Central among the tools and approaches used for ligand discovery and design are Molecular Dynamics (MD) simulations, which follow the dynamic changes in molecular structure in response to the environmental condition, interactions with other proteins,...
BtuCD–BtuF from Escherichia coli is a binding protein-dependent adenosine triphosphate (ATP)-binding cassette (ABC) transporter system that uses the energy of ATP hydrolysis to transmit vitamin B12 across cellular membranes. Experimental studies hav...
Folded proteins show a high degree of structural order and undergo (fairly constrained) collective motions related to their functions. On the other hand, intrinsically disordered proteins (IDPs), while lacking a well-defined three-dimensional structu...
The conformational landscape of 3-indoleacetamide, a key intermediate in plant hormone biosynthesis, has been comprehensively investigated using state-of-the-art laser-ablation chirped-pulse Fourier transform microwave (LA-CP-FTMW) and laser-ablation...
It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the pre...
The dynamical response of a tethered semiflexible polymer with self-attractive interactions and subjected to an external force field is numerically investigated by varying stiffness and self-interaction strength. The chain is confined in two spatial...
The high sensitivity of silicon microcantilever sensors has expanded their use in areas ranging from gas sensing to bio-medical applications. Photochromic molecules also represent promising candidates for a large variety of sensing applications. In t...
The deterministic sequence → structure → function relationship is not applicable to describe how proteins dynamically adapt to different cellular conditions. A stochastic model is required to capture functional promiscuity, redundant sequen...
Protein machines are clusters of protein assemblies that function in order to control the transfer of matter and energy in cells. For a specific protein machine, its working mechanisms are not only determined by the static crystal structures, but als...
The double-stranded B-form and A-form have long been considered the two most important native forms of DNA, each with its own distinct biological roles and hence the focus of many areas of study, from cellular functions to cancer diagnostics and drug...
Recent developments in studies concerning cell-sized vesicles, such as liposomes with a lipid bilayer and water-in-oil droplets covered by a lipid monolayer, aim to realize the real-world modeling of living cells. Compartmentalization with a membrane...
Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contri...
Nanoaperture optical tweezers (NOTs) were used to analyze conalbumin in various forms. By analyzing the power spectrum of the NOT-transmitted laser signal, differences between iron and iron-free conalbumin were observed; the corner frequency extrapol...
The formation of hemoglobin (Hb) and myoglobin (Mb) supramolecular complexes is examined. These key proteins for oxygen transport and storage undergo conformational transitions, some of which are induced by stress factors, particularly redox-active a...
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and...
Arginine kinase is a key phosphagen kinase in invertebrates that facilitates rapid ATP regeneration by reversibly transferring phosphate groups between phosphoarginine and ADP. Structural studies have shown that the enzyme adopts distinct conformatio...
Most neurodegenerative diseases have the characteristics of protein folding disorders, i.e., they cause lesions to appear in vulnerable regions of the nervous system, corresponding to protein aggregates that progressively spread through the neuronal...
A super-diffusive Vicsek model is introduced in this paper that incorporates Levy flights with exponent α. The inclusion of this feature leads to an increase in the fluctuations of the order parameter, ultimately resulting in the disorder phase...
We seek a simple but physically motivated model of strongly interacting matter applicable in atomic nuclei and the dense matter in the core of neutron stars. For densities below and somewhat above normal nuclear density, energy density functional (ED...
Protein sequence, structure, and function are inherently linked through evolution and population genetics. Our knowledge of protein structure comes from solved structures in the Protein Data Bank (PDB), our knowledge of sequence through sequences fou...
Dendrons consisting of two phosphonate functions and three oligo(ethylene glycol) (OEG) chains grafted on a central phenoxyethylcarbamoylphenoxy group were synthesized and investigated as Langmuir monolayers at the surface of water. The OEG chain in...
Silvopastoral systems (SPS), an integrated farming system in which tropical grasses are combined with trees and shrubs, have been implemented in the last years in the Amazon region in order to mitigate the impacts generated by the traditional cattle...
Structural elements inserted in proteins are essential to define folding/unfolding mechanisms and partner recognition events governing signaling processes in living organisms. Here, we present an original approach to model the folding mechanism of th...
The polypeptide Nisin is characterized by antibacterial properties, making it a compound with many applications, mainly in the food industry. As a result, a deeper understanding of its behaviour, especially after its dissolution in water, is of the u...
Cytochrome P450 3A7 (CYP3A7) is a fetal/neonatal liver enzyme that participates in estriol synthesis, clearance of all-trans retinoic acid, and xenobiotic metabolism. Compared to the closely related major drug-metabolizing enzyme in adult liver, CYP3...
The voltage-gated potassium channel Kv1.1, which is abundant in the CNS and peripheral nervous system, controls neuronal excitability and neuromuscular transmission and mediates a number of physiological functions in non-excitable cells. The developm...
Na+,K+-ATPase is the only known receptor of cardiotonic steroids (CTS) whose interaction with catalytic α-subunits leads to inhibition of this enzyme. As predicted, CTS affect numerous cellular functions related to the maintenance of the transmembran...
Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2)...
The relationship between chemical structure and spin state in a transition metal complex has an important bearing on mechanistic bioinorganic chemistry, catalysis by base metals, and the design of spin crossover materials. The latter provide an ideal...
Defects in wound closure can be related to the failure of keratinocytes to re-epithelize. Potential mechanisms driving this impairment comprise unbalanced cytokine signaling, including Transforming Growth Factor-β (TFG-β). Although the etio...
The structure-function and materials paradigms drive research on the understanding of structures and structural heterogeneity of molecules and solids from materials science to structural biology. Functional insights into complex architectures are oft...
The continuous down-scaling of complementary metal oxide semiconductor (CMOS) field effect transistors (FETs) had been suffering two fateful technical issues, one relative to the thinning of gate dielectric and the other to the aggressive shortening...
Lipopolysaccharide (LPS) endotoxin is a well-characterized microbe-associated molecular pattern (MAMP) that forms the outer membrane of both pathogenic and commensal Gram-negative bacteria. It plays a crucial role in triggering inflammatory disorders...
Optimal vision remains one of the most essential elements of the sensory system continuously threatened by many ocular pathologies. Various pharmacological agents possess the potential to effectively treat these ophthalmic conditions; however, the us...
Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structure...
The epithelial-to-mesenchymal transition (EMT) is a cell-biological program that occurs during the progression of several physiological processes and that can also take place during pathological situations such as carcinogenesis. The EMT program cons...
Ship collisions often result in huge losses of life, cargo and ships, as well as serious pollution of the water environment. Meanwhile, it is estimated that between 75% and 86% of maritime accidents are related to human factors. Thus, it is necessary...
The progress in polymer science and nanotechnology yields new colloidal and macromolecular objects and their combinations, which can be defined as complex polymer materials. The complexity may include a complicated composition and architecture of mac...
Cellular life is reliant upon rapid and efficient responses to internal and external conditions. The basic molecular events associated with these processes are the structural transitions of the proteins (structural protein allostery) involved. From t...