Interaction of β-Sheet Folds with a Gold Surface

The adsorption of proteins on inorganic surfaces is of fundamental biological importance. Further, biomedical and nanotechnological applications increasingly use interfaces between inorganic material and polypeptides. Yet, the underlying adsorption mechanism of polypeptides on surfaces is not well understood and experimentally difficult to analyze. Therefore, we investigate here the interactions of polypeptides with a gold(111) surface using computational molecular dynamics (MD) simulations with a polarizable gold model in explicit water. Our focus in this paper is the investigation of the interaction of polypeptides with β-sheet folds. First, we concentrate on a β-sheet forming model peptide. Second, we investigate the interactions of two domains with high β-sheet content of the biologically important extracellular matrix protein fibronectin (FN). We find that adsorption occurs in a stepwise mechanism both for the model peptide and the protein. The positively charged amino acid Arg facilitates the initial contact formation between protein and gold surface. Our results suggest that an effective gold-binding surface patch is overall uncharged, but contains Arg for contact initiation. The polypeptides do not unfold on the gold surface within the simulation time. However, for the two FN domains, the relative domain-domain orientation changes. The observation of a very fast and strong adsorption indicates that in a biological matrix, no bare gold surfaces will be present. Hence, the bioactivity of gold surfaces (like bare gold nanoparticles) will critically depend on the history of particle administration and the proteins present during initial contact between gold and biological material. Further, gold particles may act as seeds for protein aggregation. Structural re-organization and protein aggregation are potentially of immunological importance

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.Comment: 32 pages, 11 figures, submitted to Macromolecule

Multiple tests of association with biological annotation metadata

We propose a general and formal statistical framework for multiple tests of association between known fixed features of a genome and unknown parameters of the distribution of variable features of this genome in a population of interest. The known gene-annotation profiles, corresponding to the fixed features of the genome, may concern Gene Ontology (GO) annotation, pathway membership, regulation by particular transcription factors, nucleotide sequences, or protein sequences. The unknown gene-parameter profiles, corresponding to the variable features of the genome, may be, for example, regression coefficients relating possibly censored biological and clinical outcomes to genome-wide transcript levels, DNA copy numbers, and other covariates. A generic question of great interest in current genomic research regards the detection of associations between biological annotation metadata and genome-wide expression measures. This biological question may be translated as the test of multiple hypotheses concerning association measures between gene-annotation profiles and gene-parameter profiles. A general and rigorous formulation of the statistical inference question allows us to apply the multiple hypothesis testing methodology developed in [Multiple Testing Procedures with Applications to Genomics (2008) Springer, New York] and related articles, to control a broad class of Type I error rates, defined as generalized tail probabilities and expected values for arbitrary functions of the numbers of Type I errors and rejected hypotheses. The resampling-based single-step and stepwise multiple testing procedures of [Multiple Testing Procedures with Applications to Genomics (2008) Springer, New York] take into account the joint distribution of the test statistics and provide Type I error control in testing problems involving general data generating distributions (with arbitrary dependence structures among variables), null hypotheses, and test statistics.Comment: Published in at http://dx.doi.org/10.1214/193940307000000446 the IMS Collections (http://www.imstat.org/publications/imscollections.htm) by the Institute of Mathematical Statistics (http://www.imstat.org

Electron transport through self-assembled monolayers of tripeptides

We report how the electron transport through a solid-state metal/Gly-Gly-His tripeptide (GGH) monolayer/metal junction and the metal/GGH work function are modified by the GGH complexation with Cu2+ ions. Conducting AFM is used to measure the current-voltage histograms. The work function is characterized by combining macroscopic Kelvin probe and Kelvin probe force microscopy at the nanoscale. We observe that the Cu2+ ions complexation with the GGH monolayer is highly dependent on the molecular surface density and results in opposite trends. In the case of a high density monolayer the conformational changes are hindered by the proximity of the neighboring peptides, hence forming an insulating layer in response to copper-complexation. Whereas the slightly lower density monolayers allow for the conformational change to a looped peptide wrapping the Cu-ion, which results in a more conductive monolayer. Copper-ion complexation to the high- and low-density monolayers systematically induces an increase of the work functions. Copper-ion complexation to the low-density monolayer induces an increase of electron transport efficiency, while the copper-ion complexation to the high-density monolayer results in a slight decrease of electron transport. Both of the observed trends are in agreement with first-principle calculations. Complexed copper to low density GGH-monolayer induces a new gap state slightly above the Au Fermi energy that is absent in the high density monolayer.Comment: Full paper with supporting informatio

Synthesis and characterisation of novel polypeptide materials by the polymerisation of N-carboxyanhydrides

Advances in controlled polymerisation strategies over the last decade have allowed chemists to create materials of defined structure and architecture to probe and mimic the greatest chemist of them all ― mother nature. In this work poly-peptides have been synthesised by the polymerisation of amino acid N-carboxy anhydrides without the need for transition metal catalysts. Application of stringent reaction conditions and high-purity monomers allowed control to be imposed on the system and a series of novel homo- and block co-polypeptides to be synthesised and characterised fully. Their ability to assemble into nano- and micro-structures, apparently directed by ß-sheet stacking has been investigated in the solid state by WAXS, electron microscopy and AFM. Organo-gelation was also observed and studied in dilute concentrations of the block-co-poly-peptides. A new and improved synthesis for 7V-carboxy anhydrides bearing carbohydrate motifs was developed without the need for extensive protecting group manipulation or toxic mercury compounds, which were used previously. Finally the possibility of using water soluble polypeptides and vinyl derived polymers as mimics of antifreeze glyco-proteins in the inhibition of the recrystallisation of ice has been evaluated. This showed that not all of the complex structural features present in the native protein are required to retain at least some activity

Statistical Mechanics and Kinetics of Amyloid Fibrillation

Amyloid fibrillation is a protein self-assembly phenomenon that is intimately related to well-known human neurodegenerative diseases. During the past few decades, striking advances have been achieved in our understanding of the physical origin of this phenomenon and they constitute the contents of this review. Starting from a minimal model of amyloid fibrils, we explore systematically the equilibrium and kinetic aspects of amyloid fibrillation in both dilute and semi-dilute limits. We then incorporate further molecular mechanisms into the analyses. We also discuss the mathematical foundation of kinetic modeling based on chemical mass-action equations, the quantitative linkage with experimental measurements, as well as the procedure to perform global fitting.Comment: 68 pages, 18 figures, 201 reference

Folding by Numbers: Primary Sequence Statistics and Their Use in Studying Protein Folding

The exponential growth over the past several decades in the quantity of both primary sequence data available and the number of protein structures determined has provided a wealth of information describing the relationship between protein primary sequence and tertiary structure. This growing repository of data has served as a prime source for statistical analysis, where underlying relationships between patterns of amino acids and protein structure can be uncovered. Here, we survey the main statistical approaches that have been used for identifying patterns within protein sequences, and discuss sequence pattern research as it relates to both secondary and tertiary protein structure. Limitations to statistical analyses are discussed, and a context for their role within the field of protein folding is given. We conclude by describing a novel statistical study of residue patterning in β-strands, which finds that hydrophobic (i,i+2) pairing in β-strands occurs more often than expected at locations near strand termini. Interpretations involving β-sheet nucleation and growth are discussed