension in a turbulent fluid have trajectories that do not follow the pathlines of the flow exactly. We investigate the statistics of the angle of deviation ϕ between the particle and fluid velocities. We show that, when the effects of particle inertia are small, the probability distribution function (PDF) P_{ϕ} of this deviation angle shows a power-law region in which P_{ϕ}∼ϕ^{-4}. We also find that the PDFs of the trajectory curvature κ and modulus θ of the torsion ϑ have power-law tails that scale, respectively, as P_{κ}∼κ^{-5/2}, as κ→∞, and P_{θ}∼θ^{-3}, as θ→∞: These exponents are in agreement with those previously observed for fluid pathlines. We propose a way to measure the complexity of heavy-particle trajectories by the number N_{I}(t,St) of points (up until time t) at which the torsion changes sign. We present numerical evidence that n_{I}(St)≡lim_{t→∞}N_{I}(t,St)/t∼St^{-Δ} for large St, with Δ≃0.5.