Search for: All records

Structural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein–DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein–DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein–DNA interactions).

 

The use of Millimeter-wave (mmWave) spectrum in cellular communications has recently attracted growing interest to support the expected massive increase in traffic demands. However, the high path-loss at mmWave frequencies poses severe challenges. In this paper, we analyze the potential coverage gains of using unmanned aerial vehicles (UAVs), as hovering relays, in integrated access and backhaul (IAB) mmWave cellular scenarios. Specifically, we utilize the WinProp software package, which employs ray tracing methodology, to study the propagation characteristics of outdoor mmWave channels at 30 and 60 GHz frequency bands in a Manhattan-like environment. In doing so, we propose the implementation of amplify-and-forward (AF) and decode-and-forward (DF) relaying mechanisms in the WinProp software. We show how the 3D deployment of UAVs can be defined based on the coverage ray tracing maps at access and backhaul links. Furthermore, we propose an adaptive UAV transmission power for the AF relaying. We demonstrate, with the aid of ray tracing simulations, the performance gains of the proposed relaying modes in terms of downlink coverage, and the received signal to interference and noise ratio (SINR). 

There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid‐state NMR restraints with physics‐based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi‐quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid‐state NMR data for the model protein GB1 labeled with Cu²⁺‐EDTA at six different sites. We are able to determine the structure to 0.9 Å accuracy within a single day of computation on a GPU cluster. We further show that in some cases, the data from only a single paramagnetic tag are sufficient for accurate folding.

 

There is a pressing need for new computational tools to integrate data from diverse experimental approaches in structural biology. We present a strategy that combines sparse paramagnetic solid‐state NMR restraints with physics‐based atomistic simulations. Our approach explicitly accounts for uncertainty in the interpretation of experimental data through the use of a semi‐quantitative mapping between the data and the restraint energy that is calibrated by extensive simulations. We apply our approach to solid‐state NMR data for the model protein GB1 labeled with Cu²⁺‐EDTA at six different sites. We are able to determine the structure to 0.9 Å accuracy within a single day of computation on a GPU cluster. We further show that in some cases, the data from only a single paramagnetic tag are sufficient for accurate folding.