相关论文: Hidden Thermodynamic Information in Protein Amino …
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
Protein function depends on both protein structure and amino acid (aa) sequence. Here we show that modular features of both structure and function can be quantified from the aa sequence alone for the amyloid 770 aa precursor protein A4.…
In this study, the thermal relaxation of the 20 naturally occurring amino-acids in water is investigated using transient non-equilibrium molecular-dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the…
Thermodynamic tools are well suited to connecting evolution of protein functionalities to mutations of amino acid sequences, especially for neuronal network structures. These tools enable one to quantify changes in modular structure and…
De novo prediction of protein folding is an open scientific challenge. Many folding models and force fields have been developed, yet all face difficulties converging to native conformations. Hydrophobicity scales (HSs) play a crucial role…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Forward modeling is often used to interpret substructures observed in protoplanetary disks. To ensure the robustness and consistency of the current forward modeling approach from the community, we conducted a systematic comparison of…
We perform molecular dynamics simulations of 512 water-like molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic…
Thermodynamic profiles, based on bioinformatic hydropathicity scales and membrane-fitted sliding windows, exhibit accurately level sets of hydrophobic peaks or valleys in the constant fragment Fc of monoclonal antibodies. These sets provide…
Protein conformational stability and function depend on non-covalent interactions that are strongly influenced by the surrounding environment. To explore protein properties, amino acids are often utilized as model systems. In this study, we…
Based on neutron wide-angle diffraction and small-angle neutron scattering experiments, we show that there is a correlation between the preparational conditions of amorphous ice structures, their microscopic structural properties, the…
Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code,…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
By balancing the average energy gap with its typical change due to mutations for protein-like heteropolymers with M residues, we show that native states are unstable to mutations on a scale M* ~ (lambda/sigma_mu)^(1/zeta_s), where lambda is…
The thermodynamic properties of a spin S=1/2 tetrameric Heisenberg antiferromagnetic chain with alternating interactions AF1-AF2-AF1-F (AF and F denote the antiferromagnetic and ferromagnetic couplings, respectively) are studied by means of…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
Thermodynamic properties of the one-dimensional Kondo lattice model at half-filling are studied by the density matrix renormalization group method applied to the quantum transfer matrix. Spin susceptibility, charge susceptibility, and…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
We study the combined influence of amino acid composition and chain length on the thermal stability of protein structures. A new parameterization of the internal free energy is considered, as the sum of hydrophobic effect, hydrogen-bond and…