Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation.

This work introduces a new faster implementation of the hydrogen bond network (complex arrangement of hydrogen bonds between or within molecules) search algorithm in biomacromolecules and their environment. Existing implementation of such an algorithm in GROMACS [Abraham et al. .

DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories.

This work describes a fast implementation of a software algorithm associated with determination of protein secondary structure based on the Define Secondary Structure of Proteins (DSSP) algorithm. This implementation is fully compatible with the DSSP v.4 and DSSP v.

An IoT-Enabled E-Nose for Remote Detection and Monitoring of Airborne Pollution Hazards Using LoRa Network Protocol.

Detection and monitoring of airborne hazards using e-noses has been lifesaving and prevented accidents in real-world scenarios. E-noses generate unique signature patterns for various volatile organic compounds (VOCs) and, by leveraging artificial intelligence, detect the presence of various VOCs, gases, and smokes onsite. Widespread monitoring of airborne hazards across many remote locations is possible by creating a network of gas sensors using Internet connectivity, which consumes significant power.

A Smart Card-Based Two-Factor Mutual Authentication Scheme for Efficient Deployment of an IoT-Based Telecare Medical Information System.

The integration of the Internet of Things (IoT) and the telecare medical information system (TMIS) enables patients to receive timely and convenient healthcare services regardless of their location or time zone. Since the Internet serves as the key hub for connection and data sharing, its open nature presents security and privacy concerns and should be considered when integrating this technology into the current global healthcare system. Cybercriminals target the TMIS because it holds a lot of sensitive patient data, including medical records, personal information, and financial information.

NOMA-Based VLC Systems: A Comprehensive Review.

The enhanced proliferation of connected entities needs a deployment of innovative technologies for the next generation wireless networks. One of the critical concerns, however, is the spectrum scarcity, due to the unprecedented broadcast penetration rate nowadays. Based on this, visible light communication (VLC) has recently emerged as a viable solution to secure high-speed communications.

A Survey of Deep Learning Based NOMA: State of the Art, Key Aspects, Open Challenges and Future Trends.

Non-Orthogonal Multiple Access (NOMA) has become a promising evolution with the emergence of fifth-generation (5G) and Beyond-5G (B5G) rollouts. The potentials of NOMA are to increase the number of users, the system's capacity, massive connectivity, and enhance the spectrum and energy efficiency in future communication scenarios. However, the practical deployment of NOMA is hindered by the inflexibility caused by the offline design paradigm and non-unified signal processing approaches of different NOMA schemes.

Caught red handed: modeling and confirmation of the myeloperoxidase ceruloplasmin alpha-thrombin complex.

The work is devoted to the study of the structural characteristics of the myeloperoxidase-ceruloplasmin-thrombin complex using small-angle neutron scattering methods in combination with computer modeling, as well as surface plasmon resonance and solid-phase enzyme assay. We have previously shown that the functioning of active myeloperoxidase during inflammation, despite the presence in the blood of an excess of ceruloplasmin which inhibits its activity, is possible due to the partial proteolysis of ceruloplasmin by thrombin. In this study, the myeloperoxidase-ceruloplasmin-thrombin heterohexamer was obtained in vitro.

Zero-Padding and Spatial Augmentation-Based Gas Sensor Node Optimization Approach in Resource-Constrained 6G-IoT Paradigm.

Ultra-low-power is a key performance indicator in 6G-IoT ecosystems. Sensor nodes in this eco-system are also capable of running light-weight artificial intelligence (AI) models. In this work, we have achieved high performance in a gas sensor system using Convolutional Neural Network (CNN) with a smaller number of gas sensor elements.

Thermostability improvement of Aspergillus awamori glucoamylase via directed evolution of its gene located on episomal expression vector in Pichia pastoris cells.

Novel thermostable variants of glucoamylase (GA) from filamentous fungus Aspergillus awamori X100 were constructed using the directed evolution approach based on random mutagenesis by error-prone PCR of the catalytic domain region of glucoamylase gene located on a new episomal expression vector pPEHα in Pichia pastoris cells. Out of 3000 yeast transformants screened, six new thermostable GA variants with amino acid substitutions Val301Asp, Thr390Ala, Thr390Ala/Ser436Pro, Leu7Met/His391Tyr, Asn9His/Ile82Phe and Ser8Arg/Gln338Leu were identified and studied. To estimate the effect of each substitution in the double mutants, we have constructed the relevant single mutants of GA by site-directed mutagenesis and analyzed their thermal properties.

A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation.

Communicated by Ramaswamy H. Sarma.

The amyloidogenicity of the influenza virus PB1-derived peptide sheds light on its antiviral activity.

The influenza virus polymerase complex is a promising target for new antiviral drug development. It is known that, within the influenza virus polymerase complex, the PB1 subunit region from the 1st to the 25th amino acid residues has to be is in an alpha-helical conformation for proper interaction with the PA subunit. We have previously shown that PB1(6-13) peptide at low concentrations is able to interact with the PB1 subunit N-terminal region in a peptide model which shows aggregate formation and antiviral activity in cell cultures.

Triazavirine supramolecular complexes as modifiers of the peptide oligomeric structure.

In this study, we present molecular dynamics simulations of the antiviral drug triazavirine, that affects formation of amyloid-like fibrils of the model peptide (SI). According to our simulations, triazavirine is able to form linear supramolecular structures which can act as shields and prevent interactions between SI monomers. This model, as validated by simulations, provides an adequate explanation of triazavirine's mechanism of action as it pertains to SI peptide fibril formation.

Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering.

Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA.

Large-scale conformational flexibility determines the properties of AAA+ TIP49 ATPases.

The TIP49a and TIP49b proteins belong to the family of AAA+ ATPases and play essential roles in vital processes such as transcription, DNA repair, snoRNP biogenesis, and chromatin remodeling. We report the crystal structure of a TIP49b hexamer and the comparative analysis of large-scale conformational flexibility of TIP49a, TIP49b, and TIP49a/TIP49b complexes using molecular modeling and molecular dynamics simulations in a water environment. Our results establish key principles of domain mobility that affect protein conformation and biochemical properties, including a mechanistic basis for the downregulation of ATPase activity upon protein hexamerization.