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Protein and DNA Sequence Determinants of Thermophilic Adaptation
An exhaustive study of the relationship between amino acid composition of proteomes, nucleotide composition of DNA, and optimal growth temperature (OGT) of prokaryotes finds strong and independent correlation between OGT and the frequency with which pairs of A and G nucleotides appear as nearest neighbors in genome sequences.
Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
An analysis of molecular evolution of five of the most populated protein folds: immunoglobulin fold, oligonucleotide-binding fold, Rossman fold, alpha/beta plait, and TIM barrels is provided, based on a new concept of "conservatism-of-conservatism".
A biophysical protein folding model accounts for most mutational fitness effects in viruses
Contrary to neutral network theory, it is found that, in mutation/selection/drift steady state, high mutation rates lead to less stable proteins and a more dispersed DFE (i.e., less mutational robustness).
How does a protein fold?
A lattice Monte Carlo model in which the global minimum (native state) is known guarantees thermodynamic stability of the native state at a temperature where the chain does not get trapped in local minima and suggest principles for the folding of real proteins.
Common activation mechanism of class A GPCRs
By analyzing the conformational changes in 234 structures from 45 class A GPCRs, this work discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues, which unifies previous findings into a common activation mechanism and strings together the scattered key motifs.
The folding mechanics of a knotted protein.
Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.
It is shown that successful folding does not require certain attributes that have been previously proposed as necessary for folding; these include a high number of short versus long-range contacts in the native state, a high content of the secondary structure in the original structure, a strong correlation between the native contact map and the interaction parameters, and the existence of aHigh number of low energy states with near-native conformation.
Engineering of stable and fast-folding sequences of model proteins.
It is shown that this can be obtained by proper selection of protein sequences and a simple practical way to find these sequences is suggested.
Protein stability imposes limits on organism complexity and speed of molecular evolution
- K. Zeldovich, Peiqiu Chen, E. Shakhnovich
- BiologyProceedings of the National Academy of Sciences
- 28 May 2007
Classical population genetics a priori assigns fitness to alleles without considering molecular or functional properties of proteins that these alleles encode. Here we study population dynamics in a…
How to derive a protein folding potential? A new approach to an old problem.
It is argued that more detail of protein structure and energetics should be taken into account to achieve energy gaps and the suggested method is general enough to allow us to systematically derive parameters for more sophisticated energy functions.