Update and Supplementary Articles Proteins of SARS CoV-2, Which Causes COVID-19, and the Interacting Proteins.

Coronavirus disease 2019 (COVID-19), which is the pandemic caused by the virus, severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), first appearing in December 2019, continues to confound the world. In this update we provide insights into how some of the new mutant variant strains of SARS CoV-2 have evolved to be more infective. We also introduce our supplement of the special issue on the topic of the proteins of SARS CoV-2 in the Protein Journal, which follows this introduction.

Nitroxide Spin-Labelling and Its Role in Elucidating Cuproprotein Structure and Function.

Copper is one of the most abundant biological metals, and its chemical properties mean that organisms need sophisticated and multilayer mechanisms in place to maintain homoeostasis and avoid deleterious effects. Studying copper proteins requires multiple techniques, but electron paramagnetic resonance (EPR) plays a key role in understanding Cu(II) sites in proteins. When spin-labels such as aminoxyl radicals (commonly referred to as nitroxides) are introduced, then EPR becomes a powerful technique to monitor not only the coordination environment, but also to obtain structural information that is often not readily available from other techniques. This information can contribute to explaining how cuproproteins fold and misfold. The theory and practice of EPR can be daunting to the non-expert; therefore, in this mini review, we explore how nitroxide spin-labelling can be used to help the inorganic biochemist gain greater understanding of cuproprotein structure and function in vitro and how EPR imaging may help improve understanding of copper homoeostasis in vivo.

From spin-labeled proteins to in vivo EPR applications.

This is a historical overview of the advent of applications of spin labeling to biological systems and the subsequent developments from the perspective of a scientist who was working as a Ph.D. student when the technique was conceived and was fortunate enough to participate in its development. In addition, the historical development of in vivo applications of EPR on animals and other living systems is described from a personal perspective.

How to improve nature: study of the electrostatic properties of the surface of alpha-lactalbumin.

It was recently shown that alpha-lactalbumin interacts with histones and simple models of histone proteins such as positively charged polyamino acids, suggesting that some fundamental aspects of the protein surface electrostatics may come into play. In the present work, the energies of charge-charge interaction in apo- and Ca(2+)-loaded alpha-lactalbumin were calculated using a Tanford-Kirkwood algorithm with either solvent accessibility correction or using a finite difference Poisson-Boltzmann method. The analysis revealed two major regions of alpha-lactalbumin that possessed highly unfavorable electrostatic potentials: (a) the Ca(2+)-binding loop and its neighboring residues and (b) the N-terminal region of the protein. Several individual mutants were prepared to neutralize specific individual surface acidic amino acids at both the N-terminus and Ca(2+)-binding loop of bovine alpha-lactalbumin. These mutants were characterized by intrinsic fluorescence, differential scanning microcalorimetry and circular dichroism. The structural and thermodynamic data agree in every case with the theoretical predictions, confirming that the N-terminal region is very sensitive to changes in charge. For example, desMet D14N mutation destabilizes protein and decreases its calcium affinity. On the other hand, desMet E1M and desMet D37N substitutions increase the thermal stability and calcium affinity. The Met E1Q is characterized by a marked increase in protein stability, whereas desMet E7Q and desMet E11L display a slight increase in calcium affinity and thermal stability. Examination of the unfavorable energy contributed by Glu1 and the energetically favorable consequences of neutralizing this residue suggests that nature may have made an error with bovine alpha-lactalbumin from the viewpoint of stabilizing structure and conformation.

Conversion of human alpha-lactalbumin to an apo-like state in the complexes with basic poly-amino acids: toward understanding of the molecular mechanism of antitumor action of HAMLET.

It was recently shown that alpha-lactalbumin associated with oleic acid (HAMLET) interacts with core histones thereby triggering apoptosis of tumor cells (J. Biol. Chem. 2003, 278, 42131). In previous work, we revealed that monomeric alpha-lactalbumin in the absence of fatty acids can also interact with histones and, moreover, with basic poly-amino acids (poly-Lys and poly-Arg) that represent simple models of histone proteins (Biochemistry 2004, 43, 5575). Association of alpha-lactalbumin with histone or poly-Lys(Arg) essentially changes its properties. In the present work, the character of the changes in structural properties and conformational stability of alpha-lactalbumin in the complex with poly-Lys(Arg) has been studied in detail by steady-state fluorescence, circular dichroism, and differential scanning calorimetry. Complex formation strongly depends on ionic strength, confirming its electrostatic nature. Experiments with the poly-amino acids of various molecular masses demonstrated a direct proportionality between the number of alpha-lactalbumin molecules bound per poly-Lys(Arg) and the surface area of the poly-amino acid random coil. The binding of the poly-amino acids to Ca2+-saturated human alpha-lactalbumin decreases its thermal stability down to the level of its free apo-form and decreases Ca2+-affinity by 4 orders of magnitude. The conformational state of alpha-lactalbumin in a complex with poly-Lys(Arg), named alpha-LActalbumin Modified by Poly-Amino acid (LAMPA), differs from all other alpha-lactalbumin states characterized to date, representing an apo-like (molten globule-like) state with substantially decreased affinity for calcium ion. The requirement for efficient conversion of alpha-lactalbumin to the LAMPA state is a poly-Lys(Arg) chain consisting of several tens of amino acid residues.

Aspartame and aspartame derivatives effect human thrombin catalytic activity.

The study of small Asp-Phe analogs was undertaken since this dipeptide sequence is critical in fibrinogen recognition and catalysis. The inhibition of clotting activity by Asp-Phe-methyl ester (aspartame), formyl-Asp-Phe-methyl ester and acetyl-Asp-Phe was biphasic in all cases, indicating the presence of at least two binding sites. The N-terminally blocked derivatives are stronger inhibitors than aspartame. In contrast, tosyl-Gly-Pro-Arg-p'-nitroanilide hydrolysis was inhibited minimally by Asp-Phe-methyl, ester [Ki(app)=98 mM]. Acetyl-Asp-Phe inhibition of thrombin amidase activity was biphasic, tenfold stronger and appeared to be strongly cooperative. These results are discussed with respect to the inhibition of alpha-thrombin by ATP.

Detection of bioradicals by in vivo L-band electron spin resonance spectrometry.

The applications of in vivo electron paramagnetic resonance (EPR) or electron spin resonance (ESR) spectroscopy have been impressive over a relatively short period despite the many obstacles which had to be overcome, such as dielectric absorption and biodestruction. The loop-gap resonators and modified loop coil systems have emerged as the most suitable resonators for in vivo EPR experiments. This paper briefly discusses instrumental aspects as a prelude to several examples related to the in vivo monitoring and detection of bioradicals. Recent progress in detection of bioradicals induced by drugs or chemicals is discussed with regard to nitrosocompounds, nitric oxide and metals in vivo. A clinical EPR application is also discussed.