An official website of the United States government
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 CO 2 . 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 CO 2 , which would permit effective O 2 unloading to tissues in response to an increase in metabolism during intense activity and diving. Although the Hbs of all crocodilians exhibit similar intrinsic O 2 -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 NH 2 -terminal acetylation. Whereas chloride appears to be a potent allosteric effector of all crocodile Hbs, ATP has a strong, chloride-independent effect on Hb-O 2 affinity only in caimans. Modeling suggests that allosteric ATP binding has a somewhat different structural basis in crocodilian and mammalian Hbs.
more »
« less
Parameter sensitivity analysis for CO-mediated sickle cell de-polymerization
This study investigates the impact of melting/binding rates (referred to hereafter as the parameters) over the polymers and monomers on the dynamics of carbon-monoxide-mediated sickle cell hemoglobin (HbS) de-polymerization. Two approaches, namely the traditional sensitivity analysis (TSA) and the multi-parameter sensitivity analysis (MPSA), have been developed and applied to the mathematical model system to quantify the sensitivities of polymers and monomers to the parameters. The Runge-Kutta method and the Monte-Carlo simulation are employed for the implementation of the sensitivity analyses. The TSA utilizes the traditional sensitivity functions (TSFs). The MPSA enumerates the overall effect of the model input parameters on the output by perturbing the model input parameters simultaneously within large ranges. All four concentrations (namely, de-oxy HbS monomers, CO-bound HbS monomers, de-oxy Hbs polymer and CO-bound HbS polymer) as model outputs, and all four binding/melting rates (namely, the CO binding and melting rates for polymers and monomers) as input parameters are considered in this study. The sensitivity results suggest that TSA and MPSA are essentially consistent.
more »
« less
- Award ID(s):
- 1719498
- PAR ID:
- 10638650
- Publisher / Repository:
- Institute of Mathematics and Informatics at the Bulgarian Academy of Sciences
- Date Published:
- Journal Name:
- BIOMATH
- Volume:
- 13
- Issue:
- 1
- ISSN:
- 1314-684X
- Page Range / eLocation ID:
- 2312036
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Schaeffer, Josie; Zhang, Fei (Ed.)Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form complexes (polymers). Rather than employing free-energy parameters for each polymer, we focus on the athermic setting where all interactions preserve enthalpy. This setting aligns with the strongly bonded (domain-based) regime in DNA nanotechnology when strands can bind in different ways, but always with maximum overall bonding - and is consistent with the saturated configurations in the Thermodynamic Binding Networks (TBNs) model. Within this context, we develop an iterative algorithm for assigning polymer concentrations to satisfy detailed-balance, where on-target (desired) polymers are in high concentrations and off-target (undesired) polymers are in low. Even if not directly executed, our algorithm provides effective insights into upper bounds on concentration of off-target polymers, connecting combinatorial arguments about discrete configurations such as those in the TBN model to real-valued concentrations. We conclude with an application of our method to decreasing leak in DNA logic and signal propagation. Our results offer a new framework for design and verification of equilibrium concentrations when configurations are distinguished by entropic forces.more » « less
-
The objective of this work was to computationally predict the melting temperature and melt properties of thermosetting monomers used in aerospace applications. In this study, we applied an existing voids method by Solca. to examine four cyanate ester monomers with a wide range of melting temperatures. Voids were introduced into some simulations by removal of molecules from lattice positions to lower the free-energy barrier to melting to directly simulate the transition from a stable crystal to amorphous solid and capture the melting temperature. We validated model predictions by comparing melting temperature against previously reported literature values. Additionally, the torsion and orientational order parameters were used to examine the monomers’ freedom of motion to investigate structure–property relationships. Ultimately, the voids method provided reasonable estimates of melting temperature while the torsion and order parameter analysis provided insight into sources of the differing melt properties between the thermosetting monomers. As a whole, the results shed light on how freedom of molecular motions in the monomer melt state may affect melting temperature and can be utilized to inspire the development of thermosetting monomers with optimal monomer melt properties for demanding applications.more » « less
-
Hydrogen bonds (HB)s are the most abundant motifs in biological systems. They play a key role in determining protein–ligand binding affinity and selectivity. We designed two pharmaceutically beneficial HB databases, database A including ca. 12,000 protein–ligand complexes with ca. 22,000 HBs and their geometries, and database B including ca. 400 protein–ligand complexes with ca. 2200 HBs, their geometries, and bond strengths determined via our local vibrational mode analysis. We identified seven major HB patterns, which can be utilized as a de novo QSAR model to predict the binding affinity for a specific protein–ligand complex. Glycine was reported as the most abundant amino acid residue in both donor and acceptor profiles, and N–H⋯O was the most frequent HB type found in database A. HBs were preferred to be in the linear range, and linear HBs were identified as the strongest. HBs with HB angles in the range of 100–110°, typically forming intramolecular five-membered ring structures, showed good hydrophobic properties and membrane permeability. Utilizing database B, we found a generalized Badger’s relationship for more than 2200 protein–ligand HBs. In addition, the strength and occurrence maps between each amino acid residue and ligand functional groups open an attractive possibility for a novel drug-design approach and for determining drug selectivity and affinity, and they can also serve as an important tool for the hit-to-lead process.more » « less
-
Stereocomplexation is a useful strategy for the enhancement of polymer properties by the co-crystallization of polymer strands with opposed chirality. Yet, with the exception of PLA, stereocomplexes of biodegradable polyesters are relatively underexplored and the relationship between polymer microstructure and stereocomplexation remains to be delineated, especially for copolymers comprising two different chiral monomers. In this work, we resolved the two enantiomers of a non-symmetric chiral anhydride (CPCA) and prepared a series of polyesters from different combinations of racemic and enantiopure epoxides and anhydrides, via metal-catalyzed ring-opening copolymerization (ROCOP). Intriguingly, we found that only specific chiral combinations between the epoxide and anhydride building blocks result in the formation of semicrystalline polymers, with a single stereocenter inversion inducing a change from amorphous to semicrystalline copolymers. Stereocomplexes of the latter were prepared by mixing an equimolar amount of the two enantiomeric copolymers, yielding materials with increased melting temperatures (ca. 20 °C higher) compared to their enantiopure constituents. Following polymer structure optimization, the stereocomplex of one specific copolymer combination exhibits a particularly high melting temperature (Tm = 238 °C).more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.55630/j.biomath.2023.12.036
