Biology subjects

Crain, J.

Publications and source records attributed to Crain, J..

11 recordsLinked to original sources

bioRxiv2025

Functional specialization of the hippocampus along its dorso-ventral axis: from span to supraspan in working memory capacity

Working memory (WM) is characterized by a limited capacity or span, beyond which performance deteriorates, the supraspan condition. Human neuropsychology and neuroimaging studies have implicated the medial temporal lobe (MTL), including the hippocampus (HPC), in WM particularly when memory load exceeds span, yet no animal model has been established to investigate supraspan mechanisms. Here, we present a novel rodent model of supraspan memory and examine the distinct roles of dorsal and ventral HPC. Using selective NMDA lesions in mice combined with object recognition tasks and a modified radial arm maze (RAM), we manipulated memory load and strategy constraints to assess span and supraspan performance. Dorsal HPC lesions impaired object memory span, while ventral lesions spared this ability. In the RAM, span performance (number of correct arm visits before the first error) was unaffected by either lesion under allocentric conditions. However, once animals exceeded span, following the first error, here defined as the supraspan condition, both dorsal and ventral lesions caused catastrophic disorientation and error escalation. Under free-choice conditions, ventral HPC lesions selectively reduced the occurrence of trials with no errors in the first 5 choices, increased errors overall, and disrupted sequential egocentric strategies. Together, these results demonstrate that supraspan performance can be modeled in rodents, revealing a dorsal contribution to object memory under high load, a ventral contribution to egocentric spatial strategies, and a shared hippocampal role in supraspan memory performance. This paradigm provides a translational framework for investigating supraspan deficits observed in MTL patients and Alzheimers disease.

neuroscience↗

bioRxiv2023

Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl- Channel

Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 Cl- channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. Here, we implement the fully polarizable forcefield AMOEBA in MD simulations on different conformations of hBest1. This forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion-{pi} interactions. We show that key biophysical properties of the channel can only be simulated when electronic polarization is included in the molecular models and that Cl- permeation through the neck of the pore is achieved through hydrophobic solvation concomitant with partial ion dehydration. Furthermore, we demonstrate how such polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures and that neglecting polarization places Cl- at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems, especially channels and pores that selectively permeate anions. Statement of SignificanceIon channels are nanoscale protein pores that enable the selective passage of charged ions across cell membranes. Understanding the underlying mechanisms for selective anion permeation through such pores remains a challenge. To simulate their behavior efficiently in silico, fixed charge models are typically employed. However, this approach is insufficient for the study of anions. Here, we use simulations with explicit treatment of electrostatics to investigate the interactions of chloride ions in the human bestrophin 1 channel. We find that electronic polarization tunes the state of the channel and affects the interactions of chloride ions thereby revealing a mechanism for permeation. Furthermore, these simulations can be used to resolve experimental ambiguity in ion-like densities from cryo-EM structures.

biophysics↗

bioRxiv2023

Influence of Electronic Polarization on the Binding of Anions to a Chloride-Pumping Rhodopsin

The functional properties of some biological ion channels and membrane transport proteins are proposed to exploit anion-hydrophobic interactions. Here, we investigate a chloride-pumping rhodopsin (ClR) as an example of a membrane protein known to contain a defined anion binding site composed predominantly of hydrophobic residues. Using molecular dynamics simulations, we explore Cl- binding to this hydrophobic site and compare the dynamics arising when electronic polarization is neglected (CHARMM36 (c36) fixed-charge force field), included implicitly (via the prosECCo force field), or included explicitly (through the polarizable force field, AMOEBA). Free energy landscapes of Cl- moving out of the binding site and into bulk solution demonstrate that the inclusion of polarization results in stronger ion binding and a second metastable binding site in ClR. Simulations focused on this hydrophobic binding site also indicate longer binding durations and closer ion proximity when polarization is included. Furthermore, simulations reveal that Cl- within this binding site interacts with an adjacent loop to facilitate rebinding events that are not observed when polarization is neglected. These results demonstrate how the inclusion of polarization can influence the behavior of anions within protein binding sites and thereby reveal novel mechanisms. Statement of SignificanceMolecular simulations based on classical (Newtonian) mechanics represent the most common method of visualizing the behavior of water and ions within channels and nanopores. Although computationally efficient, many of the approximations required mean that these simulations often do not fully capture the complex and dynamic interactions involved. Here, we use the prosECCo force field that offers an improved electronic description whilst maintaining computational efficiency. We show that using this method to include the effects of polarization greatly influences the binding dynamics of anions to a protein binding site and yields results similar to more accurate but computationally demanding methods.

biophysics↗

bioRxiv2022

Structure adaptation in Omicron SARS-CoV-2/hACE2:Biophysical origins of evolutionary driving forces

Since its emergence, the Covid19 pandemic has been sustained by a series of transmission waves initiated by new variants of the SARS-CoV-2 virus. Some of these arise with higher transmissivity and/or increased disease severity. Here we use molecular dynamics simulations to examine the modulation of the fundamental interactions between the receptor binding domain (RBD) of the spike glycoprotein and the host cell receptor (human angiotensin-converting enzyme 2: hACE2) arising from Omicron variant mutations (BA.1 and BA.2) relative to the original wild type strain. We find significant structural differences in the complexes which overall bring the spike protein and its receptor into closer proximity. These are consistent with and attributed to the higher positive charge on the RBD conferred by BA.1 and BA.2 mutations relative to the wild type. However, further differences between sub-variants BA.1 and BA.2 (which have equivalent RBD charges) are also evident: Mutations affect interdomain interactions between the up-chain and its clockwise neighbor chain, resulting in enhanced flexibility for BA.2. Consequently, additional close contacts arise in BA.2 which include binding to hACE2 by a second spike protein monomer, in addition to the up-chain - a motif not found in BA.1. Finally, the mechanism by which the glycans stabilize the up state of the Spike protein differs for the wild type and the Omicrons. We also found the glycan on N90 of hACE2 turns from inhibiting, to facilitating the binding to Omicron spike protein. These structural and electrostatic differences offer further insight into the mechanisms by which viral mutations modulate host cell binding and provide a biophysical basis for evolutionary driving forces.

biophysics↗

bioRxiv2022

Multiple lineages of Monkeypox virus detected in the United States, 2021-2022

Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of Monkeypox virus (MPXV) among nine 2021 and 2022 U.S. monkeypox cases. A 2021 case was highly similar to the 2022 MPXV outbreak variant, suggesting a common ancestor. Analysis of mutations among these two lineages revealed an extreme preference for GA-to-AA mutations indicative of APOBEC3 cytosine deaminase activity that was shared among West African MPXV since 2017 but absent from Congo Basin lineages. Poxviruses are not thought to be subject to APOBEC3 editing; however, these findings suggest APOBEC3 activity has been recurrent and dominant in recent West African MPXV evolution.

genomics↗

bioRxiv2022

Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat

Barley yellow dwarf (BYD) is one of the major viral diseases of cereals. Phenotyping BYD in wheat is extremely challenging due to similarities to other biotic and abiotic stresses. Breeding for resistance is additionally challenging as the wheat primary germplasm pool lacks genetic resistance, with most of the few resistance genes named to date originating from a wild relative species. The objectives of this study were to, i) evaluate the use of high-throughput phenotyping (HTP) from unmanned aerial systems to improve BYD assessment and selection, ii) identify genomic regions associated with BYD resistance, and iii) evaluate genomic prediction models ability to predict BYD resistance. Up to 107 wheat lines were phenotyped during each of five field seasons under both insecticide treated and untreated plots. Across all seasons, BYD severity was lower with the insecticide treatment and plant height (PTHTM) and grain yield (GY) showed increased values relative to untreated entries. Only 9.2% of the lines were positive for the presence of the translocated segment carrying resistance gene Bdv2 on chromosome 7DL. Despite the low frequency, this region was identified through association mapping. Furthermore, we mapped a potentially novel genomic region for resistance on chromosome 5AS. Given the variable heritability of the trait (0.211 - 0.806), we obtained relatively good predictive ability for BYD severity ranging between 0.06 - 0.26. Including Bdv2 on the predictive model had a large effect for predicting BYD but almost no effect for PTHTM and GY. This study was the first attempt to characterize BYD using field-HTP and apply GS to predict the disease severity. These methods have the potential to improve BYD characterization and identifying new sources of resistance will be crucial for delivering BYD resistant germplasm.

genetics↗

bioRxiv2021

Influence of effective polarization on ion and water interactions within a biomimetic nanopore

Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are suggested to play a key role in the movement of ions across biological membranes. Previous molecular dynamics (MD) simulations have shown that the affinity of polarizable anions to aqueous/hydrophobic interfaces can be markedly influenced by including polarization effects through an electronic continuum correction (ECC). Here, we designed a model biomimetic nanopore to imitate the polar pore openings and hydrophobic gating regions found in pentameric ligand-gated ion channels. MD simulations were then performed using both a non-polarizable force field and the ECC method to investigate the behavior of water, Na+ and Cl- ions confined within the hydrophobic region of the nanopore. Number density distributions revealed preferential Cl- adsorption to the hydrophobic pore walls, with this interfacial layer largely devoid of Na+. Free energy profiles for Na+ and Cl- permeating the pore also display an energy barrier reduction associated with the localization of Cl- to this hydrophobic interface, and the hydration number profiles reflect a corresponding reduction in the first hydration shell of Cl-. Crucially, these ion effects were only observed through inclusion of effective polarization which therefore suggests that polarizability may be essential for an accurate description for the behavior of ions and water within hydrophobic nanoscale pores, especially those that conduct Cl-.

biophysics↗

bioRxiv2021

Small molecules enhance the potency of natural antimicrobial peptides

The skin-associated microbiome plays an important role in general well-being and in a variety of treatable conditions. In this regard, endogenous antimicrobial peptides have a role in controlling the microbial population. We demonstrate here that certain small molecular species can amplify the potency of naturally-occurring antimicrobial peptides. For example, Niacinamide is a vitamin B3 analogue naturally found in foods and widely used in topical skin care products, and here we have investigated its cooperativity with the human antimicrobial peptide LL37 on the bacterium Staphylococcus aureus. We have also studied two other structurally related B3 analogs. We observed a clear synergistic effect of niacinamide and, to some extent, methyl niacinamide, whereas isonicotinamide showed no significant cooperativity with LL37. Adaptively-biased molecular dynamics simulations revealed that the analogs partition into the head group region of an anionic bilayer used to mimic the bacterial membrane. The observed effects on the physical properties of the membrane are well correlated with experimental activity. In contrast, the analogs have little effect on zwitterionic bilayers which mimic a mammalian membrane. We conclude that these vitamin B3 analogues can potentiate the activity of host peptides by modulating the physical properties of the bacterial membrane, and to a lesser extent through direct interactions with the peptide. The level of cooperativity is strongly dependent on the detailed chemistry of the additive, suggesting an opportunity to fine-tune the behaviour of host peptides.

molecular biology↗

bioRxiv2020

Naa12 rescues embryonic lethality in Naa10-Deficient Mice in the amino-terminal acetylation pathway

Amino-terminal acetylation is catalyzed by a set of N-terminal acetyltransferases (NATs). The NatA complex (including X-linked Naa10 and Naa15) is the major acetyltransferase, with 40-50% of all mammalian proteins being potential substrates. However, the overall role of amino-terminal acetylation on a whole-organism level is poorly understood, particularly in mammals. Male mice lacking Naa10 show no globally apparent in vivo amino-terminal acetylation impairment and do not exhibit complete embryonic lethality. Rather Naa10 nulls display increased neonatal lethality, and the majority of surviving undersized mutants exhibit a combination of hydrocephaly, cardiac defects, homeotic anterior transformation, piebaldism and urogenital anomalies. Naa12 is a previously unannotated Naa10-like paralogue with NAT activity that genetically compensates for Naa10. Mice deficient for Naa12 have no apparent phenotype, whereas mice deficient for Naa10 and Naa12 display embryonic lethality. The discovery of Naa12 adds to the currently known machinery involved in amino-terminal acetylation in mice.

developmental biology↗

bioRxiv2020

Modified Bacterial Lipids Which Alter Membrane Surface Charge Reduce Binding of Antimicrobial Peptides

Antimicrobial peptides (AMPs) initiate killing of bacteria by binding to and destabilizing their membranes. The multiple peptide resistance factor (MprF) provides a defence mechanism for bacteria against a broad range of AMPs. MprF reduces the negative charge of both Gram-positive and Gram--negative bacterial membranes through enzymatic conversion of the anionic lipid phosphatidyl glycerol (PG) to either zwitterionic alanyl-phosphatidyl glycerol (Ala-PG) or cationic lysylphosphatidyl glycerol (Lys-PG). The resulting change in membrane charge is suggested to reduce AMP-membrane binding and hinder downstream AMP activity. Using molecular dynamics to investigate the effects of these modified lipids on AMP-binding to model membranes, we show that AMPs have substantially reduced affinity for model membranes containing Ala-PG or Lys-PG. A total of ~7000 simulations are used to define the relationship between bilayer composition and binding for 5 different membrane active peptides. The reduction of degree of interaction of a peptide with the membrane is shown to correlate with the change in membrane surface charge density. Free energy profile (potential of mean force) calculations reveal that these lipid modifications alter the energy barrier to peptide helix penetration of the bilayer. These results will enable us to guide design of novel peptides which address the issue of resistance via MprF-mediated membrane modification.

biophysics↗

bioRxiv2017

Not by systems alone: identifying functional outliers in rare disease pedigrees

In characterizing a disease, it is common to search for dysfunctional genes by assaying the transcriptome. The resulting differentially expressed genes are typically assessed for shared features, such as functional annotation or co-expression. While useful, the reliability of these systems methods is hard to evaluate. To better understand shared disease signals, we assess their replicability by first looking at gene-level recurrence and then pathway-level recurrence along with co-expression signals across six pedigrees of a rare homogeneous X-linked disorder, TAF1 syndrome. We find most differentially expressed genes are not recurrent between pedigrees, making functional enrichment largely distinct in each pedigree. However, we find two highly recurrent \"functional outliers\" (CACNA1I and IGFBP3), genes acting atypically with respect to co-expression and therefore absent from a systems-level assessment. We show this occurs in re-analysis of Huntingtons disease, Parkinsons disease and schizophrenia. Our results suggest a significant role for genes easily missed in systems approaches.

systems biology↗