Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2

Hemoglobins (Hbs) of crocodilians are reportedly characterized by unique mechanisms of allosteric regulatory control, but there are conflicting reports regarding the importance of different effectors, such as chloride ions, organic phosphates, and CO₂. Progress in understanding the unusual properties of crocodilian Hbs has also been hindered by a dearth of structural information. Here, we present the first comparative analysis of blood properties and Hb structure and function in a phylogenetically diverse set of crocodilian species. We examine mechanisms of allosteric regulation in the Hbs of 13 crocodilian species belonging to the families Crocodylidae and Alligatoridae. We also report new amino acid sequences for the α- and β-globins of these taxa, which, in combination with structural analyses, provide insights into molecular mechanisms of allosteric regulation. All crocodilian Hbs exhibited a remarkably strong sensitivity to CO₂, which would permit effective O₂ unloading to tissues in response to an increase in metabolism during intense activity and diving. Although the Hbs of all crocodilians exhibit similar intrinsic O₂-affinities, there is considerable variation in sensitivity to Cl^- ions and ATP, which appears to be at least partly attributable to variation in the extent of NH₂-terminal acetylation. Whereas chloride appears to be a potent allosteric effector of all crocodile Hbs, ATP has a strong, chloride-independent effect on Hb-O₂ affinity only in caimans. Modeling suggests that allosteric ATP binding has a somewhat different structural basis in crocodilian and mammalian Hbs.

Lack of conventional oxygen-linked proton and anion binding sites does not impair allosteric regulation of oxygen binding in dwarf caiman hemoglobin

In contrast to other vertebrate hemoglobins (Hbs) whose high intrinsic O2 affinities are reduced by red cell allosteric effectors (mainly protons, CO2, organic phosphates, and chloride ions), crocodilian Hbs exhibit low sensitivity to organic phosphates and high sensitivity to bicarbonate (HCO3(-)), which is believed to augment Hb-O2 unloading during diving and postprandial alkaline tides when blood HCO3(-) levels and metabolic rates increase. Examination of α- and β-globin amino acid sequences of dwarf caiman (Paleosuchus palpebrosus) revealed a unique combination of substitutions at key effector binding sites compared with other vertebrate and crocodilian Hbs: β82Lys→Gln, β143His→Val, and β146His→Tyr. These substitutions delete positive charges and, along with other distinctive changes in residue charge and polarity, may be expected to disrupt allosteric regulation of Hb-O2 affinity. Strikingly, however, P. palpebrosus Hb shows a strong Bohr effect, and marked deoxygenation-linked binding of organic phosphates (ATP and DPG) and CO2 as carbamate (contrasting with HCO3(-) binding in other crocodilians). Unlike other Hbs, it polymerizes to large complexes in the oxygenated state. The highly unusual properties of P. palpebrosus Hb align with a high content of His residues (potential sites for oxygenation-linked proton binding) and distinctive surface Cys residues that may form intermolecular disulfide bridges upon polymerization. On the basis of its singular properties, P. palpebrosus Hb provides a unique opportunity for studies on structure-function coupling and the evolution of compensatory mechanisms for maintaining tissue O2 delivery in Hbs that lack conventional effector-binding residues.

Time-symmetric quantum theory of smoothing

Smoothing is an estimation technique that takes into account both past and future observations and can be more accurate than filtering alone. In this Letter, a quantum theory of smoothing is constructed using a time-symmetric formalism, thereby generalizing prior work on classical and quantum filtering, retrodiction, and smoothing. The proposed theory solves the important problem of optimally estimating classical Markov processes coupled to a quantum system under continuous measurements, and is thus expected to find major applications in future quantum sensing systems, such as gravitational wave detectors and atomic magnetometers.

Statistical theory of nonadiabatic transitions

Based on results of the preceding paper, and assuming fast equilibration in phase space to the temperature of the surrounding media compared to the time scale of a reaction, we formulate a statistical theory of intramolecular nonadiabatic transitions. A classical mechanics description of phase space dynamics allows for an ab initio treatment of multidimensional reaction coordinates and easy combination with any standard molecular dynamics (MD) method. The presented approach has several features that distinguishes it from existing methodologies. First, the applicability limits of the approach are well defined. Second, the nonadiabatic transitions are treated dynamically, with full account of detailed balance, including zero-point energy, quantum coherence effects, arbitrarily long memory, and change of the free energy of the bath. Compared to popular trajectory surface hopping schemes, our MD-based algorithm is more efficient computationally, and does not use artificial ad hoc constructions like a "fewest switching" algorithm, and rescaling of velocities to conserve total energy. The enhanced capabilities of the new method are demonstrated considering a model of two coupled harmonic oscillators. We show that in the rate regime and at moderate friction the approach precisely reproduces the free-energy-gap law. It also predicts a general trend of the reaction dynamics in the low friction limit, and is valid beyond the rate regime.

Theory of solvent influence on reaction dynamics

A generalization of the recently published quantum-classical approximation [A. A. Neufeld, J. Chem. Phys., 119, 2488 (2003)] for the purposes of reaction dynamics in condensed phase is presented. The obtained kinetic equations treat a solvent influence in a nonphenomenological way, account for the change of the free energy of the surrounding media, allow for different solvent dynamics in each reaction channel, and constitute a powerful framework for an accurate modeling of solvent effects, including ultrafast processes. The key features of the approach are its differential form, which considerably facilitates practical applications, and well defined wide applicability limits. The developed methodology fully accounts for an arbitrary long memory of the canonical bath and covers solvent-induced processes from a subpicosecond time scale.