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We simulate the aggregation of large systems containing palindromic peptides from the Syrian hamster prion protein SHaPrP 113–120 (AGAAAAGA) and the mouse prion protein MoPrP 111–120 (VAGAAAAGAV) and eight sequence variations: GAAAAAAG, (AG)4, A8, GAAAGAAA, A10, V10, GAVAAAAVAG, and...
Despite the many protein structures solved successfully by nuclear magnetic resonance (NMR) spectroscopy, quality control of NMR structures is still by far not as well established and standardized as in crystallography. Therefore, there is still the need for new, independent, and unbiased...
Understanding protein function is one of the keys to understanding life at the molecular level. It is also important in the context of human disease because many conditions arise as a consequence of alterations of protein function. The recent availability of relatively inexpensive sequencing...
Hydrogen exchange (HX) is recognized today as one of the most powerful and versatile tools available to protein scientists, especially for studying protein conformational change. This short history traces the beginnings of the HX method and the basic problems that faced the founders. Protein HX...
A recent crystal structure of HIV‐1 protease (HIVp) was the first to experimentally observe a ligand targeting an open‐flap conformation. Researchers studying a symmetric pyrrolidine inhibitor found that two ligands cocrystallized with the protease, forcing an unusual configuration and unique...
The human immunodeficiency virus type 1 (HIV‐1) genome encodes 18 proteins and 2 peptides. Four of these proteins encode high‐affinity calmodulin‐binding sites for which direct interactions with calmodulin have already been described. In this study, the HIV‐1 proteome is queried using an...
The hypermodified nucleoside N6‐threonylcarbamoyladenosine resides at position 37 of tRNA molecules bearing U at position 36 and maintains translational fidelity in the three kingdoms of life. The N6‐threonylcarbamoyl moiety is composed of L‐threonine and bicarbonate, and its synthesis was...
We describe here definitions of “local helical axis” and “straightness” that are developed using a simple quaternion‐based analysis of protein structure without resort to least‐squares fitting. As part of this analysis, it is shown how quaternion differences can be visualized to...
Protecting osmolytes are widespread small organic molecules able to stabilize the folded state of most proteins against various denaturing stresses in vivo. The osmophobic model explains thermodynamically their action through a preferential exclusion of the osmolyte molecules from the protein...
Recognizing the limits of trying to achieve chemical accuracy for pKa calculations with a purely electrostatic model, we include empirical corrections into the Poisson–Boltzmann solver macroscopic electrostatics with atomic detail (Bashford, Biochemistry 1990;29:10219–10225), to improve the...
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