Related papers: 'Perfectly' curvilinear profiles for binding as de…
Data for voltage-activation of a potassium channel (Matulef et al. Proc Natl Acad Sci USA 110: 17886-17891. 2013) were, as conventionally done, fitted by the authors by a Boltzmann function, i.e. by a curvilinear profile. Reanalysis of the…
In a study of the role that voltage-dependent K+ channels may have in the mechanosensation of living cells (Schmidt et al. Proc Soc Natl Acad Sci USA 109: 10352-10357. 2012), the data were as conventionally done fitted by a Boltzmann…
A wide variety of biological as well as non-biological processes and phenomena involving ion channels, binding, pH, folding/unfolding and effects of chain length are well represented by multiphasic profiles, a series of straight lines…
The nucleotides guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) bind to target proteins to promote bacterial survival (Corrigan et al. 2016). Thus, the binding of the nucleotides to RsgA, a GTPase, inhibits the…
Reanalysis of data (Bruice and York 1961) for the pH dependences of the calculated apparent second-order rate constants (k2) for the reaction of tris-(hydroxymethyl)-aminomethane (TRIS) with phenyl esters reveals that the pH profiles are…
2D conjugated polyphthalocyanines can be obtained as two distinctly different types of material with specific molecular structures and different morphological properties. It was believed that the temperature is the key factor affecting the…
Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed…
The preceding paper (Nissen 2017) shows multiphasic profiles, straight lines separated by discontinuous transitions, for the ion activities of NaCl and KCl at 15, 25, 35 and 45oC based on very precise tabular data of Lee et al. (2002). In…
Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to…
When plotted in linear transformations of the Michaelis-Menten equation, ion uptake in plants has been shown to be multiphasic, i.e. to be represented by a series of straight lines separated by discontinuous transitions (Nissen 1971, 1974,…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…
Starting from a protein solution which is metastable with respect to the crystalline phase, the effect of adding semidilute non-adsorbing polymer is considered. It is found to increase the chemical potential of the protein by a few tenths…
The new generation of manufacturing technologies such as e.g. additive manufacturing and automated fiber placement has enabled the development of material systems with desired functional and mechanical properties via particular designs of…
Determining the structure of a protein has been a decades-long open question. A protein's three-dimensional structure often poses nontrivial computation costs, when classical simulation algorithms are utilized. Advances in the transformer…
Recently many important biopolymers have been found to possess intrinsic curvature. Tubulin protofilaments in animal cells, FtsZ filaments in bacteria and double stranded DNA are examples. We examine how intrinsic curvature influence the…
Protein structure determination has long been one of the primary challenges of structural biology, to which deep machine learning (ML)-based approaches have increasingly been applied. However, these ML models generally do not incorporate…
The \emph{ab initio} path integral Monte Carlo (PIMC) approach is one of the most successful methods in quantum many-body theory. A particular strength of this method is its straightforward access to imaginary-time correlation functions…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
The study of protein functions attributed to the conformation and fluctuation that are ruled by both the amino acid sequence and thermodynamics, requires thermodynamic quantities given by calorimetry using thermometric techniques. The…
Single-crystal X-ray diffraction was employed to study the structural-electronic phase transition of IrTe$_2$ at approximately 270 K. The low-temperature structure was found to be a triclinic (space group $P\bar{1}$) characterized by the…