Journal ArticleDOI
Small-world view of the amino acids that play a key role in protein folding.
TLDR
Geometrical considerations are used to provide a different perspective on the fact that a few selected amino acids act as nucleation centers for protein folding and show that they have the "small-world" feature of having a limited set of vertices with large connectivity.Abstract:
We use geometrical considerations to provide a different perspective on the fact that a few selected amino acids, the so-called "key residues," act as nucleation centers for protein folding. By constructing graphs corresponding to protein structures we show that they have the "small-world" feature of having a limited set of vertices with large connectivity. These vertices correspond to the key residues that play the role of "hubs" in the network of interactions that stabilize the structure of the transition state.read more
Citations
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The “New” Science of Networks
TL;DR: In recent years, the analysis and modeling of networks, and also networked dynamical systems, have been the subject of considerable interdisciplinary interest, yielding several hundred papers in physics, mathematics, computer science, biology, economics, and sociology journals as mentioned in this paper.
Journal ArticleDOI
Network analysis of protein structures identifies functional residues.
Gil Amitai,Arye Shemesh,Einat Sitbon,Maxim Shklar,Dvir Netanely,Ilya Venger,Shmuel Pietrokovski +6 more
TL;DR: This work transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges, and found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values.
Journal ArticleDOI
A Network Representation of Protein Structures: Implications for Protein Stability
TL;DR: The hubs identified are found to play a role in bringing together different secondary structural elements in the tertiary structure of the proteins, and could be crucial for the folding and stability of the unique three-dimensional structure of proteins.
Journal ArticleDOI
Small-World Communication of Residues and Significance for Protein Dynamics
TL;DR: In this article, the authors show that residues in folded proteins are distributed according to a "small-world" topology, and that the core residues have the same local packing arrangements irrespective of protein size.
Journal ArticleDOI
The protein folding network.
Francesco Rao,Amedeo Caflisch +1 more
TL;DR: The conformation space of a 20 residue antiparallel beta-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways.
References
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Book
Structure and Mechanism in Protein Science
TL;DR: The three-dimensional structure of proteins chemical catalysis the basic equations of enzyme kinetics measurement and magnitude of enzymatic rate constants the pH dependence of enzyme catalysis practical kinetics detection of intermediaries in reactions by kinetics stereochemistry of enzymes reactions active-site-directed and enzyme-activated irreversible inhibitors - affinity labels and suicide inhibitors conformational change, allosteric regulation, motors and work forces between molecules, and enzymesubstrate binding energies enzyme-substrate complementarity and the use of binding energy in catalysis specificity and editing mechanisms recombinant DNA technology case studies of enzyme
BookDOI
Structure and Mechanism in Protein Science : a guide to enzyme catalysis and protein folding
TL;DR: The three-dimensional structure of proteins chemical catalysis, kinetics measurement and magnitude of enzymatic rate constants, and the use of binding energy in catalysis specificity and editing mechanisms are studied.
Metabolic engineering of plant alkaloid biosynthesis. Proc Natl Acad Sci U S A
Ken-ichi Tamura,Yasuyuki Yamada,Takashi Hashimoto,Akira Hachiya,Kum-Boo Choi,Fumihiko Sato,Takashi Morishige,Hideki Fujimoto +7 more