生物大分子
The isoelectric point (IEP or pI) is the pH where the net charge on the molecular ensemble of peptides and proteins is zero. This physical-chemical property is dependent on protonable/deprotonable sidechains and their pKa values. Here an pI…
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and…
The CryoEM single particle imaging method has recently received broad attention in the field of structural biology for determining the structures of biological molecules. The structures can be resolved to near-atomic resolutions after…
Atomic radii and charges are two major parameters used in implicit solvent electrostatics and energy calculations. The optimization problem for charges and radii is under-determined, leading to uncertainty in the values of these parameters…
Background. Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly, thus aiding…
We propose to develop mean field theory in combination with Glauber algorithm, to model and interpret protein dynamics and structure formation in small to wide angle x-ray scattering (S/WAXS) experiments. We develop the methodology by…
Modern algorithms for de novo prediction of protein structures typically output multiple full-length models (decoys) rather than a single solution. Subsequent clustering of such decoys is used both to gauge the success of the modelling and…
Transcription factors are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional…
In this paper we work out a parameterization of the environment noise within the Haken-Strobl-Reinenker (HSR) model for the PE545 light-harvesting complex based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We…
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…
This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
It is acknowledged that co-evolutionary nucleotide-nucleotide interactions are essential for RNA structures and functions. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequence from its homologous sequence…
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises…
DNA shape readout is an important mechanism of target site recognition by transcription factors, in addition to the sequence readout. Several models of transcription factor-DNA binding which consider DNA shape have been developed in recent…
Pure and homogeneous biological macromolecules (i.e. proteins, nucleic acids, protein-protein or protein-nucleic acid complexes, and functional assemblies such as ribosomes and viruses) are the key for consistent and reliable biochemical…
We have introduced a Pareto sorting algorithm into Synopsis, a de novo design program that generates synthesizable molecules with desirable properties. We give a detailed description of the algorithm and illustrate its working in 2…
Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for…
The elucidation of entropic contribution to enzyme catalysis has been debated over decades. The recent experimentally measured activation enthalpy and entropy, for chorismate rearrangement reaction in PchB brings up a hotly debated issue…
Natural IgM autoantibodies have been proposed to convey protection from autoimmune pathogenesis. Herein, we investigated the IgM responses in 396 systemic lupus erythematosus (SLE) patients, divided into subgroups based on distinct…