Biology subjects

Cretu, A.

Publications and source records attributed to Cretu, A..

3 recordsLinked to original sources

bioRxiv2022

AlphaFold2 and RoseTTAFold Predict Posttranslational modifications. Chromophore Formation in GFP-like Proteins.

AlphaFold2 and RoseTTAfold are able to predict, based solely on their sequence whether GFP-like proteins will post-translationally form a chromophore or not. Their training has not only taught them protein structure and folding, but also chemistry. The structures of 21 sequences of GFP-like fluorescent proteins that will post-translationally form a chromophore and of 23 GFP-like non-fluorescent proteins that do not have the residues required to form a chromophore were determined by AlphaFold2 and RoseTTAfold. The resultant structures were mined for a series of geometric measurements that are crucial to chromophore formation. Statistical analysis of these measurements showed that both programs conclusively distinguished between chromophore forming and non-chromophore forming proteins. A clear distinction between sequences capable of forming a chromophore and those that do not have the residues required for chromophore formation can be obtained by examining a single measurement - the RMSD of the overlap of the central alpha helices of the crystal structure of S65T GFP and the AlphaFold2 determined structure.

biochemistry↗

bioRxiv2019

The effects of a TMS double lesion to a cortical network

Transcranial magnetic stimulation (TMS) has contributed to our understanding of the functions of individual brain regions, but its use to examine distributed functions throughout a network has been more limited. We assess the functional consequences of a TMS pulse to the oculomotor network which was first perturbed by continuous theta-burst stimulation (cTBS), to examine the potential for additive effects from lesions to two network nodes. Twenty-three humans performed pro-(look towards) and anti-(look away) saccades after receiving cTBS to right frontal eye fields (FEF), dorsolateral prefrontal cortex (DLPFC) or somatosensory cortex (S1) (control). On a subset of trials, a TMS pulse was applied to right posterior parietal cortex (PPC). We assessed changes in saccade amplitudes, performance (percentage correct) and reaction times, as these parameters relate to computations in networks involving these nodes. We observed impairments in ipsilateral anti-saccade amplitudes following DLPFC cTBS that were enhanced by a PPC pulse, but that were not enhanced relative to the effect of the PPC pulse alone. There was no evidence for effects from the double lesion to performance or reaction times. This suggests that computations are distributed across the network, such that even a single lesion is consequential.

neuroscience↗

bioRxiv2018

Motor resonance in primary motor cortex reflects the integration of kinematic and contextual information in accordance to a Bayesian predictive coding framework

Contextual information accompanying others actions modulates \"motor resonance\", i.e. neural activity within motor areas that is elicited by movement observation. One possibility is that we weight and combine such information in a Bayesian manner according to their relative uncertainty. Therefore, contextual information becomes particularly useful when others actions are ambiguous. It is unclear, however, whether this uncertainty modulates the neural activity in primary motor cortex (M1) during movement observation. Here we applied single-pulse transcranial magnetic stimulation (TMS) while subjects watched different grasping actions. We operationalized motor resonance as grip specific modulation of corticomotor excitability measured in the index (FDI) versus the little finger abductor (ADM). We experimentally modulated either the availability of kinematic information (Exp. 1) or the reliability of contextual cues (Exp. 2). Our results indicate that even in the absence of movement kinematics, reliable contextual information is enough to trigger significant muscle-specific corticomotor excitability changes in M1 (p<.0001) which are strongest when both kinematics and contextual information are available (p<.005). These findings suggest that bottom-up mechanisms that activate motor representations as a function of the observed kinematics, and top-down mechanisms which activate motor representations associated with arbitrary cues converge in M1 in a statistically optimal manner.

neuroscience↗