Modeling and simulation of protein–surface interactions: achievements and challenges

M Ozboyaci, DB Kokh, S Corni… - Quarterly reviews of …, 2016 - cambridge.org
Understanding protein–inorganic surface interactions is central to the rational design of new
tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant …

Molecular simulation of adsorption and its implications to protein chromatography: A review

L Zhang, Y Sun - Biochemical Engineering Journal, 2010 - Elsevier
Adsorption on solid surface is of fundamental importance in the research and development
of chromatographic science and technology. Due to the limitation of the currently available …

High-resolution atomic force microscopy and spectroscopy of native membrane proteins

CA Bippes, DJ Muller - Reports on Progress in Physics, 2011 - iopscience.iop.org
Membranes confining cells and cellular compartments are essential for life. Membrane
proteins are molecular machines that equip cell membranes with highly sophisticated …

Structure prediction of protein− solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite

K Makrodimitris, DL Masica, ET Kim… - Journal of the American …, 2007 - ACS Publications
A molecular description of protein− surface interactions could open new avenues in
bionanotechnology and provide a deeper understanding of in vivo phase boundary …

Parallel tempering Monte Carlo simulations of lysozyme orientation on charged surfaces

Y **e, J Zhou, S Jiang - The Journal of chemical physics, 2010 - pubs.aip.org
In this work, the parallel tempering Monte Carlo (PTMC) algorithm is applied to accurately
and efficiently identify the global-minimum-energy orientation of a protein adsorbed on a …

Effects of surface tethering on protein folding mechanisms

M Friedel, A Baumketner… - Proceedings of the …, 2006 - National Acad Sciences
The folding mechanisms of proteins are increasingly being probed through single-molecule
experiments in which the protein is immobilized on a surface. Nevertheless, a clear …

[HTML][HTML] An entropic perspective of protein stability on surfaces

TA Knotts, N Rathore, JJ De Pablo - Biophysical Journal, 2008 - cell.com
The interaction of proteins with surfaces regulates numerous processes in nature, science,
and technology. In many applications, it is desirable to place proteins on surfaces in an …

[HTML][HTML] Confinement effects on the thermodynamics of protein folding: Monte Carlo simulations

N Rathore, TA Knotts, JJ de Pablo - Biophysical journal, 2006 - cell.com
The effects of chaperonin-like cage-induced confinement on protein stability have been
studied for molecules of varying sizes and topologies. Minimalist models based on Gō-like …

[HTML][HTML] A coarse grain model for protein-surface interactions

S Wei, TA Knotts - The Journal of chemical physics, 2013 - pubs.aip.org
The interaction of proteins with surfaces is important in numerous applications in many fields—
such as biotechnology, proteomics, sensors, and medicine—but fundamental understanding …

[HTML][HTML] Thermodynamics of DNA hybridization on surfaces

TJ Schmitt, TA Knotts - The Journal of chemical physics, 2011 - pubs.aip.org
Hybridization of single-stranded DNA (ssDNA) targets to surface-tethered ssDNA probes
was simulated using an advanced coarse-grain model to identify key factors that influence …