Biology subjects

Gray, C. J.

Publications and source records attributed to Gray, C. J..

3 recordsLinked to original sources

bioRxiv2026

RheoScale 2.0: Revealing the Hidden Roles of Protein Positions via Substitution Patterns

A central challenge in molecular biology is understanding how amino acid substitutions modulate various features of protein function and stability. To illuminate the complexities of this relationship, high-throughput (HTP) assays are increasingly used to assess site-saturating mutagenesis libraries. A common downstream analysis is to average the set of twenty outcomes at each amino acid position for comparison with structural and evolutionary features. Average values clearly identify positions that tolerate most substitutions (neutral positions) and positions where most substitutions abolish activity (toggle positions). However, average values conceal the existence of rheostat positions, where different amino acid substitutions sample a wide range of outcomes. To quantitatively identify rheostat positions, we previously developed a histogram-based analysis that we here expand by: (i) incorporating new position classes observed in experimental studies of rheostat positions; (ii) formalizing a hierarchy of class assignments; (iii) refining error-based identification of neutral positions; and (iv) statistically assessing the robustness of class assignments to changes in experimental and computational parameters. RheoScale 2.0 is implemented in Excel and newly implemented in Python for facile integration with existing HTP pipelines; all parameters are customizable. Example analyses are shown for three HTP datasets of the SARS-CoV-2 papain-like protease. Results illustrate two aspects that influence interpretation of HTP data: First, position assignments (and substitution outcomes) depend highly on the measured feature. Second, many protein positions play multiple roles in the sequence-structure-function relationship. The recognition of varied position roles will advance understanding of pathogen evolution, protein engineering, and variant interpretation for personalized medicine. SummaryRheoScale 2.0 improves how high-throughput mutational data are interpreted by identifying protein positions where amino acid substitutions act like biological dimmer switches. By enabling more nuanced assignment of position behavior, beyond neutral or deleterious outcomes, this analysis framework advances studies of sequence-structure-function relationships and has broad relevance for understanding protein evolution, engineering proteins with desired properties, and interpreting variants linked to human disease. SOFTWARE AVAILABILITYhttps://github.com/liskinsk/RheoScale-calculator

biochemistry↗

bioRxiv2025

Human brown adipose tissue demonstrates substantial 18F-fluorocholine uptake at room temperature for phosphatidylcholine synthesis

ObjectiveBrown Adipose Tissue (BAT) is composed of mitochondrial-rich, multilocular adipocytes, which dissipate energy to produce heat. Quantification of BAT mass is most commonly performed by 18F-fluorodeoxyglucose positron emission tomography (PET), which requires antecedent cold exposure. We hypothesized that 18F-fluorocholine PET could detect human BAT due to its requirement for considerable phosphatidylcholine synthesis, secondary to brown adipocytes high mitochondrial density and multiple lipid droplets. Methods1) Six healthy men with detectable 18F-fluorodeoxyglucose uptake by BAT were recruited to a randomised crossover study investigating 18F-fluorocholine uptake by BAT during warm and cold exposure. 2) 18F-fluorocholine uptake by supraclavicular adipose tissue was quantified in 76 patients who had undergone 18F-fluorocholine PET/CT scanning. 3) Choline transporter expression was quantified in human BAT and white adipose tissue (WAT), and in brown and white adipocytes. 4) Lipidomics was performed on human brown adipocytes incubated with 15N-choline to determine phospholipid synthesis. Results1) 18F-Fluorocholine uptake by BAT was substantially greater than by WAT during both warm and cold exposure. 2) 18F-Fluorocholine uptake by supraclavicular adipose tissue was higher in the colder seasons, inversely associated with body mass index, and positively associated with tissue radiodensity. 3) Expression of the choline transporter SLC44A3 was higher in human supraclavicular BAT than WAT, while SLC44A2 was expressed more highly in human brown than white adipocytes. 4) 15N-choline tracing in human brown adipocytes identified incorporation into >30 phosphatidylcholine species. Conclusions18F-fluorocholine PET may be a novel method to quantify human BAT at room temperature. HighlightsO_LI18F-Fluorocholine (FCH) PET can detect human BAT without the need for cold exposure. C_LIO_LI18F-FCH uptake by supraclavicular AT is inversely associated with body mass index. C_LIO_LIThe choline transporter SLC44A3 is more highly expressed in BAT than WAT. C_LIO_LIHuman brown adipocytes utilise choline for phosphatidylcholine synthesis. C_LI O_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC="FIGDIR/small/671970v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@11e85forg.highwire.dtl.DTLVardef@1aec87forg.highwire.dtl.DTLVardef@1ed3bf3org.highwire.dtl.DTLVardef@1fadbd1_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG

physiology↗

bioRxiv2017

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

Molecular modelling is routinely employed to assign 3D structures to collision cross sections (CCSs) derived from ion mobility mass spectrometry experiments (IM-MS). The assignment of model structures to the experimental CCSs remains an ambiguous task, where one of several methods may be used to obtain a CCS from a given set of coordinates. The most reliable of the commonly used techniques, the Trajectory Method, starts with atomic coordinates which can be accompanied by partial atomic charges, obtained using ab initio methods. Here, we use lithiated - and {beta}-glucose ions as exemplar molecules to detect the effect conformational modification and changes to the partial charge distribution have on computed collision cross sections. Six popular charge schemes (Mulliken, APT, CHelpG, MK, HLY and NPA) were examined in combination with three functionals (Hartree-Fock, B3LYP and M05) and five basis sets (STO-3G, 3-21G, 6-31G, 6-31+G and 6-31G*) on twenty unique structures. Our findings indicate that molecular conformation makes a significant contribution to fluctuations of partial charges in Electrostatic Potential (ESP) and Mulliken charge scheme; Partial charges derived using Natural Population Analysis (NPA) and ESP methods are largely independent of functional and basis set selection; and both selection of the charge scheme and functional/basis set combination play a large role in the resultant CCS, often causing few percent fluctuations in the computed values.

biochemistry↗