Sequence determinants of amyloid fibril formation
M López de la Paz, L Serrano - Proceedings of the National …, 2004 - National Acad Sciences
The establishment of rules that link sequence and amyloid feature is critical for our
understanding of misfolding diseases. To this end, we have performed a saturation …
understanding of misfolding diseases. To this end, we have performed a saturation …
Basic units of protein structure, folding, and function
IN Berezovsky, E Guarnera, Z Zheng - Progress in biophysics and …, 2017 - Elsevier
Study of the hierarchy of domain structure with alternative sets of domains and analysis of
discontinuous domains, consisting of remote segments of the polypeptide chain, raised a …
discontinuous domains, consisting of remote segments of the polypeptide chain, raised a …
[HTML][HTML] The origin of the genetic code and of the earliest oligopeptides
EN Trifonov - Research in microbiology, 2009 - Elsevier
Reconstruction of the earliest proteins in the ancient binary alphabet [glycine family G,
alanine family A] leads to repeats of G alternating with repeats of A. In addition, omnipresent …
alanine family A] leads to repeats of G alternating with repeats of A. In addition, omnipresent …
[HTML][HTML] Living in trinity of extremes: genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation
A Amangeldina, ZW Tan, IN Berezovsky - Current Research in Structural …, 2024 - Elsevier
Since nucleic acids and proteins of unicellular prokaryotes are directly exposed to extreme
environmental conditions, it is possible to explore the genomic-proteomic compositional …
environmental conditions, it is possible to explore the genomic-proteomic compositional …
Conservation and diversity in allosteric fingerprints of proteins for evolutionary-inspired engineering and design
Hand-in-hand work of physics and evolution delivered protein universe with diversity of
forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an …
forms, sizes, and functions. Pervasiveness and advantageous traits of allostery made it an …
[HTML][HTML] Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery
Background Extant life depends greatly on the binding of small molecules (such as ligands)
with macromolecules (such as proteins), and one ligand can bind multiple proteins …
with macromolecules (such as proteins), and one ligand can bind multiple proteins …
A simple semiempirical model for the effect of molecular confinement upon the rate of protein folding
M Hayer-Hartl, AP Minton - Biochemistry, 2006 - ACS Publications
A simple two-state model for the dependence of the rate of folding of a polypeptide confined
within a spherical cavity upon the size of the cavity relative to that of the polypeptide is …
within a spherical cavity upon the size of the cavity relative to that of the polypeptide is …
[HTML][HTML] Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic …
G Schneider, G Neuberger, M Wildpaner, S Tian… - BMC …, 2006 - Springer
Background Manually finding subtle yet statistically significant links to distantly related
homologues becomes practically impossible for very populated protein families due to the …
homologues becomes practically impossible for very populated protein families due to the …
[HTML][HTML] Back in time to the Gly-rich prototype of the phosphate binding elementary function
Z Zheng, A Goncearenco, IN Berezovsky - Current Research in Structural …, 2024 - Elsevier
Binding of nucleotides and their derivatives is one of the most ancient elementary functions
dating back to the Origin of Life. We review here the works considering one of the key …
dating back to the Origin of Life. We review here the works considering one of the key …
Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins
A Goncearenco, IN Berezovsky - Bioinformatics, 2011 - academic.oup.com
Motivation: Enzymes are complex catalytic machines, which perform sequences of
elementary chemical transformations resulting in biochemical function. The building blocks …
elementary chemical transformations resulting in biochemical function. The building blocks …