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Showing papers in "Biopolymers in 2008"


Journal ArticleDOI
TL;DR: Recent developments in the analysis of protein secondary structures, including features of the DICHROWEB analysis webserver are discussed, which greatly improve and facilitate the analyses of CD spectra.
Abstract: Circular dichroism (CD) spectroscopy has been a valuable method for the analysis of protein secondary structures for many years. With the advent of synchrotron radiation circular dichroism (SRCD) and improvements in instrumentation for conventional CD, lower wavelength data are obtainable and the information content of the spectra increased. In addition, new computation and bioinformatics methods have been developed and new reference databases have been created, which greatly improve and facilitate the analyses of CD spectra. This article discusses recent developments in the analysis of protein secondary structures, including features of the DICHROWEB analysis webserver.

2,112 citations


Journal ArticleDOI
TL;DR: Collagen type I, with selective removal of its telopeptides, has been shown to have many advantageous features for both of these approaches to tissue engineering for regeneration of tissues and organs.
Abstract: There are two major approaches to tissue engineering for regeneration of tissues and organs. One involves cell-free materials and/or factors and one involves delivering cells to contribute to the regeneraion process. Of the many scaffold materials being investigated, collagen type I, with selective removal of its telopeptides, has been shown to have many advantageous features for both of these approaches. Highly porous collagen lattice sponges have been used to support in vitro growth of many types of tissues. Use of bioreactors to control in vitro perfusion of medium and to apply hydrostatic fluid pressure has been shown to enhance histogenesis in collagen scaffolds. Collagen sponges have also been developed to contain differentiating-inducing materials like demineralized bone to stimulate differentiation of cartilage tissue both in vitro and in vivo.

701 citations


Journal ArticleDOI
TL;DR: The crystallinity values obtained from the XRD patterns of a wide range of native starches using this fitting technique are very similar to the double helix contents as measured by 13C solid state NMR, suggesting that double helices in granular starches are present within irregular crystals.
Abstract: A peak fitting procedure has been implemented for calculating crystallinity in granular starches. This methodology, widely used for synthetic polymers, is proposed to better reflect the crystalline content of starches than the method normally used, in which it is assumed that relatively perfect crystalline domains are interspersed with amorphous regions. The new approach takes into account irregularities in crystals that are expected to exist in semicrystalline materials. Therefore, instead of assuming that the amorphous background extends up to the base of diffraction peaks, the whole X-ray diffraction (XRD) profile is fitted to an amorphous halo and several discrete crystalline diffraction peaks. The crystallinity values obtained from the XRD patterns of a wide range of native starches using this fitting technique are very similar to the double helix contents as measured by (13)C solid state NMR, suggesting that double helices in granular starches are present within irregular crystals. This contrasts with previous descriptions of crystalline and noncrystalline double helices that were based on the analysis of XRD profiles as perfect crystals interspersed in a noncrystalline background. Furthermore, with this fitting methodology it is possible to calculate the contribution from the different crystal polymorphs of starch to the total crystallinity.

524 citations


Journal ArticleDOI
TL;DR: The results show that the number of positively charged residues on the polar face and net charge are both important for both antimicrobial activity and hemolytic activity.
Abstract: In our previous study, we utilized a 26-residue amphipathic α-helical antimicrobial peptide L-V13K (Chen et al., Antimicrob Agents Chemother 2007, 51, 1398−1406) as the framework to study the effects of peptide hydrophobicity on the mechanism of its antimicrobial action. In this study, we explored the effects of net charge and the number of positively charged residues on the hydrophilic/polar face of L-V13K on its biological activity (antimicrobial and hemolytic) and biophysical properties (hydrophobicity, amphipathicity, helicity, and peptide self-association). The net charge of V13K analogs at pH 7 varied between −5 and +10 and the number of positively charged residues varied from 1 to 10. The minimal inhibitory concentrations (MIC) against six strains of Pseudomonas aeruginosa as well as other gram-negative and gram-positive bacteria were determined along with the maximal peptide concentration that produces no hemolysis of human red blood cells (MHC). Our results show that the number of positively charged residues on the polar face and net charge are both important for both antimicrobial activity and hemolytic activity. The most dramatic observation is the sharp transition of hemolytic activity on increasing one positive charge on the polar face of V13K i.e., the change from +8 to +9 resulted in greater than 32-fold increase in hemolytic activity (250 μg/ml to <7.8 μg/ml, respectively).

385 citations


Journal ArticleDOI
TL;DR: This work is a review of the Poisson–Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding, and discusses the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT.
Abstract: This work is a review of the Poisson-Boltzmann (PB) continuum electrostatics theory and its modifications, with a focus on salt effects and counterion binding. The PB model is one of the mesoscopic theories that describes the electrostatic potential and equilibrium distribution of mobile ions around molecules in solution. It serves as a tool to characterize electrostatic properties of molecules, counterion association, electrostatic contributions to solvation, and molecular binding free energies. We focus on general formulations which can be applied to large molecules of arbitrary shape in all-atomic representation, including highly charged biomolecules such as nucleic acids. These molecules present a challenge for theoretical description, because the conventional PB model may become insufficient in those cases. We discuss the conventional PB equation, the corresponding functionals of the electrostatic free energy, including a connection to DFT, simple empirical extensions to this model accounting for finite size of ions, the modified PB theory including ionic correlations and fluctuations, the cell model, and supplementary methods allowing to incorporate site-bound ions in the PB calculations.

306 citations


Journal ArticleDOI
TL;DR: This work considers the main results in intracellular delivery of TATp-mediated delivery of liposomes and DNA, and addresses the development of "smart" stimuli-sensitive nanocarriers, where cell-penetrating function can be activated by the decreased pH only inside the biological target minimizing thus the interaction of drug-loaded nanoccarriers with nontarget cells.
Abstract: Cell-penetrating peptides (CPPs) including TAT peptide (TATp) have been successfully used for intracellular delivery of a broad variety of cargos including various nanoparticulate pharmaceutical carriers (liposomes, micelles, nanoparticles). Here, we will consider the main results in this area, with a special emphasis on TATp-mediated delivery of liposomes and DNA. We will also address the development of “smart” stimuli-sensitive nanocarriers, where cell-penetrating function can be activated by the decreased pH only inside the biological target minimizing thus the interaction of drug-loaded nanocarriers with nontarget cells. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 604–610, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

264 citations


Journal ArticleDOI
TL;DR: Research on peptide models of turns is reviewed to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding, as well as factors that correlate with the importance of turns in folding.
Abstract: Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein’s structure.

183 citations


Journal ArticleDOI
TL;DR: The dependence of collagen triple-helix stability on the residues in its (Gly-X-Y)(n) repeating sequence has been investigated by measuring melting temperatures of host-guest peptides and an on-line collagen stability calculator is now available.
Abstract: Peptides have been an integral part of the collagen triple-helix structure story, and have continued to serve as useful models for biophysical studies and for establishing biologically important sequence-structure-function relationships. High resolution structures of triple-helical peptides have confirmed the basic Ramachandran triple-helix model and provided new insights into the hydration, hydrogen bonding, and sequence dependent helical parameters in collagen. The dependence of collagen triple-helix stability on the residues in its (Gly-X-Y)(n) repeating sequence has been investigated by measuring melting temperatures of host-guest peptides and an on-line collagen stability calculator is now available. Although the presence of Gly as every third residue is essential for an undistorted structure, interruptions in the repeating (Gly-X-Y)(n) amino acid sequence pattern are found in the triple-helical domains of all nonfibrillar collagens, and are likely to play a role in collagen binding and degradation. Peptide models indicate that small interruptions can be incorporated into a rod-like triple-helix with a highly localized effect, which perturbs hydrogen bonds and places the standard triple-helices on both ends out of register. In contrast to natural interruptions, missense mutations which replace one Gly in a triple-helix domain by a larger residue have pathological consequences, and studies on peptides containing such Gly substitutions clarify their effect on conformation, stability, and folding. Recent studies suggest peptides may also be useful in defining the basic principles of collagen self-association to the supramolecular structures found in tissues.

164 citations


Journal ArticleDOI
TL;DR: Results demonstrated that the intracellular delivery of anti-PGL3-Luc siRNA/PEI-HA complex could be facilitated by the HA receptor mediated endocytosis.
Abstract: A novel target specific small interfering RNA (siRNA) delivery system was successfully developed using polyethyleneimine (PEI)-hyaluronic acid (HA) conjugate. Anti-PGL3-Luc siRNA was used as a model system suppressing the PGL3-Luc gene expression. The siRNA/PEI-HA complex with an average size of ca. 21 nm appeared to be formed by electrostatic interaction between the negatively charged siRNA and the positively charged PEI of PEI-HA conjugate. The cytotoxicity of siRNA/PEI-HA complex to B16F1 cells was lower than that of siRNA/PEI complex according to the MTT assay. When B16F1 and HEK-293 cells were treated with fluorescein isothiocyanate (FITC) labeled siRNA/PEI-HA complex, B16F1 cells, with a lymphatic vessel endothelial hyaluronan receptor-1 (LYVE-1), showed higher green fluorescent intensity than HEK-293 cells because of the HA receptor mediated endocytosis of the complex. Accordingly, the PGL3-Luc gene silencing of anti-PGL3-Luc siRNA/PEI-HA complex was more efficient in B16F1 cells than in HEK-293 cells. In addition, the inhibited PGL3-Luc gene silencing effect in the presence of free HA in the transfection medium revealed that siRNA/HA-PEI complex was selectively taken up to B16F1 cells via HA receptor mediated endocytosis. All these results demonstrated that the intracellular delivery of anti-PGL3-Luc siRNA/PEI-HA complex could be facilitated by the HA receptor mediated endocytosis.

162 citations


Journal ArticleDOI
TL;DR: The present knowledge related to the structure of native as well as denatured, renatured and annealed (1,3)‐β‐D‐glucans is reviewed, and some factors hindering progress in the understanding of their biological effects or complexation abilities are pointed out.
Abstract: (1,3)-beta-D-Glucans form a group of biologically active biopolymers that exist in different structural organizations depending on the environmental conditions. The biological effect of (1,3)-beta-D-glucans is a core issue stimulating large research efforts of the molecular properties and their consequences for action as biological response modifiers. The fascination for these molecules increased further following the finding of their ability to form complexes of defined geometry with a number of structures, ranging from linear architectures as polymers or carbon nanotubes, to globular structures as gold particles or dye molecules. The fascinating information concerning the relationship between sample treatment history and molecular organization has not yet reached out to all the contributors within the field, resulting in unnecessary apparent inconsistencies in the literature. In addition to environmental conditions, the sample history is known to influence on the precise structural organization of these molecules. The present knowledge related to the structure of native as well as denatured, renatured and annealed (1,3)-beta-D-glucans is reviewed. The influence of their structural organization on the biological activity and complexation abilities is discussed, and some factors hindering progress in the understanding of their biological effects or complexation abilities are pointed out.

153 citations


Journal ArticleDOI
TL;DR: The present work reviews the latest chemical and biochemical developments for the site‐specific covalent attachment of proteins onto solid supports.
Abstract: Immobilization of proteins onto surfaces is of great importance in numerous applications, including protein analysis, drug screening, and medical diagnostics, among others. The success of all these technologies relies on the immobilization technique employed to attach a protein to the corresponding surface. Non-specific physical adsorption or chemical cross-linking with appropriate surfaces results in the immobilization of the protein in random orientations. Site-specific covalent attachment, on the other hand, leads to molecules being arranged in a definite, orderly fashion and allows the use of spacers and linkers to help minimize steric hindrances between the protein and the surface. The present work reviews the latest chemical and biochemical developments for the site-specific covalent attachment of proteins onto solid supports.

Journal ArticleDOI
TL;DR: This review will attempt to make a bridge between the design of SMAMPs and the fundamentals of SMAMP-membrane interactions, and provide an optimistic picture for the greater challenge of general proteomimetics.
Abstract: Infectious diseases and antibiotic resistance are now considered the most imperative global healthcare problem. In the search for new treatments, host defense, or antimicrobial, peptides have attracted considerable attention due to their various unique properties; however, attempts to develop in vivo therapies have been severely limited. Efforts to develop synthetic mimics of antimicrobial peptides (SMAMPs) have increased significantly in the last decade, and this review will focus primarily on the structural evolution of SMAMPs and their membrane activity. This review will attempt to make a bridge between the design of SMAMPs and the fundamentals of SMAMP-membrane interactions. In discussions regarding the membrane interaction of SMAMPs, close attention will be paid to the lipid composition of the bilayer. Despite many years of study, the exact conformational aspects responsible for the high selectivity of these AMPs and SMAMPs toward bacterial cells over mammalian cells are still not fully understood. The ability to design SMAMPs that are potently antimicrobial, yet nontoxic to mammalian cells has been demonstrated with a variety of molecular scaffolds. Initial animal studies show very good tissue distribution along with more than a 4-log reduction in bacterial counts. The results on SMAMPs are not only extremely promising for novel antibiotics, but also provide an optimistic picture for the greater challenge of general proteomimetics.

Journal ArticleDOI
TL;DR: It is demonstrated that within cyclotide subfamilies there is a correlation between hydrophobicity of certain loop regions and HIV inhibition and charged residues in these loops impact on the activity of the cyclotides, presumably by modulating membrane binding.
Abstract: Cyclotides are disulfide rich macrocyclic plant peptides that are defined by their unique topology in which a head-to-tail cyclized backbone is knotted by the interlocking arrangement of three disulfide bonds. This cyclic cystine knot motif gives the cyclotides exceptional resistance to thermal, chemical, or enzymatic degradation.

Journal ArticleDOI
TL;DR: The,beta-defensins comprise a large family of small cationic antimicrobial peptides widely distributed in plants, mammals and insects that display multifunctional properties with implications as potential therapeutic agents.
Abstract: The beta-defensins comprise a large family of small cationic antimicrobial peptides widely distributed in plants, mammals and insects. These cysteine rich peptides display multifunctional properties with implications as potential therapeutic agents. Recent research has highlighted their role in both the innate and adaptive immune systems as well as being novel melanocortin ligands. Studies investigating structure and function provide an insight into the molecular basis of their immunological properties.

Journal ArticleDOI
TL;DR: Polymeric micelles self-assembled from cholesterol-conjugated poly(ethylene glycol) (PEG) and anchored with transcriptional activator TAT peptide (TAT-PEG-b-Col) were fabricated for delivery of antibiotics across the blood-brain barrier (BBB) and proved to cross the BBB and enter the brain.
Abstract: Polymeric micelles self-assembled from cholesterol-conjugated poly(ethylene glycol) (PEG) and anchored with transcriptional activator TAT peptide (TAT-PEG-b-Col) were fabricated for delivery of antibiotics across the blood-brain barrier (BBB). Ciprofloxacin, which demonstrated a high bactericidal effect, was efficiently loaded into the micelles by a membrane dialysis method. The ciprofloxacin-loaded micelles were characterized via dynamic light scattering and SEM. The micelles were spherical in nature, having an average diameter of smaller than 180 nm. Sustained release of ciprofloxacin was achieved over 6 h in phosphate-buffered saline (pH 7.4) at 37 degrees C. Confocal laser scanning microscopy reveals that the uptake of Fluorescein 5-isothiocyanate (FITC)-loaded TAT-PEG-b-Col micelles by human astrocytes was much higher than that of free FITC. Animal studies proved that these micelles crossed the BBB and entered the brain. The TAT-conjugated micelles may be used to deliver antibiotics across the BBB for treatment of brain infections.

Journal ArticleDOI
TL;DR: An overview of the biology and enzymology of tyrosine sulfation is provided and recent developments in preparative and analytical methods that are central to sulfoproteome research are discussed.
Abstract: Tyrosine sulfation is one of the most common post-translational modifications in secreted and transmembrane proteins and a key modulator of extracellular protein-protein interactions. Several proteins known to be tyrosine sulfated play important roles in physiological processes, and in some cases a direct link between protein function and tyrosine sulfation has been established. In blood coagulation, tyrosine sulfation of factor VIII is required for efficient binding of von Willebrand factor; in leukocyte adhesion, tyrosine sulfation of the P-selectin glycoprotein ligand-1 mediates high-affinity binding to P-selectin; and in leukocyte chemotaxis, tyrosine sulfation of chemokine receptors is required for optimal interaction with chemokine ligands. Furthermore, tyrosine sulfation has been implicated in several infectious diseases. In particular, tyrosine sulfation of the HIV-1 co-receptor CCR5 is required for viral entry into host cells and tyrosine sulfation of the Duffy antigen/receptor for chemokines is crucial for erythrocyte invasion by the malaria parasite plasmodium vivax. Despite increasing interest in tyrosine sulfation in recent years, the sulfoproteome still remains largely unexplored. To date, only a relatively small number of sulfotyrosine-containing peptides and proteins have been identified, and a specific role for tyrosine sulfation has not been established for most of these. Here, we provide an overview of the biology and enzymology of tyrosine sulfation and discuss recent developments in preparative and analytical methods that are central to sulfoproteome research.

Journal ArticleDOI
TL;DR: In this article, the authors used Raman spectroscopy with near-infrared light excitation to study normal breast tissue and tumors from 11 mice injected with a cancer cell line.
Abstract: Raman spectroscopy shows potential in differentiating tumors from normal tissue. We used Raman spectroscopy with near-infrared light excitation to study normal breast tissue and tumors from 11 mice injected with a cancer cell line. Spectra were collected from 17 tumors, 18 samples of adjacent breast tissue and lymph nodes, and 17 tissue samples from the contralateral breast and its adjacent lymph nodes. Discriminant function analysis was used for classification with principal component analysis scores as input data. Tissues were examined by light microscopy following formalin fixation and hematoxylin and eosin staining. Discriminant function analysis and histology agreed on the diagnosis of all contralateral normal, tumor, and mastitis samples, except one tumor which was found to be more similar to normal tissue. Normal tissue adjacent to each tumor was examined as a separate data group called tumor bed. Scattered morphologically suspicious atypical cells not definite for tumor were present in the tumor bed samples. Classification of tumor bed tissue showed that some tumor bed tissues are diagnostically different from normal, tumor, and mastitis tissue. This may reflect malignant molecular alterations prior to morphologic changes, as expected in preneoplastic processes. Raman spectroscopy not only distinguishes tumor from normal breast tissue, but also detects early neoplastic changes prior to definite morphologic alteration.

Journal ArticleDOI
Hyejung Mok1, Tae Gwan Park1
TL;DR: The formulation based on the self-crosslinked fusogenic peptide could be used as a biocompatible and efficient nonviral carrier for siRNA delivery and formed more stable and compact polyelectrolyte complexes with siRNA, compared with naked KALA and polyethylenimine.
Abstract: A novel self-crosslinked and reducible peptide was synthesized for stable formation of nanoscale complexes with an siRNA-PEG conjugate to enhance transfection efficiency in serum containing condition without compromising cytotoxicity. A fusogenic peptide, KALA, with two cysteine residues at both terminal ends was crosslinked via disulfide linkages under mild DMSO oxidation condition. The reducible crosslinked KALA (cl-KALA) was used to form nano-complexes with green fluorescent protein (GFP) siRNA. Size and morphology of various polyelectrolyte complexes formulated with KALA and cl-KALA were comparatively analyzed. cl-KALA exhibited more reduced cell cytotoxicity and formed more stable and compact polyelectrolyte complexes with siRNA, compared with naked KALA and polyethylenimine (PEI), probably because of its increased charge density. The extent of gene silencing was quantitatively evaluated using MDA-MB-435 cells. cl-KALA/siRNA complexes showed comparable gene silencing efficiency with those of cytotoxic PEI. In a serum containing medium, cl-KALA/siRNA-PEG conjugate complexes exhibited superior gene inhibition because of the shielding effect of PEG on the surface. The formulation based on the self-crosslinked fusogenic peptide could be used as a biocompatible and efficient nonviral carrier for siRNA delivery.

Journal ArticleDOI
TL;DR: The history of RNase and its offspring, RNase S (S‐protein/S‐peptide), will be considered as a preface to preliminary data and proposed experiments addressing topics of current interest, including entropy–enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action.
Abstract: Pancreatic ribonuclease A (EC 3.1.27.5, RNase) is, perhaps, the best-studied enzyme of the 20th century. It was isolated by Rene Dubos, crystallized by Moses Kunitz, sequenced by Stanford Moore and William Stein, and synthesized in the laboratory of Bruce Merrifield, all at the Rockefeller Institute/University. It has proven to be an excellent model system for many different types of experiments, both as an enzyme and as a well-characterized protein for biophysical studies. Of major significance was the demonstration by Chris Anfinsen at NIH that the primary sequence of RNase encoded the three-dimensional structure of the enzyme. Many other prominent protein chemists/enzymologists have utilized RNase as a dominant theme in their research. In this review, the history of RNase and its offspring, RNase S (S-protein/S-peptide), will be considered, especially the work in the Merrifield group, as a preface to preliminary data and proposed experiments addressing topics of current interest. These include entropy–enthalpy compensation, entropy of ligand binding, the impact of protein modification on thermal stability, and the role of protein dynamics in enzyme action. In continuing to use RNase as a prototypical enzyme, we stand on the shoulders of the giants of protein chemistry to survey the future. © 2007 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 90: 259–277, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Journal ArticleDOI
TL;DR: The results of this study demonstrate that collagen organization can be modified by the addition of GAG, leading to altered matrix mechanical properties.
Abstract: The ability to alter collagen organization could lead to more physiologically relevant scaffolds for tissue engineering. This study examined collagen organization in the presence of polysaccharide and the resulting effects on viscoelastic properties. Fibrillogenesis in the presence of chondroitin sulfate (CS) resulted in changes in the collagen network organization with an increase in void space present. The increased void space caused by CS addition correlated with a decreased stiffness of the collagen gel. These changes occurred with physiologically relevant ratios of collagen to CS, at physiological pH and ionic strength, and without a decrease in the amount of collagen incorporated into fibrils. The addition of dextran, an uncharged polysaccharide, yielded no change in network void space or mechanical properties. Changes in fibril diameter caused by CS or dextran were not correlated with mechanical properties. The results of this study demonstrate that collagen organization can be modified by the addition of GAG, leading to altered matrix mechanical properties.

Journal ArticleDOI
TL;DR: The results indicate that the structure of the collagen network is not a major factor in determining the diffusion through the ECM, and increasing the concentration of collagen was found to reduce the diffusion coefficient.
Abstract: The extracellular matrix (ECM) represents a major barrier for delivery of therapeutic drugs, and the transport is determined by the ECM composition, structure, and distribution. Because of the high interstitial fluid pressure in tumors, diffusion becomes the main transport mechanism through ECM. The purpose of this work was to study the impact of the structure of the collagen network on diffusion, by studying to what extent the orientation and chemical modification of the collagen network influenced diffusion. Collagen gels with a concentration of 0.2-2.0% that is comparable with the amount of collagen in the tumor ECM were used as a model system for ECM. Collagen gels were aligned in a low-strength magnetic field and geometrical confinement, and chemically modified by adding decorin or hyaluronan. Diffusion of dextran 2-MDa molecules in the collagen gels was measured using fluorescence recovery after photobleaching. Alignment of the collagen fibers in our gels was found to have no impact on the diffusion coefficient. Adding decorin reduced the diameter of the collagen fibers, but no effect on diffusion was observed. Hyaluronan also reduced the fiber diameter, and high concentration of hyaluronan (2.5 mg/ml) increased the diffusion coefficient. The results indicate that the structure of the collagen network is not a major factor in determining the diffusion through the ECM. Rather, increasing the concentration of collagen was found to reduce the diffusion coefficient. Concentration of the collagen network is more important than the structure in determining the diffusion coefficient.

Journal ArticleDOI
TL;DR: It is found that peptide conformation and membrane insertion were sequence dependent, both upon the number of Leu residues, and upon their positions along the hydrophobic core, which led to distinctions in the mechanism of actions of these CAPs for disruption of bacterial versus mammalian membranes.
Abstract: Novel cationic antimicrobial peptides (CAPs) designed in our lab-typified by sequences such as KKKKKKAAX-AAXAAXAA-NH(2), where X = Phe/Trp-display high antibacterial activity but exhibit little or no hemolytic activity towards human red blood cells even at high doses. To clarify the mechanism of their selectivity for bacterial versus mammalian membranes and to increase our understanding of the relationships between primary sequence and bioactivity, a library of derivatives was prepared by increasing segmental hydrophobicity, in which systematic substitutions of Ala for two, three, or four Leu residues were made. Conformationally constrained dimeric and cyclic derivatives were also synthesized. The peptides were examined for activity against pathogenic bacteria (Pseudomonas aeruginosa), hemolytic activity on human red blood cells, and insertion into models of natural bacterial membranes (containing anionic lipids) and mammalian membranes (containing zwitterionic lipids + cholesterol). Results were compared with corresponding properties of the natural CAPs magainin and cecropin. Using circular dichroism and fluorescence spectroscopy, we found that peptide conformation and membrane insertion were sequence dependent, both upon the number of Leu residues, and upon their positions along the hydrophobic core. Membrane disruption was likely enhanced by the fact that the peptides contain potent dimerization-promoting sequence motifs, as assessed by SDS-PAGE gel analysis. The overall results led us to identify distinctions in the mechanism of actions of these CAPs for disruption of bacterial versus mammalian membranes, the latter dependent on surpassing a "second hydrophobicity threshold" for insertion into zwitterionic membranes.

Journal ArticleDOI
TL;DR: Three modified cyclic peptides are examined, along with multiple versions of their linear control analogs, and their thermodynamic parameters when binding the same host, the third PDZ domain of the mammalian postsynaptic density-95 (PSD-95) protein to demonstrate that the entropic relationship between a macrocyclic ligand and a linear counterpart can be a complex one that is difficult to rationalize.
Abstract: It is an accepted practice in ligand design to introduce conformational constraint with the expectation of improving affinity, justified by the theoretical possibility that an unfavorable change in binding entropy will be reduced. This rationale of minimizing the entropic penalty through imposing structural constraints upon a ligand, however, has been voiced more often than verified. Here we examine three modified cyclic peptides, along with multiple versions of their linear control analogs, and determine their thermodynamic parameters when binding the same host, the third PDZ domain (PDZ3) of the mammalian postsynaptic density-95 (PSD-95) protein. To begin a two-stage investigation, the initial evaluation involved solution binding studies with isothermal titration calorimetry (ITC), which provided the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (TΔS) upon formation of the protein-ligand complex. In the second stage, a selected macrocycle along with two matched linear controls were subjected to more rigorous analysis by ITC, which included (1) change in heat of buffer ionization (ΔHion) titrations, to examine the role of proton transfer events; (2) change in heat capacity (ΔCp) determinations, to indirectly probe the nature of the binding surface; and (3) osmotic stress experiments, to evaluate desolvation effects and quantitate water release. Together, these demonstrate that the entropic relationship between a macrocyclic ligand and a linear counterpart can be a complex one that is difficult to rationalize. Further, the addition of constraint can, counterintuitively, lead to a less favorable change in binding entropy. This underscores the need to use matched linear control ligands to assure that comparisons are made in a meaningful manner. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 653–667, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Journal ArticleDOI
TL;DR: The development of collagen‐like gels by means of the self‐assembly of chemically synthesized peptides will offer possibilities for novel types of biomaterials.
Abstract: Development of artificial collagens to replace the animal-derived collagens presents a challenge in the formation of safer and functional biomaterials. We report here the development of collagen-like gels by means of the self-assembly of chemically synthesized peptides. The peptides are disulfide-linked trimers of collagenous Gly-X-Y triplet repeats with self-complementary shapes. Upon cooling the peptide solutions, hydrogels of peptide supramolecules are formed by spontaneous intermolecular triple helix formation. The thermal gel-sol transition appeared to be reversible, and the transition temperatures were found to be tunable by the design of the peptides. Our systems for the formation of artificial collagen-like gels will offer possibilities for novel types of biomaterials.

Journal ArticleDOI
TL;DR: These data, which are consistent with previous work on 4-fluoroprolines and 4-methylprolines, support the importance of stereoelectronic and steric effects in the stability of the collagen triple helix and provide another means to modulate that stability.
Abstract: Collagen is an abundant, triple-helical protein comprising three strands of the repeating sequence: Xaa–Yaa–Gly. (2S)-Proline and (2S,4R)-4-hydroxyproline (Hyp) are common in the primary structure of collagen. Here, we use nonnatural proline derivatives to reveal determinants of collagen stability. Specifically, we report high-yielding syntheses of (2S,4S)-4-chloroproline (clp) and (2S,4R)-4-chloroproline (Clp). We find that the molecular structure of Ac-Clp-OMe in the solid state is virtually identical to that of Ac-Hyp-OMe. In contrast, the conformational properties of Ac-clp-OMe are similar to those of Ac-Pro-OMe. Ac-Clp-OMe has a stronger preference for a trans amide bond than does Ac-Pro-OMe, whereas Ac-clp-OMe has a weaker preference. (Pro–Clp–Gly)10 forms triple helices that are significantly more stable than those of (Pro–Pro–Gly)10. Triple helices of (clp–Pro–Gly)10 have stability similar to those of (Pro–Pro–Gly)10. Unlike (Pro–Clp–Gly)10 and (clp–Pro–Gly)10, (clp–Clp–Gly)10 does not form a stable triple helix, presumably due to a deleterious steric interaction between proximal chlorines on different strands. These data, which are consistent with previous work on 4-fluoroprolines and 4-methylprolines, support the importance of stereoelectronic and steric effects in the stability of the collagen triple helix and provide another means to modulate that stability. © 2007 Wiley Periodicals, Inc. Biopolymers 89: 443–454, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Journal ArticleDOI
TL;DR: The effect of chemical modification of hyaluronic acid (HA) on its distribution throughout the body was successfully visualized in nude mice through real-time bioimaging using quantum dots (QDots) using near-infrared emission wavelength of 800 nm.
Abstract: The effect of chemical modification of hyaluronic acid (HA) on its distribution throughout the body was successfully visualized in nude mice through real-time bioimaging using quantum dots (QDots). Adipic acid dihydrazide modified HA (HA-ADH) was synthesized and conjugated with QDots having carboxyl terminal ligands activated with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide. The formation of HA-QDot conjugates could be confirmed by gel permeation chromatography, fluorometry, transmission electron microscopy, and ζ-size analysis. According to the real-time bioimaging of HA-QDot conjugates after subcutaneous injection to nude mice, the fluorescence of HA-QDot conjugates with a near infrared wavelength of 800 nm could be detected up to 2 months, whereas that with an emission wavelength of 655 nm disappeared almost completely within 5 days. The results can be ascribed to the fact that near-infrared light has a high penetration depth of about 5–6 cm in the body compared to that of about 7–10 mm for visible light. Thereby, using QDots with a near-infrared emission wavelength of 800 nm, the distribution of HA-QDot conjugates throughout the body was bioimaged in real-time after their tail-vein injection into nude mice. HA-QDot conjugates with 35 mol% ADH content maintaining enough binding sites for HA receptors were mainly accumulated in the liver, while those with 68 mol% ADH content losing much of HA characteristics were evenly distributed to the tissues in the body. The results are well matched with the fact that HA receptors are abundantly present in the liver with a high specificity to HA molecules. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1144–1153, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Journal ArticleDOI
TL;DR: The results suggested that the polysaccharide of AAG exists as extended chains in 0.1M NaCl aqueous solution, resulting in the increased stiffness of the chains.
Abstract: From Auricularia auricula-judae, a water soluble β-D-glucan, named as AAG, was isolated by extraction with 70% ethanol/water solution. Its chemical structure was analyzed by gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS), matrix-assisted laser desorption /ionization (MALDI)-time of flight (TOF), and 1D, 2D NMR. AAG was detected, for the first time, to be composed of a main chain of (14)-linked D-glucopyranosyl with glucopyranosyl side groups at O6. With the help of MALDI-TOF-MS, the sequence and the distribution of glucuronic acid were determined and the content of glucuronic acid is about 19%. Five fractions were prepared from the AAG sample in water by ultrasonic degradation method. Their molecular weight, size, and shape (chain conformation) were studied by dynamics light scattering (DLS), static laser light scattering (LLS), size exclusion chromatography combined LLS (SEC-LLS) and viscometry in 0.1M NaCl aqueous solution at 25°C. The dependence of intrinsic viscosity ([η]) on Mw for this polysaccharide was established to be [η] = 1.22 ×10−3Mw1.00 (cm3 g−1) in the range of Mw from 3.40 × 104 to 2.88 × 105. The conformational parameters of the AAG polysaccharide were found to be 820 nm−1 for molar mass per unit contour length (ML), 12.3 nm for persistence length (q) and 2.1 for ρ (〈s2〉1/2/Rh). The results suggested that the polysaccharide exists as extended chains in 0.1M NaCl aqueous solution. The chemical structure of AAG containing glucuronic acid and side groups led to steric hindrance, resulting in the increased stiffness of the chains. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 614–622, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Journal ArticleDOI
TL;DR: It is found that an initial random coil conformation of the SF can be readily changed into an ordered β‐sheet structure by optimizing the solution conditions, such as the SF concentration, pH, temperature, or metal‐ion content.
Abstract: The conformational transition of molecular chains of regenerated silk fibroin (SF) aqueous solution is systematically investigated by circular dichroism, Raman, IR, and UV-vis spectroscopies. It is found that an initial random coil conformation of the SF can be readily changed into an ordered beta-sheet structure by optimizing the solution conditions, such as the SF concentration, pH, temperature, or metal-ion content. Circular dichroic spectra quantitatively confirm a steadily decreased content of the random coil conformation but a significantly increased beta-sheet content after an ultrasonic or extruding treatment. Furthermore, the extrusion is more powerful to achieve high beta-sheet content than the ultrasonic. It is interesting that the polarized optical micrographs of the SF aqueous solution extruded by injection illustrate the formation and existence of liquid crystalline state. A study of extrusion in vitro could be used as a model system to understand the natural silk spinning process in silkworm.

Journal ArticleDOI
TL;DR: The blood-brain barrier (BBB) is concentrated here on the vascular BBB, which is comprised of the capillary bed of the brain specially modified to prevent the production of a plasma ultrafiltrate.
Abstract: Peptides and regulatory proteins hold great promise as therapeutic agents for the central nervous system (CNS). However, the blood-brain barrier (BBB) is a major obstacle to the delivery of these potential therapeutics to their site of action. We concentrate here on the vascular BBB, which is comprised of the capillary bed of the brain specially modified to prevent the production of a plasma ultrafiltrate. For many peptides and proteins, this physical barrier is reinforced by enzymatic activities at the BBB, CNS, and peripheral tissues, short half-lives and large volumes of distribution in the blood, binding proteins in blood, and brain-to-blood efflux systems. Nevertheless, there are pathways through which substances can cross. Small, lipid soluble substances cross by the nonsaturable mechanism of transmembrane diffusion, but even water-soluble peptides can cross to some degree. Many endogenous peptides and regulatory proteins cross the BBB by way of selective, saturable transport systems. For enzymatically resistant substances with long circulating half-lives and small volumes of distribution, such as antibodies, erythropoietin, and enzymes, substances can enter the CNS in therapeutic amounts through the residual leak of the BBB, termed the extracellular pathways. Recent examples show that the BBB transporters for peptides and regulatory substances are modifiable. This provides both a therapeutic opportunity and the potential for disease to arise from BBB dysfunctions. In the last case, the BBB itself is a therapeutic target.

Journal ArticleDOI
TL;DR: A recent survey of cyclic Cα-tetrasubstituted α-amino acids can be found in this paper with a focus on the use as conformation determining elements in peptides.
Abstract: Cα-Tetrasubstituted α-amino acids are widely used to design and prepare peptides and peptide mimics with constrained conformations. Subcategories of these compounds are cyclic Cα-tetrasubstituted α-amino acids, in which both α-substituents are covalently connected. This survey presents recent advances in the synthesis and application of cyclic Cα-tetrasubstituted α-amino acids in a systematic order beginning with cyclopropane amino acids, continuing with four, five, six membered rings, and ring structures larger than six-membered. We discuss synthetic routes to the cyclic Cα-tetrasubstituted α-amino acids and their use as conformation determining elements in peptides.