Untitled

Stöcker, Urs; Spiegel, Katrin; Gunsteren, Wilfred F. van

doi:10.1023/a:1008379605403

Cited by 55 publications

(24 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…From Figure 3.6(a), it can be seen that most features of the secondary structure were preserved for the structure in bulk solution compared with its crystal structure. As found in the work by Stocker et al [20], the behavior of a protein in solution and in crystal environment is very similar. For the structures of Cyt-c on SAM surfaces with dissociation degree of 5%, 25%, and 50%, the RMSD values are 1.71Å, 1.97Å, and 2.64Å, respectively.…”

supporting

confidence: 68%

Molecular Engineering of Surfaces for Sensing and Detection

Jiang¹

2005

View full text Add to dashboard Cite

Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. MOLECULAR ENGINEERING OF SURFACES FOR SENSING AND DETECTION AUTHOR(S)Shaoyi Jiang FUNDING NUMBERSC -F30602-01-2-0542 PE -61101E PR -E117 TA -00 WU -71 PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)University of Washington Department of Chemical Engineering Seattle Washington 98195 PERFORMING ORGANIZATION REPORT NUMBERN/A SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES)Defense There are three challenges in the development of surfaces for sensing and detection -sensitivity (i.e., low detection limit), specificity (i.e., false positives and negatives), and robustness (simultaneous detection of multiple analytes). These three issues are addressed in this work with the main focuses on control of protein orientation and creation of protein arrays. The ability to control, probe, and predict protein orientation will facilitate the development of biosensors with high sensitivity and specificity. In this work, a charge-driven protein orientation principle was proposed. Molecular simulations were first performed to predict protein orientation on a surface under a wide range of conditions. Simulation results showed that there is indeed a distinct difference in protein orientation on different charged surfaces. Surface Plasmon Resonance (SPR) and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) experiments were then performed to confirm simulation results. Protein arrays are an attractive platform for many applications in sensing and detection, yet due to challenges with fabrication, storage, and protein stability they have not realized their full potential. In this work, a novel single stranded DNA probe surface is introduced, which when used in conjunction with a simple DNA-antibody conjugate, produces a biosensor surface with superior sensitivity, protein resistance and chip stability.

show abstract

supporting

confidence: 68%

Molecular Engineering of Surfaces for Sensing and Detection

Jiang¹

2005

View full text Add to dashboard Cite

show abstract

“…In crystal structures, flexible parts appear as disorder or give rise to large values of B factors, while these regions attain low levels of electron density or almost no density at all (Branden & Tooze, 1999). Analysis of crystallographic B factors thus allows inferences concerning the relations between structure and dynamics of proteins (Frauenfelder et al, 1979;Artymiuk et al, 1979;Karplus & Schulz, 1985;Carugo & Argos, 1999;Parthasarathy & Murthy, 2000;Stocker et al, 2000;Radivojac et al, 2004;Yuan et al, 2005;Weiss, 2007).…”

Section: Introductionmentioning

confidence: 99%

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

View full text Add to dashboard Cite

Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

show abstract

“…Molecular dynamics (MD) simulations provide a more detailed way to study protein crystals, because they allow accounting for the fluctuation of protein atoms, and the structure of the diffusing molecules and ions. MD simulations have recently been used to study the structure related properties of protein crystals [17][18][19][20].…”

Section: Introductionmentioning

confidence: 99%

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

Malek¹,

Odijk²,

Coppens³

2005

Nanotechnology

View full text Add to dashboard Cite

The dynamics of water and sodium counter-ions (Na + ) in a C222 1 orthorhombic β-lactoglobulin crystal is investigated by means of 5 ns molecular dynamics simulations. The effect of the fluctuation of the protein atoms on the motion of water and sodium ions is studied by comparing simulations in a rigid and in a flexible lattice. The electrostatic interactions of sodium ions with the positively charged LYS residues inside the crystal channels significantly influence the ionic motion. According to our results, water molecules close to the protein surface undergo an anomalous diffusive motion. On the other hand, the motion of water molecules further away from the protein surface is normal diffusive. Protein fluctuations affect the diffusion constant of water, which increases from 0.646 ± 0.108 to 0.887 ± 0.41 nm 2 ns −1 , when protein fluctuations are taken into account. The pore size (0.63-1.05 nm) and the water diffusivities are in good agreement with previous experimental results. The dynamics of sodium ions is disordered. LYS residues inside the pore are the main obstacles to the motion of sodium ions. However, the simulation time is still too short for providing a precise description of anomalous diffusion of sodium ions. The results are not only of interest for studying ion and water transport through biological nanopores, but may also elucidate water-protein and ion-protein interactions in protein crystals.

show abstract

Untitled

Cited by 55 publications

References 21 publications

Molecular Engineering of Surfaces for Sensing and Detection

Molecular Engineering of Surfaces for Sensing and Detection

The active site of hen egg-white lysozyme: flexibility and chemical bonding

Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study

Contact Info

Product

Resources

About