Biology subjects

Kraskov, A.

Publications and source records attributed to Kraskov, A..

9 recordsLinked to original sources

bioRxiv2026

Structural Basis for Near Infrared Absorption and Noncanonical Photoisomerization in Neorhodopsin

In retinal proteins, light absorption leads to a double bond isomerization of the chromophore, followed by conformational relaxations that drive functional protein rearrangements. The balance between photoisomerization and radiative or non-radiative decays of the excited state is adjusted to the demands of the respective photoreceptor function. The molecular determinants controlling the excited state processes remain poorly understood and are the focus of this combined crystallographic, spectroscopic, and theoretical work on the recently discovered neorhodopsin (NeoR). NeoR exhibits a highly red-shifted and fluorescent dark state and selectively photoisomerizes from all-trans to 7-cis. We show that the local electrostatic environment reduces the negative charge density near the Schiff base and suppresses torsional motion around the canonical C13=C14 isomerization site of microbial rhodopsins. Instead, the chromophore-binding pocket permits only low-efficiency C7=C8 isomerization, accompanied by polyene inversion, {beta}-ionone ring displacement, and Schiff base deprotonation. Consequently, unlike other retinal photoreceptors, NeoR undergoes structural changes localized near the {beta}-ionone ring.

biophysics↗

bioRxiv2026

Crystal structures of a far-red photoreceptor in different light-absorbing states: insights into spectral tuning and light signaling

Cyanobacteriochromes (CBCRs) are bilin-binding photoreceptors with remarkable spectral versatility. Using phycocyanobilin (PCB) as a chromophore, CBCRs regulate diverse light-dependent processes in cyanobacteria, ranging from photosynthesis to chromatic acclimation. Although extensive studies have uncovered multiple spectral tuning mechanisms in bilin-binding proteins, recent structural studies of far-red CBCRs suggest the existence of additional tuning strategies in both the 15Z and 15E states. Here we report crystal structures of the representative far-red CBCR Anacy_2551g3 in three distinct light-absorbing states, all of which adopt a compact all-syn PCB conformation. These structures demonstrate that 15Z/15E photoisomerization in Anacy_2551g3 involves minimal chromophore rotation relative to the GAF domain, in stark contrast to other characterized bilin-based photoreceptors. To investigate the molecular basis of its far-red absorption, we examined the protonation and tautomeric states of PCB in the Pfr state using resonance Raman (RR) spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Comparisons of experimental and calculated RR spectra support a bilin lactam as the predominant tautomeric form in the Pfr state. Integrating structural, spectroscopic, computational and mutational analyses, we propose that specific protein-chromophore interactions play critical roles in modulating chromophore conjugation beyond bilin coplanarity. Structural analyses further suggest a signaling model in which light regulation by Anacy_2551g3 is mediated through reversible switching between a high-affinity Pfr state and a low-affinity Po state that does not involve large chromophore motions. Together, these results provide new insights into how protein-chromophore coupling governs spectral tuning and light signaling in bilin-based photoreceptors. Significance statementBilins are widespread biological pigments that mediate photoreception, light harvesting, and photosynthesis across diverse light environments. In a phenomenon known as spectral tuning, the optical properties of bilin-binding proteins are profoundly influenced by protein-chromophore interactions. Mechanistic understanding of spectral tuning and light signaling is important not only for advancing fundamental knowledge of light-sensitive proteins but also for developing new engineering strategies in synthetic biology and biotechnology. Recently discovered cyanobacteriochromes (CBCRs) exhibit remarkable spectral diversity and structural versatility, providing excellent model systems for dissecting the mechanisms of bilin-based photoreceptors. By integrating crystallography, spectroscopy and computational methods, this work examines three distinct light absorbing states of a representative far-red CBCR. Our findings reveal previously unrecognized mechanisms of spectral tuning and light signaling, highlighting the critical roles of protein-chromophore coupling and electrostatic interactions in regulating photoreceptor function.

biochemistry↗

bioRxiv2025

Electrophysiological Characteristics of Epidural Spinal Signals in Preclinical Models of Spinal Cord Stimulation

ObjectivesEpidural stimulation of the spinal cord evokes distinct electrophysiological responses that can be recorded epidurally. Here, we characterized evoked compound action potentials (ECAPs), doublets (secondary or tertiary ECAPs, likely of different physiological origin than primary ECAPs), evoked synaptic activity potentials (ESAPs), and electromyographic (EMG) signals in preclinical models. Our objective was to clarify the features and distinct physiological origins of these signals, in order to advance mechanistic studies and support clinical applications of spinal cord stimulation (SCS) therapy. Materials and MethodsAdult male Sprague-Dawley rats (300-440 g) were implanted with two epidural leads (caudal and rostral; each with eight electrodes) and received monopolar, biphasic stimulation (200 s pulse width) at 2 and 50 Hz, with current increased stepwise to motor threshold. Rhesus macaques (11.5 and 10.2 kg) were implanted with a single 12-electrode epidural lead and stimulated using either tripolar, triphasic pulses at 10 Hz (100 s) or tripolar, biphasic pulses at 3 Hz (80 s) up to 3xECAP threshold. Recordings were taken from non-stimulating electrodes. ResultsECAPs and EMG signals were recorded across multiple spinal segments in both rats (L1-T7) and macaques (L2-T11). Doublets presented as complex waveforms with multiple negative peaks, two in rats and three in macaques, likely representing distinct ECAPs at T11-T6 in a rat and L1-T11 in macaques. ESAPs, detectable in rats, showed anatomical specificity, over the L1/T13 vertebrae with peak responses at L1. Signal analysis included activation thresholds, amplitudes, latencies, and conduction velocities. ConclusionsThis study outlines electrophysiological signals evoked by SCS in terms of their waveform, recruitment thresholds, and putative physiological origins. We propose that, to the extent these signals reflect different aspects of spinal processing and may serve as biomarkers of dysregulated nociceptive pathways, as well as indicators of SCS efficacy or potential side effects.

neuroscience↗

bioRxiv2023

Grasp Orientation in Ambiguous Settings is Sensitive to Prior Object Motion

The hand grasp of an object is normally consistent, determined by the optimal, most efficient strategy learnt from previous experience. Yet in certain settings, despite object properties remaining constant and intention the same, the grasp chosen by an individual can vary with a lack of clear preference for a particular grasp configuration. This is referred to as motor ambiguity. Here, we compare the influence of preceding static versus dynamic visual information on participants choice between two possible hand configurations when grasping an object at various orientations. We confirm previous findings that presentation of an object in an initial static orientation prior to the grasping in ambiguous orientation causes subjects to select a grasp that would be most congruent with the initial, determinate orientation. However, we unexpectedly found that when object rotation is observed between the initial and target positions, the bias is inversed, i.e. subjects choose the alternate grasp configurations. Furthermore, the inverse bias strength was found to be independent of the motion magnitude, and persists even when greater decision time is allowed. We provide evidence that this bias effect is not a perceptual phenomenon, and suggest it is potentially a behavioural manifestation of inhibitory circuits that delay decisions in conditions of motor ambiguity.

neuroscience↗

bioRxiv2020

Top-down contextual requirement to suppress self-movement influences grasp-specific modulation of corticospinal excitability during action observation

Action observation modulates corticospinal excitability (CSE) measured via transcranial magnetic stimulation (TMS) in humans, which presumably exposes the effect of mirror neuron activation on corticospinal pathways. These responses can consist of both facilitation and suppression, and the balance of these two may restrict the outflow of activity into movement. Evidence also suggests that task context can considerably influence CSE changes during action observation. Here, we assessed whether embedding action observation within a Go-NoGo paradigm, emphasizing movement withholding on observation and NoGo trials, influenced CSE modulation. Fourteen healthy subjects received single pulse TMS over left primary motor cortex (M1) during a baseline period, grasp observation onset, or after a NoGo cue, while performing, observing, or withholding two distinct reach-to-grasp actions. We assessed modulation of motor evoked potentials (MEPs) in three intrinsic hand muscles, which were recruited in a grasp-specific manner during action execution. CSE modulation was limited, and predominantly suppressive in nature during grasp observation. Seven subjects performed the same task without the NoGo condition ("Go-only" block) immediately before the "Go&NoGo" block. We found evidence for grasp-specific modulation of CSE, which matched the recruitment pattern of the muscles during action execution. Within these subjects, modulation was attenuated when the NoGo condition was introduced, but was still distinct from modulation in the first group. These results suggest that bottom-up grasp-specific modulation of MEPs during action observation is attenuated by the top-down contextual requirement to suppress self-movement, and facilitation and suppression effects are determined by the balance between these two processes. SIGNIFICANCE STATEMENTAction observation can activate specific pathways in the motor system of the observer, which are also used to perform the same action. This motor resonance, measured via changes in corticospinal excitability using transcranial magnetic stimulation, is susceptible to task context. In this study, we show that observing grasping actions results in grasp-specific changes in excitability, consistent with mirror neuron activation, but this effect is masked when observation is interleaved within a Go-NoGo paradigm, which emphasises suppression of ones own movement. Top-down task requirements to withhold movement within and across trials, which are present in most action observation studies, likely influence the extent of motor resonance, urging caution in the design and interpretation of results in TMS action observation experiments.

neuroscience↗

bioRxiv2019

Movement initiation and grasp representation in premotor and primary motor cortex mirror neurons

Pyramidal tract neurons (PTNs) within macaque rostral ventral premotor cortex (F5) and primary motor cortex (M1) provide direct input to spinal circuitry and are critical for skilled movement control, but surprisingly, can also be active during passive action observation. We recorded from single neurons, including identified PTNs in the hand and arm area of primary motor cortex (M1) (n=189), and in premotor area F5 (n=115) of two adult male macaques, while they executed, observed, or simply withheld (NoGo) reach-to-grasp and hold actions. We found that F5 maintains a more sustained, similar representation of grasping actions during both execution and observation. In contrast, although some M1 neurons mirrored during the grasp and hold, M1 population activity during observation contained signatures of a withholding state. This suggests that M1 and its output may dissociates signals required for the initiation of movement from those associated with the representation of grasp in order to flexibly guide behaviour. Significance StatementVentral premotor cortex (area F5) maintains a similar representation of grasping actions during both execution and observation. Primary motor cortex and its outputs dissociate between movement and non-movement states.

bioinformatics↗

bioRxiv2019

Slowly-conducting pyramidal tract neurons in macaque and rat

Anatomical studies report a large proportion of fine myelinated fibres in the primate pyramidal tract (PT), while very few pyramidal tract neurons (PTNs) with slow conduction velocities (CV) (< [~]10 m/s) are reported electrophysiologically. This discrepancy might reflect recording bias towards fast PTNs or prevention of antidromic invasion by recurrent inhibition of slow PTNs from faster axons. We investigated these factors in recordings made with a polyprobe (32 closely-spaced contacts) from motor cortex of anaesthetised rats (n=2) and macaques (n=3), concentrating our search on PTNs with long antidromic latencies. We identified 21 rat PTNs with antidromic latencies > 2.6 ms and estimated CV 3-8 m/s, and 67 macaque PTNs (> 3.9ms, CV 6-12 m/s). Spikes of most slow PTNs were small and present on only some recording contacts, while spikes from simultaneously recorded fast-conducting PTNs were large and appeared on all contacts. Antidromic thresholds were similar for fast and slow PTNS, while spike duration was considerably longer in slow PTNs. Most slow PTNs showed no signs of failure to respond antidromically. A number of tests, including intracortical microinjection of bicuculline (GABAA antagonist), failed to provide any evidence that recurrent inhibition prevented antidromic invasion of slow PTNs. Our results suggest that recording bias is the main reason why previous studies were dominated by fast PTNs.

physiology↗

bioRxiv2019

Time-dependent modulation of spinal excitability during action observation in the macaque monkey

Neurons in the primate motor cortex, including identified pyramidal tract neurons projecting to the spinal cord, respond to the observation of others actions, yet this does not cause movement in the observer. Here, we investigated changes in spinal excitability during action observation by monitoring short latency electromyographic responses produced by single shocks delivered directly to the pyramidal tract. Responses in hand and digit muscles were recorded from two adult rhesus macaques while they performed, observed or withheld reach-to-grasp and hold actions. We found modest grasp-specific facilitation of hand muscle responses during hand shaping for grasp, which persisted when the grasp was predictable but obscured from the monkeys vision. We also found evidence of a more general inhibition before observed movement onset, and the size of this inhibition effect was comparable to the inhibition after an explicit NoGo signal. These results confirm that the spinal circuitry controlling hand muscles is modulated during action observation, and this may be driven by internal representations of actions. The relatively modest changes in spinal excitability during observation suggest net corticospinal outflow exerts only minor, sub-threshold changes on hand motoneuron pools, thereby preventing any overflow of mirror activity into overt movement.

animal behavior and cognition↗

bioRxiv2018

On the interpretation of tractography-based parcellations

Connectivity-based parcellation of subcortical structures using diffusion tractography is now a common paradigm in neuroscience. These analyses often imply voxel-level specificity of connectivity, and the formation of compact, spatially coherent clusters is often taken as strong imaging-based evidence for anatomically distinct subnuclei in an individual. In this study, we demonstrate that internal structure in diffusion anisotropy is not necessary for a plausible parcellation to be obtained, by spatially permuting diffusion parameters within the thalami and repeating the parcellation. Moreover, we show that, in a winner-takes-all paradigm, most voxels receive the same label before and after this shuffling process--a finding that is stable across image acquisitions and tractography algorithms. We therefore suggest that such parcellations should be interpreted with caution.

neuroscience↗