Surface analysis by X-ray photoelectron spectroscopy of sol-gel silica modified with covalently bound peptides

Chemical surface characterization of biologically modified sol-gel derived silica is critical but somewhat limited. This work demonstrates the ability of x-ray photoelectron spectroscopy (XPS) to characterize the surface chemistry of peptide modified sol-gel thin films based on the example of four different free peptide-silanes, denoted RGD, NID, KDI ,and YIG. The N 1s and C 1s peaks were found to be good fingerprints of the peptides, whereas O 1s overlapped with the signal of substrate oxygen and, therefore, the O 1s peak was not informative in the case of the thin films. The C 1s peak was fitted and the contribution of the residual hydrocarbons was sorted out. The curve-fitting procedure of the C 1s peak accounted for the different chemical states of carbon atoms in the peptide structure. The curve-fitting procedure was validated by analyzing free peptides in the powder form and was then applied to the characterization of the peptide-modified thin films. The XPS measured ratio between nitrogen and carbon for the peptide thin film was similar to the corresponding value calculated from the peptide structures. Angle resolved XPS confirmed the surface nature of peptides in modified thin films. The coverage and thickness of the peptides on the thin film surface depended on the peptide sequence. The coverage was in the range of 10% of a monolayer, and the layer thickness varied from 10 to 30 A. We believe that the different thicknesses and surface coverage are due to the local structure of the peptides, with the RGD and NID peptides taking a globule conformation and the YIG and KDI peptides adopting a more linear structure.     

Hydration of small peptides

The results for the sequential hydration of small peptides (<15 residues) obtained in our group are reviewed and put in perspective with other work published in the literature where appropriate. Our findings are based on hydration equilibrium measurements in a high-pressure drift cell inserted into an electrospray mass spectrometer and on calculations employing molecular mechanics and density functional theory methods. It is found that the ionic functional groups typically present in peptides, the ammonium, guanidinium, and carboxylate groups, are the primary target of water molecules binding to peptides. Whereas the water–guanidinium binding energy is fairly constant at 9 ± 1 kcal/mol, the water binding energy of an ammonium group ranges from 7 to 15 kcal/mol depending on how exposed the ammonium group is. A five-residue peptide containing an ammonium group is in favorable cases large enough to fully self-solvate the charge, but a pentapeptide containing a guanidinium group is too small to efficiently shield the charge of this much larger ionic group. The water–carboxylate interaction amounts to 13 kcal/mol with smaller values for a shielded carboxylate group. Both water bound to water in a second solvation shell and charge remote water molecules on the surface of the peptide are bound by 7–8 kcal/mol. The presence of several ionic groups in multiply charged peptides increases the number of favorable hydration sites, but does not enhance the water–peptide binding energy significantly. Water binding energies measured for the first four water molecules bound to protonated bradykinin do not show the declining trend typically observed for other peptides but are constant at 10 kcal/mol, a result consistent with a molecule containing a salt bridge with several good hydration sites. Questions regarding peptide structural changes as a function of number of solvating water molecules are discussed. Not much is known at present about the effect of individual water molecules on the conformation of peptides and on the stability of peptide zwitterions.     

Lipid-protein interactions in the membrane: studies with model peptides

We have used fluorescence quenching of tryptophan-containing trans-membrane peptides by bromine-containing phospholipids to study the specificity of peptide-lipid interactions. We have synthesized peptides Ac-K2GLm WLnK2A-amide where m = 7 and n = 9 (L16) and m = 10 and n = 12 (L22). Binding constants of L22 for dioleoylphosphatidylserine [di(C18 : 1)PS] or dioleoylphosphatidic acid [di(C18 : 1)PA] relative to dieoleoylphosphatidylcholine [di(C18 : 1)PC] were close to 1. However, for L16, whilst the bulk of the di(C18 : 1)PA molecules bound with a binding constant relative to di(C18 : 1)PC close to 1, a small number of di(C18 : 1)PA molecules bound much more strongly. Assuming just one high affinity binding site on L16 for anionic lipid, the affinity of the site for di(C18 : 1)PS was calculated to be ca. 8 times that for di (C18 : 1)PC. The relative binding constant was little affected by ionic strength and close contact between the anionic headgroup of di(C18 : 1)PS and a lysine residue on the peptide was suggested. The relative binding constant for di(C18 : 1)PS at this high affinity site was less than for di(C18 : 1)PA. Cholesterol interacts with L22 with an affinity about 0.7 of that of di(C18 : 1)PC. The structure of the peptide itself is important. The peptide Ac-KKGYL6WL8YKKA-amide (Y2L14) incorporated into bilayers of dinervonylphosphatidylcholine [di(C24 : 1)PC] whereas L16 did not incorporate into this lipid. It is suggested that thinning of a lipid bilayer around a peptide to give optimal hydrophobic matching is less energetically unfavourable when a Tyr residue is located in the lipid/water interfacial region.     

Identification of small molecule binding sites within proteins using phage display technology

Affinity selection of peptides displayed on phage particles was used as the basis for mapping molecular contacts between small molecule ligands and their protein targets. Analysis of the crystal structures of complexes between proteins and small molecule ligands revealed that virtually all ligands of molecular weight 300 Da or greater have a continuous binding epitope of 5 residues or more. This observation led to the development of a technique for binding site identification which involves statistical analysis of an affinity-selected set of peptides obtained by screening of libraries of random, phage-displayed peptides against small molecules attached to solid surfaces. A random sample of the selected peptides is sequenced and used as input for a similarity scanning program which calculates cumulative similarity scores along the length of the putative receptor. Regions of the protein sequence exhibiting the highest similarity with the selected peptides proved to have a high probability of being involved in ligand binding. This technique has been employed successfully to map the contact residues in multiple known targets of the anticancer drugs paclitaxel (Taxol), docetaxel (Taxotere) and 2-methoxyestradiol and the glycosaminoglycan hyaluronan, and to identify a novel paclitaxel receptor [1]. These data corroborate the observation that the binding properties of peptides displayed on the surface of phage particles can mimic the binding properties of peptides in naturally occurring proteins. It follows directly that structural context is relatively unimportant for determining the binding properties of these disordered peptides. This technique represents a novel, rapid, high resolution method for identifying potential ligand binding sites in the absence of three-dimensional information and has the potential to greatly enhance the speed of development of novel small molecule pharmaceuticals.     

Crossing borders to bind proteins—a new concept in protein recognition based on the conjugation of small organic molecules or short peptides to polypeptides from a designed set

A new concept for protein recognition and binding is highlighted. The conjugation of small organic molecules or short peptides to polypeptides from a designed set provides binder molecules that bind proteins with high affinities, and with selectivities that are equal to those of antibodies. The small organic molecules or peptides need to bind the protein targets but only with modest affinities and selectivities, because conjugation to the polypeptides results in molecules with dramatically improved binder performance. The polypeptides are selected from a set of only sixteen sequences designed to bind, in principle, any protein. The small number of polypeptides used to prepare high-affinity binders contrasts sharply with the huge libraries used in binder technologies based on selection or immunization. Also, unlike antibodies and engineered proteins, the polypeptides have unordered three-dimensional structures and adapt to the proteins to which they bind. Binder molecules for the C-reactive protein, human carbonic anhydrase II, acetylcholine esterase, thymidine kinase 1, phosphorylated proteins, the D-dimer, and a number of antibodies are used as examples to demonstrate that affinities are achieved that are higher than those of the small molecules or peptides by as much as four orders of magnitude. Evaluation by pull-down experiments and ELISA-based tests in human serum show selectivities to be equal to those of antibodies. Small organic molecules and peptides are readily available from pools of endogenous ligands, enzyme substrates, inhibitors or products, from screened small molecule libraries, from phage display, and from mRNA display. The technology is an alternative to established binder concepts for applications in drug development, diagnostics, medical imaging, and protein separation.     

Sliding on DNA: From Peptides to Small Molecules

Many DNA binding proteins utilize one‐dimensional (1D) diffusion along DNA to accelerate their DNA target recognition. Although 1D diffusion of proteins along DNA has been studied for decades, a quantitative understanding is only beginning to emerge and few chemical tools are available to apply 1D diffusion as a design principle. Recently, we discovered that peptides can bind and slide along DNA—even transporting cargo along DNA. Such molecules are known as molecular sleds. Here, to advance our understanding of structure–function relationships governing sequence nonspecific DNA interaction of natural molecular sleds and to explore the potential for controlling sliding activity, we test the DNA binding and sliding activities of chemically modified peptides and analogs, and show that synthetic small molecules can slide on DNA. We found new ways to control molecular sled activity, novel small‐molecule synthetic sleds, and molecular sled activity in N‐methylpyrrole/N‐methylimidazole polyamides that helps explain how these molecules locate rare target sites.     

Combining conformational sampling and selection to identify the binding mode of zinc-bound amyloid peptides with bifunctional molecules

The pathogenesis of Alzheimer's disease (AD) has been suggested to be related with the aggregation of amyloid β (Aβ) peptides. Metal ions (e.g. Cu, Fe, and Zn) are supposed to induce the aggregation of Aβ. Recent development of bifunctional molecules that are capable of interacting with Aβ and chelating biometal ions provides promising therapeutics to AD. However, the molecular mechanism for how Aβ, metal ions, and bifunctional molecules interact with each other is still elusive. In this study, the binding mode of Zn(2+)-bound Aβ with bifunctional molecules was investigated by the combination of conformational sampling of full-length Aβ peptides using replica exchange molecular dynamics simulations (REMD) and conformational selection using molecular docking and classical MD simulations. We demonstrate that Zn(2+)-bound Aβ((1-40)) and Aβ((1-42)) exhibit different conformational ensemble. Both Aβ peptides can adopt various conformations to recognize typical bifunctional molecules with different binding affinities. The bifunctional molecules exhibit their dual functions by first preferentially interfering with hydrophobic residues 17-21 and/or 30-35 of Zn(2+)-bound Aβ. Additional interactions with residues surrounding Zn(2+) could possibly disrupt interactions between Zn(2+) and Aβ, which then facilitate these small molecules to chelate Zn(2+). The binding free energy calculations further demonstrate that the association of Aβ with bifunctional molecules is driven by enthalpy. Our results provide a feasible approach to understand the recognition mechanism of disordered proteins with small molecules, which could be helpful to the design of novel AD drugs.     

Compressed matrix thin film (CMTF)-assisted laser desorption ionization mass spectrometric analysis

The inhomogeneous re-crystallization process of matrix materials is the major concerns associated with matrix assisted laser desorption/ionization (MALDI) analysis. We describe here the approach termed compressed matrix thin film (CMTF) in order to make a uniform matrix deposition. In this approach, solid matrix particles are compressed under 10 MPa of pressure by a compressor that is regularly used in infrared spectroscopic analysis. Then aqueous samples can be deposited on the surface of the matrix film. Major advantages of the CMTF approach are summarized as follows. (1) Reproducible sample preparation procedure. Size and thickness of matrix thin films can be controlled by using a fixed mold.force and known amount of matrix materials. (2) Significantly decreased shot-to-shot variations and enhanced reproducibility. (3) Tolerance for in situ salt washing. Because matrix materials are hydrophobic, salts can be washed away while proteins or peptides are retained on the surface of matrix thin films through hydrophobic interactions. (4) Improved sensitivity. The hydrophobic coating of MALDI sample plate by matrix thin films prevents the spreading of samples across the plate and confines analytes to a small area, leading to increased local concentration. (5) A new means for tissue analysis. Tissue sections can be directly transferred to the uniform surface of matrix materials for reproducible and quantitative comparison of different molecules in different localization. The proposed CMTF should be an enabling technique for mass spectrometric analysis with improved correlations between signal intensities and sample quantities.     

Novel, highly selective gold nanoparticle patterning on surfaces using pure water

We present a simple, novel procedure to selectively deposit gold nanoparticles using pure water. It enables patterning of nanoparticle monolayers with a remarkably high degree of selectivity on flat as well as microstructured oxide surfaces. We demonstrate that water molecules form a thin "capping" layer on exposed thiol molecules within the mercaptan self-assembled layer. This reversible capping of water molecules locally "deactivates" the thiol groups, therewith inhibiting the binding of metallic gold nanoparticles to these specific areas. This amazing role of water molecules can be used as a tool to pattern flat as well as structured surfaces with gold nanoparticles.     

Peptide Ligands Stabilized by Small Molecules

Bicyclic peptides generated through directed evolution by using phage display offer an attractive ligand format for the development of therapeutics. Being nearly 100‐fold smaller than antibodies, they promise advantages such as access to chemical synthesis, efficient diffusion into tissues, and needle‐free application. However, unlike antibodies, they do not have a folded structure in solution and thus bind less well. We developed bicyclic peptides with hydrophilic chemical structures at their center to promote noncovalent intramolecular interactions, thereby stabilizing the peptide conformation. The sequences of the peptides isolated by phage display from large combinatorial libraries were strongly influenced by the type of small molecule used in the screen, thus suggesting that the peptides fold around the small molecules. X‐ray structure analysis revealed that the small molecules indeed formed hydrogen bonds with the peptides. These noncovalent interactions stabilize the peptide–protein complexes and contribute to the high binding affinity.     

Investigations on geometrical features in induced ordering of collagen by small molecules

Binding energies of the interaction of collagen like triple helical peptides with a series of polyphenols, viz. gallic acid, catechin, epigallocatechingallate and pentagalloylglucose have been computed using molecular modelling approaches. A correlation of calculated binding energies with the interfacial molecular volumes involved in the interaction is observed. Calculated interface surface areas for the binding of polyphenols with collagen-like triple helical peptides vary in the range of 60–210 ?² and hydrogen bond lengths vary in the range of 2.7–3.4 ?. Interfacial molecular volumes can be calculated from the solvent inaccessible surface areas and hydrogen bond lengths involved in the binding of polyphenols to collagen. Molecular aggregation of collagen in the presence of some polyphenols and chromium (III) salts has been probed experimentally in monolayer systems. The monolayer arrangement of collagen seems to be influenced by the presence of small molecules like formaldehyde, gluteraldehyde, tannic acid and chromium (III) salts. A fractal structure is observed on account of two-dimensional aggregation of collagen induced by tanning species. Atomic force microscopy has been employed to probe the topographic images of two-dimensional aggregation of collagen induced by chromium (III) salts. A case is made that long-range ordering of collagen by molecular species involved in its stabilisation is influenced by molecular geometries involved in its interaction with small molecules. Dedicated to Professor C N R Rao on his 70th birthday     

Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach

Peptides bound to MHC molecules on the surface of cells convey critical information about the cellular milieu to immune system T cells. Predicting which peptides can bind an MHC molecule, and understanding their modes of binding, are important in order to design better diagnostic and therapeutic agents for infectious and autoimmune diseases. Due to the difficulty of obtaining sufficient experimental binding data for each human MHC molecule, computational modeling of MHC peptide-binding properties is necessary. This paper describes a computational combinatorial design approach to the prediction of peptides that bind an MHC molecule of known X-ray crystallographic or NMR-determined structure. The procedure uses chemical fragments as models for amino acid residues and produces a set of sequences for peptides predicted to bind in the MHC peptide-binding groove. The probabilities for specific amino acids occurring at each position of the peptide are calculated based on these sequences, and these probabilities show a good agreement with amino acid distributions derived from a MHC-binding peptide database. The method also enables prediction of the three-dimensional structure of MHC-peptide complexes. Docking, linking, and optimization procedures were performed with the XPLOR program [1].     

Sequential hydration of small protonated peptides

The sequential addition of water molecules to a series of small protonated peptides was studied by equilibrium experiments using electrospray ionization combined with drift cell techniques. The experimental data were compared to theoretical structures of selected hydrated species obtained by molecular mechanics simulations. The sequential water binding energies were measured to be of the order of 7-15 kcal/mol, with the largest values for the first water molecule adding to either a small nonarginine containing peptide (e.g., protonated dialanine) or to a larger peptide in a high charge state (e.g., triply protonated neurotensin). General trends are (a) that the first water molecules are more strongly bound than the following water molecules, (b) that very small peptides (2-3 residues) bind the first few water molecules more strongly than larger peptides, (c) that the first few water molecules bind more strongly to higher charge states than to lower charge states, and (d) that water binds less strongly to a protonated guanidino group (arginine containing peptides) than to a protonated amino group. Experimental differential entropies of hydration were found to be of the order of -20 cal/mol/K although values vary from system to system. At constant experimental conditions the number of water molecules adding to any peptide ion is strongly dependent on the peptide charge state (with higher charge states adding proportionally more water molecules) and only weakly dependent on the choice of peptide. For small peptides molecular mechanics calculations indicate that the first few water molecules add preferentially to the site of protonation until a complete solvation shell is formed around the charge. Subsequent water molecules add either to water molecules of the first solvation shell or add to charge remote functional groups of the peptide. In larger peptides, charge remote sites generally compete more effectively with charge proximate sites even for the first few water molecules.     

Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction

Peptides based on the amino acid sequences found at protein-protein interaction sites make excellent leads for antagonist development. A statistical picture of amino acids involved in protein-protein interactions indicates that proteins recognize and interact with one another through the restricted set of specialized interface amino acid residues, Pro, Ile, Tyr, Trp, Asp and Arg. These amino acids represent residues from each of the three classes of amino acids, hydrophobic, aromatic and charged, with one anionic and one cationic residue at neutral pH. The use of peptides as drug leads has been successfully used to search for antagonists of cell-surface receptors. Peptide, peptidomimetic, and non-peptide organic inhibitors of a class of cell surface receptors, the integrins, currently serve as therapeutic and diagnostic imaging agents. In this review, we discuss the structural features of protein-protein interactions as well as the design of peptides, peptidomimetics, and small organic molecules for the inhibition of protein-protein interactions. Information gained from studying inhibitors of integrin functions is now being applied to the design and testing of inhibitors of other protein-protein interactions. Most drug development progress in the past several decades has been made using the enzyme binding-pocket model of drug targets. Small molecules are designed to fit into the substrate-binding pockets of proteins based on a lock-and-key, induced-fit, or conformational ensemble model of the protein binding site. Traditionally, enzymes have been used as therapeutic drug targets because it was easier to develop rapid, sensitive screening assays, and to find low molecular weight inhibitors that blocked the active site. However, for proteins which interact with other proteins, rather than with small substrate molecules, the lack of binding pockets means that this approach will not generally succeed. There exist many diseases in which the inhibition of protein-protein interactions would provide therapeutic benefit, but there are no general methods available to address such problems. The focus of the first part of this review is to discuss the features of protein-protein interactions which may serve as general guidelines for the development and design of inhibitors for protein-protein interactions. In the second part we focus on the design of peptides (lead compounds) and their conversion into peptidomimetics or small organic molecules for the inhibition of protein-protein interactions. We draw examples from the important and emerging area of integrin-based cell adhesion and show how the principles of protein-protein interactions are followed in the discovery, optimization and usage of specific protein interface peptides as drug leads.     

Cyclic Peptides as Drugs for Intracellular Targets: The Next Frontier in Peptide Therapeutic Development

Developing macrocyclic peptides that can reach intracellular targets is a significant challenge. This review discusses the most recent strategies used to develop cell permeable cyclic peptides that maintain binding to their biological target inside the cell. Macrocyclic peptides are unique from small molecules because traditional calculated physical properties are unsuccessful for predicting cell membrane permeability. Peptide synthesis and experimental membrane permeability is the only strategy that effectively differentiates between cell permeable and cell impermeable molecules. Discussed are chemical strategies, including backbone N-methylation and stereochemical changes, which have produced molecular scaffolds with improved cell permeability. However, these improvements often come at the expense of biological activity as chemical modifications alter the peptide conformation, frequently impacting the compound's ability to bind to the target. Highlighted is the most promising approach, which involves side-chain alterations that improve cell permeability without impact binding events.     

Transformation of low-affinity lead compounds into high-affinity protein capture agents

A simple and potentially general approach to the isolation of high-affinity and -specificity protein binding synthetic molecules is presented. A modest affinity lead compound is appended to the end of each molecule in a combinatorial library of oligomeric compounds, such as peptides or peptoids. The library is then screened under conditions too demanding for the lead to support robust binding to the protein target. It was anticipated that this procedure would select for bivalent ligands in which the oligomer library provides both a second binding element as well as an appropriate linker between this element and the lead compound. We report here synthetic ligands for the Mdm2 protein and ubiquitin able to capture their target proteins from dilute solutions in the presence of a large excess of other proteins.     

QDs标记免疫调节肽及其与T细胞作用的表征

量子点是直径为1~10 nm的球形半导体纳米晶体, 也被称为半导体量子点, 简称QDs. 与有机荧光染料相比, QDs具有激发光谱单一、 荧光谱线窄、 发光效率高、 发光颜色可调、 可进行多色联合标记, 并且光稳定性好等优点, 所以量子点是非常有前途的生物标记物[^1,2]. 研究结果表明, 量子点可以与许多生物分子如蛋白质、多肽、核酸及小分子配体等偶联. 现已有许多关于量子点标记生物分子的报道, 如用量子点标记木瓜蛋白酶、 胰蛋白酶、 天花粉蛋白和表皮生长因子等^[3-5].用量子点标记生物分子作为荧光探针已成功地应用于多种生物分析, 如DNA杂交监测、 免疫分析和用QDs检测ATP推动的反应等^[4,6,7]. 目前, 对量子点标记生物分子的报道多为对大分子蛋白质的标记, 而对小分子肽标记的报道却很少.     

Gas-phase binding energies for non-covalent Aβ-40 peptide/small molecule complexes from CID mass spectrometry and RRKM theory

The gas-phase binding of small molecules to the Amyloid β-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This study discusses a simple procedure used to theoretically model the experimental breakdown diagrams for the Aβ-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-β-carbolin-2-yl)propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-β-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino)propane-1-sulfonic acid. An alternative procedure employing an extrapolation procedure for k(E) is also discussed.     

The Effect of Chemical Structure on the DNA Binding Behavior of Tricyclic Heteroaromatic Ligands

It is well-known that small organic ligands can bind to the double-stranded nucleic acids by three modes, i.e.s grooving binding, intercalation, and electrostatic binding. Usually, intercalation of the ligands into the double helix involves the insertion of a planar atomatic cation into base stack of the helix, while groove binding of small molecules is pertaining to the docking of thin ribbon-like molecules in the minor groove of the helix. In both cases, electrostatic and hydrophobic interactions can afford additional stabilization for the binding.     

Aptamer‐Based SERS Assay of ATP and Lysozyme by Using Primer Self‐Generation

A simple bifunctional surface‐enhanced Raman scattering (SERS) assay based on primer self‐generation strand‐displacement polymerization (PS‐SDP) is developed to detect small molecules or proteins in parallel. Triphosphate (ATP) and lysozyme are used as the models of small molecules and proteins. Compared to traditional bifunctional methods, the method possesses some remarkable features as follows: 1) by virtue of the simple PS‐SDP reaction, a bifunctional aptamer assembly binding of trigger 1 and trigger 2 was used as a functional structure for the simultaneous sensing of ATP or lysozyme. 2) The concept of isothermal amplification bifunctional detection has been first introduced into SERS biosensing applications as a signal‐amplification tool. 3) The problem of high background induced by excess bio‐barcodes is circumvented by using magnetic beads (MBs) as the carrier of signal‐output products and massive of hairpin DNA binding with SERS active bio‐barcodes relied on Au nanoparticles (Au NPs), SERS signal is significantly enhanced. Overall, with multiple amplification steps and one magnetic‐separation procedure, this flexible biosensing system exhibited not only high sensitivity and specificity, with the detection limits of ATP and lysozyme of 0.05 nM and 10 fM , respectively.