Jesper Brask

Backbone Amide Linker in Solid-Phase Synthesis

2.1.5. Deactivated BAL, BAL Mimics 2099 2.1.6. Photocleavable BAL 2099 2.2. BAL with a Naphthyl Core 2099 2.2.1. Dialkoxynaphthalene BAL 2100 2.2.2. Trialkoxynaphthalene BAL 2100 2.2.3. Tetraalkoxynaphthalene BAL 2101 2.3. BAL with a Heteroaryl Core 2101 2.3.1. Indole BAL 2101 2.3.2. Safety-Catch Indole BAL 2102 2.3.3. Thiophene BAL 2102 3. Applications in Peptide Synthesis 2103 3.1. Linear and Branched Peptides 2104 3.2. Cyclic Peptides 2104 3.2.1. Diketopiperazines (DKPs) 2105 3.2.2. Head-to-tail Monocyclic Peptides 2105 3.2.3. Cyclic Peptides from -Amino Acids 2105 3.2.4. Other Cyclic Peptide Structures 2106 3.3. C-Terminally Modified Peptides 2106 3.3.1. Peptide Aldehydes 2106 3.3.2. Peptide Thioesters 2107 3.3.3. Other C-Terminally Modified Peptides and Conjugates 2108

Softening of POPC membranes by magainin

Magainin 2 belongs to the family of peptides, which interacts with the lipid membranes. The present work deals with the effect of this peptide on the mechanical properties of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine Giant Unilamellar Vesicle, characterized by the bending stiffness modulus. The bending elastic modulus is measured by Vesicle Fluctuation Analysis at biologically relevant pH and physiological buffer conditions and shows a dramatic decrease with increasing peptide concentration. The observed bilayer softening is interpreted in terms of a continuum model describing perturbations on the membrane organization. Our analysis suggests that the adsorbed peptides give rise to considerable local curvature disruptions of the membrane.

Carbopeptides: chemoselective ligation of peptide aldehydes to an aminooxy-functionalized D-galactose template.

Multifunctional, topological template molecules such as linear and cyclic peptides have been used for the attachment of peptide strands to form novel protein models of, for example, 4‐α‐helix bundles. The concept of carbohydrates as templates for de novo design of potential protein models has been previously described and these novel chimeric compounds were termed carbopeptides. Here, a second generation strategy in which carbopeptides are synthesized by chemoselective ligation of a peptide aldehyde to an aminooxy‐functionalized α‐D‐galactopyranoside is described. This template was prepared by per‐O‐acylation of methyl α‐D‐galactopyranoside with N,N‐Boc2‐aminooxyacetic acid to form a tetra‐functionalized template, followed by treatment with TFA‐CH2Cl2 to release the aminooxy functionality. The peptide aldehydes Fmoc‐Ser‐Gly‐Gly‐H and H‐Ala‐Leu‐Ala‐Lys‐Leu‐Gly‐Gly‐H were synthesized by a BAL strategy. Four identical copies of peptide aldehyde were smoothly attached to the template by chemoselective ligation to form a 2.1 and a 2.9 kDa carbopeptide, respectively. Copyright

Carboproteins: A 4-α-helix bundle protein model assembled on a d-galactopyranoside template

Abstract We have recently introduced the concept of monosaccharides as templates for de novo design of protein models and described the synthesis of a model ‘carbopeptide’. Here, we report the synthesis of a 64 amino acid (AA) ‘carboprotein’ by chemoselective ligation of a C-terminal hexadecapeptide aldehyde to a tetra-aminooxy functionalized methyl α- d -galactopyranoside ( d -Gal p ) template. Biophysical characterizations by CD spectroscopy and NMR amide H–D exchange experiments indicated that the four-stranded carboprotein forms a 4-α-helix bundle structure.

Carbohydrates as templates for control of distance-geometry in de novo-designed proteins.

Abstract. An understanding of very complex natural systems can often only be achieved through detailed studies of systems with a reduced complexity. Thus, de novo design of proteins allows the study of fundamental forces determining protein folding and stability, as well as protein-protein interactions, by analyses of protein models of structural motifs. In addition, de novo design may lead to new biomimetic molecules with novel properties. In a synthetic approach to achieve structural economy, rigid templates, sometimes called topological scaffolds, have been used to connect secondary-structure elements, most notably α-helices. By positioning the helices on the template, the unfavorable entropy of protein folding is reduced. In a novel class of chimeric molecules called carboproteins, carbohydrates are used as templates for de novo design of protein models. Recently, a strategy relying on chemoselective ligation of C-terminal peptide aldehydes to tetra-aminooxy functionalized monosaccharides has provided 7-kDa 4-α-helix bundle carboproteins.

Farnesylated peptides in model membranes: a biophysical investigation

Protein prenylation plays an important role in signal transduction, protein–protein interactions, and the localization and association of proteins with membranes. Using three different techniques, this study physically characterizes the interactions between model dimyristoylphosphatidylcholine membranes and a series of farnesylated peptides. Magic angle spinning nuclear Overhauser enhancement spectroscopy and differential scanning calorimetry reveal that both charged [Ac-Asn-Lys-Asn-Cys-(farnesyl)-OMe and Ac-Asn-Lys-Asn-Cys-(farnesyl)-NH2] and uncharged [Ac-Cys-(farnesyl)-OMe and farnesol] species partition into dimyristoylphosphatidylcholine bilayers. Calorimetry and vesicle fluctuation analysis of giant unilamellar vesicles show that the charged peptides modestly decrease the main gel–fluid phase transition and markedly increase the bending rigidity of large unilamellar vesicles. Uncharged species, on the other hand, dramatically decrease the main phase transition and modestly decrease the bending rigidity. No difference with carboxyl methylation is detected.

Commentary : Farnesylated peptides in model membranes: a biophysical investigation (vol 33, pg 300, 2003)

Protein prenylation plays an important role in signal transduction, protein-protein interactions, and the localization and association of proteins with membranes. Using three different techniques, this study physically characterizes the interactions between model dimyristoylphosphatidylcholine membranes and a series of farnesylated peptides. Magic angle spinning nuclear Overhauser enhancement spectroscopy and differential scanning calorimetry reveal that both charged [Ac-Asn-Lys-Asn-Cys-(farnesyl)-OMe and Ac-Asn-Lys-Asn-Cys-(farnesyl)-NH(2)] and uncharged [Ac-Cys-(farnesyl)-OMe and farnesol] species partition into dimyristoylphosphatidylcholine bilayers. Calorimetry and vesicle fluctuation analysis of giant unilamellar vesicles show that the charged peptides modestly decrease the main gel-fluid phase transition and markedly increase the bending rigidity of large unilamellar vesicles. Uncharged species, on the other hand, dramatically decrease the main phase transition and modestly decrease the bending rigidity. No difference with carboxyl methylation is detected.

Monolayers of a de novo designed 4-α-helix bundle carboprotein and partial structures on Au(111)-surfaces

Mapping of structure and function of proteins adsorbed on solid surfaces is important in many contexts. Electrochemical techniques based on single-crystal metal surfaces and in situ scanning probe microscopies (SPM) have recently opened new perspectives for mapping at the single-molecule level. De novo design of model proteins has evolved in parallel and holds promise for test and control of protein folding and for new tailored protein structural motifs. These two strategies are combined in the present report. We present a synthetic scheme for a new 4-alpha-helix bundle carboprotein built on a galactopyranoside derivative with a thiol anchor aglycon suitable for surface immobilization on gold. The galactopyranoside with thiol anchor and the thiol anchor alone were prepared for comparison. Voltammetry of the three molecules on Au(111) showed reductive desorption peaks caused by monolayer adsorption via thiolate-Au bonding. In situ STM of the thiol anchor disclosed an ordered adlayer with clear domains and molecular features. This holds promise, broadly for single-molecule voltammetry and the SPM and scanning tunnelling microscopy (STM) of natural and synthetic proteins.

Protein Models on Carbohydrate Templates: Effect of the Template

De novo design is a valuable tool for the systematic study of factors controlling protein structure and function [1]. We have previously described [2–4] the concept of carbohydrates as templates for de novo design of protein models and introduced the terms carbopeptides and carboproteins for this class of template-assembled synthetic proteins [5]. The chemoselective oxime ligation [6] of tetraaminooxyacetyl functionalized carbohydrates and amphiphilic C-terminal peptide aldehydes provided carboproteins that fold to form 4-α-helix bundles according to CD spectroscopy and NMR H-D exchange studies [4].