相关论文: Universality of fold-encoded localized vibrations …
Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We show that the efficient excitation energy transfer in the Fenna-Matthews-Olson molecular aggregate under realistic physiological conditions is fueled by underdamped vibrations of the embedding proteins. For this, we present numerically…
There is a crescent use of enzymes in multiple industries and sciences, ranging from materials and fuel synthesis to pharmaceutical and food production. Their applicability in this variety of fields depends not only on their biochemical…
Despite the rapid pace of computationally and experimentally discovering new two-dimensional layered materials, a general criteria for a given compound to prefer a layered structure over a non-layered one remains unclear. Articulating such…
Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we…
Two recent experimental (Li, J.~\emphj{et al}, \emph{Proc.\ Natl.\ Acad.\ Sci.\ U.~S.~A.} {\bf 2014}, 111, 1282-1287) and theoretical studies (B\^aldea, I, \emph{Phys.\ Chem.\ Chem.\ Phys.}\ {\bf 2014}, 16, 25942-25949) have addressed the…
Protein motions occur on multiple time and distance scales. Large-scale motions of protein tertiary-structure elements, i.e. domains, are particularly intriguing as they are essential for the catalytic activity of many enzymes and for the…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Calculations of highly excited and delocalized molecular vibrational states are computationally challenging tasks, which strongly depends on the choice of coordinates for describing vibrational motions. We introduce a new method that…
Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in…
Local changes in pH are known to significantly alter the state and activity of proteins and in particular enzymes. pH variations induced by pulses propagating along soft interfaces (e.g. the lipid bilayer) would therefore constitute an…
Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…
Free energy landscapes decisively determine the progress of enzymatically catalyzed reactions[1]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [2-4] because both can be…
Unique catalytic potential of metal surfaces has encouraged a great number of basic and applied studies. The manuscript highlights the general regularities in a field on the grounds of strong interrelation between catalytic, kinetic and…
We present a unified framework for folding kinetics of proteins and RNA. The basis for this framework relies on the notion of topological frustration, which gives rise to several competing basins of attraction (CBA) in addition to the…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
The biological activity and functional specificity of proteins depend on their native three-dimensional structures determined by inter- and intra-molecular interactions. In this paper, we investigate the geometrical factor of protein…
It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that…