Chiroptical signatures of life and fundamental physics

This paper aims to inspire experimentalists to carry out proposed new chiroptical experiments springing from the theoretical study of the role of parity violation in the origin of biomolecular homochirality and to provide a brief update on the current status of calculations of the electroweak parity-violating energy difference (PVED) between enantiomers. If the PVED did select life's handedness, we would expect to find life on other planets consistently using the same hand as terrestrial biochemistry. Much more importantly, even finding the "wrong" hand (rather than a racemic mixture) on another planet could be the homochiral signature of life, and we discuss our proposal for chiroptical detection of life on extra-solar planets. The PVED may also have an exciting future as a "molecular footprint" of fundamental physics: comparison of calculated PVEDs with measured values could one day allow chemists to do "table-top particle physics" more cheaply with improved chiroptical techniques instead of ever larger particle accelerators. We discuss our proposed chiroptical method to measure the PVED by using molecular beams. To our knowledge, optical rotation has not yet been measured in molecular beams, but the rewards of doing so include a host of other "first ever" results in addition to measurement of the PVED. Chirality 24:764-769, 2012. ? 2012 Wiley Periodicals, Inc.     

LncRNA GABPB1‑IT1 inhibits the tumorigenesis of renal cancer via the miR-21/PTEN axis

Long noncoding RNA (lncRNA) (GABPB1‑IT1) has been reported to be downregulated in lung cancer, while its expression and function in other cancers are unknown. In this study, the expression levels of GABPB1‑IT1 in tissue samples from 62 ccRCC patients were measured by performing RT-qPCR. Potential base pairing formed between GABPB1‑IT1 and miR-21 was explored using the online program IntaRNA 2.0 and further confirmed by Dual-luciferase activity assay and RNA pulldown assay. The role of GABPB1‑IT1 and miR-21 in regulating the expression of PTEN was evaluated by RT-qPCR and Western blot. The role of GABPB1‑IT1, miR-21, and PTEN in regulating the proliferation of Caki-2 cells was explored by CCK-8 assay. It was observed that GABPB1‑IT1 was downregulated in ccRCC and predicted poor survival. GABPB1‑IT1 directly interacted with miR-21, while it did not regulate the expression of each other. Moreover, upregulation of PTEN, which is a target of miR-21, was observed in ccRCC cells with overexpression of GABPB1‑IT1. Overexpression of GABPB1‑IT1 and PTEN decreased the proliferation rates of ccRCC cells. In addition, overexpression of GABPB1‑IT1 reduced the enhancing effects of miR-21 on cell proliferation. Therefore, GABPB1‑IT1 may upregulate PTEN by sponging miR-21 in ccRCC to inhibit cancer cell proliferation. Our study characterized a novel GABPB1‑IT1/miR-21/PTEN axis in ccRCC.     

Enantioselective autocatalysis. IV. Implications for parity violation effects

Historically, parity violation at the contemporary biomolecular level (i.e., only L-amino acids in proteins and D-sugars in DNA and RNA) has been postulated to be the inevitable result of parity violations at the elementary particle level, involving either-decay electrons or parity violating energy differences (PVEDs)between enantiomers. These two chiral biases have in turn allegedly impressed a small but persistent chirality onto prebiotic chemistry which, after appropriate amplification, has culminated in our contemporary homochiral biopolymers. Experiments and controversies pertaining to the efficacy of these two chiral biases are reviewed briefly, with the conclusions that: a) there is no experimental evidence supporting the capability of-decay electrons or other spinpolarized chiral particles to generate chiral molecules, and b) only theoretical calculations, but no experimental evidence, support the allegation of a causal relation between PVEDs and biomolecular homochirality. We here attempt to examine the latter allegation experimentally. Spontaneous resolution under racemization conditions (SRURC) during the crystallization of the bromofluoro-1,4-benzodiazepinooxazole derivativeI is capable of affording products of high enantiomeric purity. This process, which involves very efficient stereoselective autocatalysis, has now been examined statistically. If PVED effects are operative, the SRURC of racemicI should provide, either exclusively or with a strong and consistent bias, only one enantiomer of crystallineI. However, crystallization experiments of racemicI showed no bias in its SRURC, leading to the conclusion that PVED effects are ineffective in dictating a preferred chirality in this system. Several earlier experiments in the literature leading to a similar conclusion as to the inefficacy of PVED effects in promoting a preferred chirality are noted.     

Enantioselective Autocatalysis. V. The Spontaneous Resolution of Tri-o-Thymotide

We have attempted to appraise experimentally the allegation that minute chemical and physical differences due to the parity violating energy difference (PVED) between enantiomers are, after suitable autocatalytic amplification, ultimately responsible for the homochirality of contemporary biomolecules. The autocatalytic amplification technique employed involved the spontaneous resolution under racemizing conditions (SRURC) of a conglomerate during crystallization, and the system studied was the known crystallization of P(+)- or M(–)-tri-o-thymotide (TOT) as its optically active inclusion compound (clathrate) with benzene. Our premise was that if a PVED effect were operative, there should be a strong and consistent bias favoring the crystallization of one enantiomer of the TOT-benzene clathrate. Repetitive preparations of the clathrate, however, yielded crystalline products showing random optical activity. These results thus afford no evidence whatsoever for stereoselective bias due to a PVED, and are in accord with earlier statistical studies demonstrating random SRURC in other conglomerate crystallizations, again indicating the inefficacy of PVEDs to promote a preferred chirality in such systems.     

Critical effects of polar fluorescent probes on the interaction of DHA with POPC supported lipid bilayers

The understanding of lipid bilayer structure and function has been advanced by the application of molecular fluorophores. However, the effects of these probe molecules on the physicochemical properties of membranes being studied are poorly understood. A quartz crystal microbalance with dissipation monitoring instrument was used in this work to investigate the impact of two commonly used fluorescent probes, 1‑palmitoyl‑2‑{12‑[(7‑nitro‑2‑1,3‑benzoxadiazol‑4‑yl)amino]dodecanoyl}‑sn‑glycero‑3‑phosphocholine (NBD-PC) and 1,2‑dipalmitoyl‑sn‑glycero‑3‑phosphoethanolamine‑n‑(lissamine rhodamine‑B‑sulfonyl) (Lis-Rhod PE), on the formation and physicochemical properties of a 1‑palmitoyl‑2‑oleoyl‑sn‑glycero‑3‑phosphocholine supported lipid bilayer (POPC-SLB). The interaction of the POPC-SLB and fluorophore-modified POPC-SLB with docosahexaenoic acid, DHA, was evaluated. The incorporation of DHA into the POPC-SLB was observed to significantly decrease in the presence of the Lis-Rhod PE probe compared with the POPC-SLB. In addition, it was observed that the small concentration of DHA incorporated into the POPC:NBD-PC SLB can produce rearrangement processes followed by the lost not only of DHA but also of POPC or NBD-PC molecules or both during the washing step. This work has significant implications for the interpretation of data employing fluorescent reporter molecules within SLBs.     

Molecular chirality and the fundamental symmetries of physics: influence of parity violation on rovibrational frequencies and thermodynamic properties.

We introduce the topic of fundamental symmetries of physics in relation to molecular chirality by a brief review of the development and current status of the theory of parity violation in chiral molecules. We then discuss in some detail CHBrClF (bromochlorofluoromethane) as a test case, to which the work of André Collet has contributed importantly. For this molecule and its isotopomers, we report here the first detailed theoretical calculations of the influence of parity violation on statistical thermodynamic properties. High-quality ab initio calculations (RPA, random phase approximation, and CASSCF, complete-active-space self-consistent-field) were performed to determine the small energy difference between R- and S-enantiomers of H and D isotopomers of bromochlorofluoromethane (CHBrClF, CDBrClF), and fluorooxirane ((1)H(3)C(2)OF) introduced by the parity-violating weak interaction. Together with vibrational and rotational frequency shifts caused by parity violation, these were used to determine the statistical thermodynamic quantities from the corresponding partition functions within the separable harmonic and in part also anharmonic adiabatic approximation. Temperature-dependent equilibrium constants for the stereomutation were calculated and are discussed in relation to biochemical homochirality.     

Electrostatic and hydrophobic interactions of lipid-associated α-synuclein: The role of a water-limited interfaces in amyloid fibrillation

Human α‑synuclein (αSyn) is an intrinsically disordered protein (IDP) whose biological and pathological functions in brain neuronal cells have not yet been fully elucidated. αSyn intrinsically participates in aiding neurotransmitter trafficking through αSyn the association with lipid membranes. However, lipid-associated states of αSyn also induce amyloid self-assembly that is linked to the pathogenesis of various synucleinopathies. These contradicting actions arise from the limited water content near lipid-water interfaces that controls αSyn electrostatic and hydrophobic interactions. Thus, understanding the molecular interactions between αSyn and lipid membranes in the presence of water molecules is critical in elucidating the pivotal role of lipid-associated αSyn in amyloid self-assembly. In this review, we describe how the membrane interface controls electrostatic and hydrophobic interactions of lipid-associated αSyn. Moreover, membrane amyloid self-assembly of αSyn will be further discussed with regards to the structural dynamics of lipid-associated αSyn and water molecules near the interface.     

Evaluation of Coupled Perturbed and Density Functional Methods of Computing the Parity-Violating Energy Difference between Enantiomers

We present new coupled-perturbed Hartree-Fock (CPHF) and density functional theory (DFT) computations of the parity-violating energy difference (PVED) between enantiomers for H₂O₂ and H₂S₂. Our DFT PVED computations are the first for H₂S₂ and the first with the new HCTH and OLYP functionals. Like other “second generation” PVED computations, our results are an order of magnitude larger than the original “first generation” uncoupled-perturbed Hartree-Fock computations of Mason and Tranter. We offer an explanation for the dramatically larger size in terms of cancellation of contributions of opposing signs, which also explains the basis set sensitivity of the PVED, and its conformational hypersensitivity (addressed in the following paper). This paper also serves as a review of the different types of “second generation” PVED computations: we set our work in context, comparing our results with those of four other groups, and noting the good agreement between results obtained by very different methods. DFT PVEDs tend to be somewhat inflated compared to the CPHF values, but this is not a problem when only sign and order of magnitude are required. Our results with the new OLYP functional are less inflated than those with other functionals, and OLYP is also more efficient computationally. We therefore conclude that DFT computation offers a promising approach for low-cost extension to larger biosystems, especially polymers. The following two papers extend to terrestrial and extra-terrestrial amino acids respectively, and later work will extend to polymers.     

Neutral currents in weak interactions and molecular asymmetry

Weak interactions are parity violating forces, i.e. they differentiate between mirror images. Therefore it is a very attractive hypothesis to invoke weak interactions in explaining the origin of molecular asymmetry. It is, however, not clear whether weak interactions may operate between electrons and/or between electrons and protons? For these types of interactions so called neutral currents are needed. Recent experiments with muon neutrinos at CERN gave some evidence for the existence of neutral currents. Thus we may suppose that parity violating forces are active in molecules. In the first part of this paper a very elementary theory of weak interactions is outlined with special reference to the discovery of neutral currents. In the second part we show how weak interactions may differentiate between mirror image molecules. The asymmetrically distributed static charges in chiral molecules represent a helical potential field. This potential field may exert an effect on the orbital electrons and therefore coupling of spins and momenta occurs. Thus the enantiomers are parity transformed images not only as geometrical bodies, but their orbital electrons are parity transformed too as "a helical electron gas". Weak interactions will differentiate between L and D forms because their orbital electrons have a nonzero spin polarization with respect to their velocity.     

Molecular homochirality and the parity-violating energy difference. A critique with new proposals

Previous proposals for the origin of molecular homochirality, based on the effect of the weak neutral current (WNC) on enantiomers, and the amplification of the resultant parity-violating energy difference (PVED), are possibly flawed. The additive amplification of PVED in crystals and polymers ("Yamagata hypothesis") cannot lead to detectable levels of optical activity, the original theory apparently overestimating PVED by a factor equal to Avogadro's number. An alternative theory based on the irreversible and spontaneous evolution of a dynamically fluctuating system is apparently impractical. However, the nonlinear amplification of PVED via autocatalytic polymerization may be possible as indicated by a simplified physico-chemical approach. This may also occur during crystallization and melting, and form the basis of the second order asymmetric transformation. (Thus, reported differences in the melting points of enantiomers in several cases may well be real). Also, the preponderance of racemic compounds over conglomerates may be based on the destabilization of the conglomerate by the action of the WNC on the crystalline lattice. The WNC may also be involved in the anomalous scattering of X-rays, which possibly arises from their circular polarization: the current theory would need to be revised accordingly.     

24S-hydroxycholesterol alters activity of large-conductance Ca2+-dependent K+ (slo1 BK) channel through intercalation into plasma membrane

Oxysterols, oxidization products of cholesterol, are regarded as bioactive lipids affecting various physiological functions. However, little is known of their effects on ion channels. Using inside-out patch clamp recording, we found that naturally occurring side-chain oxidized oxysterols, 20S‑hydroxycholesterol, 22R‑hydroxycholesterol, 24S‑hydroxycholestero, 25‑hydroxycholesterol, and 27‑hydroxycholesterol, induced current reduction of large-conductance Ca²⁺- and voltage-activated K⁺ (slo1 BK) channels heterologously expressed in HEK293T cells. In contrast with side-chain oxidized oxysterols, naturally occurring ring oxidized ones, 7α‑hydroxycholesterol and 7‑ketocholesterol were without effect. By using 24S‑hydroxycholesterol (24S‑HC), the major brain oxysterol, we explored the inhibition mechanism. 24S‑HC inhibited Slo1 BK channels with an IC₅₀ of ~2 μM, and decreased macroscopic current by ~60%. This marked current decrease was accompanied by a rightward shift in the conductance-voltage relationship and a slowed activation kinetics, with the deactivation kinetics unaltered. Furthermore, the membrane sterol scavenger γ‑cyclodextrin was found to rescue slo1 BK channels from the inhibition, implicating that 24S-HC may be intercalated into the plasma membrane to affect the channel. These findings unveil a novel physiological importance of oxysterols from a new angle that involves ion channel regulation.     

1H, 13C and 15N chemical shift assignments of Ninjurin1 Extracellular N-terminal Domain

Cell adhesion molecules play a crucial role in fundamental biological processes via regulating cell–cell interactions. Nerve injury induced protein1 (Ninjurin1) is a novel adhesion protein that has no significant homology with other known cell adhesion molecules. Here we present the assignment of an 81 aa construct for human Ninjurin1 Extracellular N-Terminal (ENT) domain, which comprises the critical adhesion domain.     

Beta-gamma decay and stereoselective molecular breaking

Summary Firm empirical evidence demonstrating that optical activity in biological molecules could result from the violation of parity in the weak interactions has yet to be produced. This effect, when mediated by beta particles or by their subsequent circularly polarized external bremsstrahlung, seems to exist, but it is too small for experimental verification. In this paper, I suggest another mechanism to transfer the dissymmetry from the nucleus to the molecule: a compound beta (or electron capture)-gamma disintegration process which, carrying also the information of parity violation, might be more efficient at the time of a selective breaking of one of the two enantiomers in a racemic mixture. A new type of experiment to test this idea is suggested.     

Superweak interactions and the biological time direction

A hypothesis is proposed in qualitative terms, according to which left helical electrons in chiral molecules, and right helical electrons in oppositely chiral molecules have different internal timings. The basis of this hypothesis stems from two facts: (1) It has been observed that the decay processes caused by superweak interactions go slower if left helical electrons are produced compared to decay processes in which right helical positrons are produced. (2) The excited states of D and L molecules are not only parity transformed but time reversed pairs as well. Re-evaluation of many data makes the hypothesis likely. The significance of this hypothesis in the origin and evolution of life is apparent since life and evolution as a whole have a special time direction.     

The Ehlers-Danlos syndrome: the extracellular matrix scaffold in question

Ehlers-Danlos syndrome (EDS) is a heterogeneous heritable connective tissue disorder characterized by hyper-extensible skin, hypermobile joints and fragile vessels. The molecular causes of this disorder are often, although not strictly, related to collagens and to the enzymes that process these proteins. The classical form of the syndrome, which will be principally discussed in this review, can be due to mutations on collagen V, a fibrillar collagen present in small amounts in affected tissues. However, collagen I and tenascin have also been demonstrated to be involved in the same type of EDS. Moreover gene disruption of several other matrix molecules (thrombospondin, SPARC, small leucine rich proteoglycans...) in mice, lead to phenotypes that mimic EDS and these molecules have thus emerged as new players. As collagen V remains the prime candidate, we discuss, based on fundamental and clinical observations, its physiological role. We also explore its potential interactions with other matrix molecules to determine tissue properties.     

Parity Violating Energetic Difference and Enantiomorphous Crystalsp-Caveats; Reinvestigation of Tyrosine Crystallization

The present article challenges reports claiming to have demonstrated the Parity Violating Energetic Difference (PVED) between enantiomorphous D- and L-crystals. Apart from PVED, the presence of minute quantities and differing profiles of impurities incorporated during their different history of preparation will affect the physical properties of D- and L-crystals. These impurities are anticipated to play a much greater role in affecting crystallization behavior than PVED. The effect of impurities on the growth and dissolution of enantiomorphous crystals is illustrated with some representative examples.Shinitzky et al. (2002) reported recently dramatic differences in the growth and dissolution properties of the D- and L-crystals of tyrosine. We have repeated these experiments using commercial samples from different sources and employing a validated enantioselective gas chromatographic technique. We attribute Shinitzky's findings either to the use of inappropriate analytical techniques for the determination of enantiomeric composition and/or to the presence of unidentified contaminants in the commercial tyrosine samples. Related caveats hold also for the recently published claims by Shinitzky (2006) and Scolnik et al. (2006) to have observed experimentally PVED between enantiomeric helices of poly-glutamic acid composed of 24 repeating units.We maintain the term enantiomorphous crystals despite the fact that D- and L crystals differ by PVED     

Parity violation and the origins of biomolecular handedness

The violation of parity by the weak interactions ensures that enantiomeric chiral molecules have inequivalent energies, one being inherently stabilized with respect to the other. These parity-violating energy differences have been calculated for a number of fundamental biomolecules including a series of alpha-amino acids, polypeptide structures, and a representative of the sugar series together with its variation over a possible prebiotic reaction path leading to alpha-amino acids. In each case the natural enantiomer found in terrestrial biochemistry was shown to be intrinsically stabilized and preferred over its unnatural enantiomer. The significance of these results in accounting for the prebiotic origins of the terrestrial biomolecular homochirality is discussed and the possible consequences of parity-violating energy differences in mineral catalysts during the prebiotic era considered.     

Electro weak enantioselection and the origin of life

All biomolecules are of one hand — but what determines which hand? Why is life based on L-amino acids and D-sugars rather than D-amino acids and L-sugars? We believe the symmetry-breaker could be the weak force, which causes enantiomers to differ very slightly in energy. In this paper we present our calculations of this parity-violating energy difference (PVED) for a range of important biomolecules, and in nearly all cases it is indeed the ‘natural’ enantiomer which is the more stable.     

Structure of a protein–detergent complex: the balance between detergent cohesion and binding

Despite the major interest in membrane proteins at functional, genomic, and therapeutic levels, their biochemical and structural study remains challenging, as they require, among other things, solubilization in detergent micelles. The complexity of this task derives from the dependence of membrane protein structure on their anisotropic environment, influenced by a delicate balance between many different physicochemical properties. To study such properties in a small protein–detergent complex, we used fluorescence measurements and molecular dynamics (MD) simulations on the transmembrane part of glycophorin A (GpAtm) solubilized in micelles of dihexanoylphosphatidylcholine (DHPC) detergent. Fluorescence measurements show that DHPC has limited ability to solubilize the peptide, while MD provides a possible molecular explanation for this. We observe that the detergent molecules are balanced between two different types of interactions: cohesive interactions between detergent molecules that hold the micelle together, and adhesive interactions with the peptide. While the cohesive interactions are detergent mediated, the adhesion to the peptide depends on the specific interactions between the hydrophobic parts of the detergent and the topography of the peptide dictated by the amino acids. The balance between these two parameters results in a certain frustration of the system and rather slow equilibration. These observations suggest how molecular properties of detergents could influence membrane protein stabilization and solubilization.     

Interplay between rolling and firm adhesion elucidated with a cell-free system engineered with two distinct receptor-ligand pairs

The firm arrest of leukocytes to the endothelium during inflammation is known to be mediated by endothelial intercellular adhesion molecules (ICAMs) binding to activated integrins displayed on leukocyte surface. Selectin-ligand interactions, which mediate rolling, are believed to be important for facilitating firm adhesion, either by activating integrins or by facilitating the transition to firm adhesion by making it easier for integrins to bind. Although leukocytes employ two distinct adhesion molecules that mediate different states of adhesion, the fundamental biophysical mechanisms by which two pairs of adhesion molecules facilitate cell adhesion is not well understood. In this work, we attempt to understand the interaction between two molecular systems using a cell-free system in which polystyrene microspheres functionalized with the selectin ligand, sialyl Lewis(X) (sLe(X)), and an antibody against ICAM-1, aICAM-1, are perfused over P-selectin/ICAM-1 coated surfaces in a parallel plate flow chamber. Separately, sLe(X)/P-selectin interactions support rolling and aICAM-1/ICAM-1 interactions mediate firm adhesion. Our results show that sLe(X)/aICAM-1 microspheres will firmly adhere to P-selectin/ICAM-1 coated surfaces, and that the extent of firm adhesion of microspheres is dependent on wall shear stress within the flow chamber, sLe(X)/aICAM-1 microsphere site density, and P-selectin/ICAM-1 surface density ratio. We show that P-selectin's interaction with sLe(X) mechanistically facilitates firm adhesion mediated by antibody binding to ICAM-1: the extent of firm adhesion for the same concentration of aICAM-1/ICAM-1 interaction is greater when sLe(X)/P-selectin interactions are present. aICAM-1/ICAM-1 interactions also stabilize rolling by increasing pause times and decreasing average rolling velocities. Although aICAM-1 is a surrogate for beta(2)-integrin, the kinetics of association between aICAM-1 and ICAM-1 is within a factor of 1.5 of activated integrin binding ICAM-1, suggesting the findings from this model system may be insightful to the mechanism of leukocyte firm adhesion. In particular, these experimental results show how two molecule systems can interact to produce an effect not achievable by either system alone, a fundamental mechanism that may pervade leukocyte adhesion biology.