Related papers: Amino Acids Stabilizing Effect on Protein and Coll…
We present and implement a distance-based clustering of amino acids within the framework of a statistically derived interaction matrix and show that the resulting groups faithfully reproduce, for well-designed sequences, thermodynamic…
Proposing beneficial amino acid substitutions, whether for mutational effect prediction or protein engineering, remains a central challenge in structural biology. Recent inverse folding models, trained to reconstruct sequences from…
We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. The…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
The three dimensional structure of a protein is an outcome of the interactions of its constituent amino acids in 3D space. Considering the amino acids as nodes and the interactions among them as edges we have constructed and analyzed…
Interactions between actin, an anionic polyelectrolyte, and lysozyme, a cationic globular protein, have been examined using a combination of synchrotron small-angle x-ray scattering and molecular dynamics simulations. Lysozyme initially…
This work unravels the atomic details of the interaction of solute atoms with nanoscale crystalline defects. The complexity of this phenomenon is elucidated through detailed atom probe tomographic investigations on epitaxially-strained,…
The understanding of protein structure, folding, and interaction with other proteins remains one of the grand challenges of modern biology. Tremendous progress has been made thanks to X-ray- or electron-based techniques that have provided…
Protein-stabilised emulsion gels can be studied in the theoretical framework of colloidal gels, because both protein assemblies and droplets may be considered as soft colloids. These particles differ in their nature, size and softness, and…
Charges and their contribution to protein-protein interactions are essential for the key structural and dynamic properties of monoclonal antibody (mAb) solutions. In fact, they influence the apparent molecular weight, the static structure…
We have studied the effect of amino acids on electron attachment properties of DNA nucleobases, taking cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the…
Inorganic nanoparticle cores are often coated with organic ligands to render them dispersible in apolar solvents. However, the effect of the ligand shell on the colloidal stability of the overall hybrid particle is not fully understood. In…
In this work it is shown that three pairs of the factors appear to be the key, i.e. main factors of a natural classification of protein (canonical) amino acids within the amino acid (genetic) code. First pair: the factors of the habit of an…
The low sliding friction of articular cartilage in the major joints , which is crucial for its homeostasis and for joint health, has been attributed to lipid bilayers forming lubricious boundary layers at its surface. The robustness of such…
Suspensions of hard colloidal particles frequently serve as model systems in studies on fundamental aspects of phase transitions. But often colloidal particles that are considered as ``hard'' are in fact weakly charged. If the colloids are…
We have used density functional theory to study the structural stability of surface alloys. Our systems consist of a single pseudomorphic layer of $M_xN_{1-x}$ on the Ru(0001) surface, where $M$ = Fe or Co, and $N$ = Pt, Au, Ag, Cd, or Pb.…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Phase separation is as familiar as watching vinegar separating from oil in vinegrette. The observation that phase separation of proteins and nucleic acids is widespread in living cells has opened an entire field of research into the…