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Witter, Raiker; Seyfart, Lydia; Greiner, Georg; Reißmann, Siegmund; Weston, Jennie; Anders, Ernst; Sternberg, Ulrich

doi:10.1023/a:1021625231147

Cited by 18 publications

(52 citation statements)

References 9 publications

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“…Likewise, (Δg c 1 , Δg c 0 ) correspond to a polypeptide that is 100% disordered coil with all H-bonds (present, missing). These latter four free energies are given by (10) …”

Section: Three-state Model For An Infinite Chainmentioning

confidence: 99%

Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions

Jacobs¹,

Wood²

2004

Biopolymers

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Thermodynamic stability in polypeptides is described using a novel Distance Constraint Model (DCM). Here, microscopic interactions are represented as constraints. A topological arrangement of constraints define a mechanical framework. Each constraint in the framework is associated with an enthalpic and entropic contribution. All accessible topological arrangements of distance constraints form an ensemble of mechanical frameworks, each representing a microstate of the polypeptide. A partition function is calculated exactly using a transfer matrix approach, where in many respects the DCM is similar to the Lifson-Roig model. The crucial difference is that the effect of network rigidity is explicitly calculated for each mechanical framework in the ensemble. Network rigidity is a mechanical interaction that provides a mechanism for long-range molecular cooperativity and enables a proper treatment of the nonadditivity of a microscopic free energy decomposition. Accounting for (1) helix ↔ coil conformation changes along the backbone similar to the Lifson-Roig model, (2) i to i + 4 hydrogen-bond formation ↔ breaking similar to the Zimm-Bragg model, and (3) structured ↔ unstructured solvent interaction (hydration effects), a six-parameter DCM describes normal and inverted helix-coil transitions in polypeptides. Under suitable mixed solvent conditions heat and cold denaturation is predicted. Model parameters are fitted to experimental data showing different degrees of cold denaturation in monomeric polypeptides in aqueous hexafluoroisopropanol (HFIP) solution at various HFIP concentrations. By assuming a linear HFIP concentration dependence (up to 6% by mole fraction) on model parameters, all essential experimentally observed features are captured.

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“…Likewise, (Δg c 1 , Δg c 0 ) correspond to a polypeptide that is 100% disordered coil with all H-bonds (present, missing). These latter four free energies are given by (10) …”

Section: Three-state Model For An Infinite Chainmentioning

confidence: 99%

Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions

Jacobs¹,

Wood²

2004

Biopolymers

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“…These pseudopeptide units allow many modifications in the chelating group, are easy to synthesize as series, are on the one hand conformationally restricted and lead on the other hand to an equilibrium of cis/trans-isomers. The conformational analysis by solution NMR shows that in the Zn-complex the cisconformer exists in a considerable amount because of the small energy difference between both forms [1]. Figure 1 shows structures of the pseudotripeptides Bz-His-qJ[CO-N(CH2)2-NH2]Gly-His-NH2 (L1) BzHis-kO[CO-N(CH2)2-COOH]Gly-His-NH2 (L2) and Bz-His-Sar-His-NH2 (L3).…”

Section: Introductionmentioning

confidence: 99%

Estimation of pseudopeptide metal ion complexation tendencies by special MS methods, HPCE and circular dichroism

et al. 2002

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SummaryTo obtain more insight into catalytic mechanisms of metallo enzymes and specific metal complexation by proteins we use linear and cyclic pseudopeptides as mimetics. Knowledge about tendencies of complex formation of different ligands with selected transition metal ions is an indispensable prerequisite for the development of homoand hetero-dinuclear metallo enzyme mimetics. Three pseudotripeptide ligands were investigated with respect to formation tendency and properties of complexes with the transition metal ions Cu 2+, Zn 2+, Ni 2+, Co 2+ and Mn 2+. To study complexation tendencies we applied different methods. One of the important prerequisites for the application in a screening of series of peptide ligands is the necessity for a minimal amount of substance. We used and compared certain masspectrometric methods for the estimation of a rank order of complexation of certain transition metal ions. We also applied spectrophotometric titration, circular dichroism measurements, capillary electrophoresis and pH-rate profile of catalytic activity in the attempt to evaluate complex formation tendencies. Except for the spectrophotometric pH-titration and the pH-profile of catalytic activity all methods were applicable, but each method has its advantages and disadvantages depending on the separation effect of the ligand from the metal complex, and depending on the spectroscopic properties of ligand and complex. The results regarding complex formation are compared to each other. Comparison of pairs by MALDI-TOF-and ESI-MS allows an estimation of the rank order of complexation tendency of one ligand with different metal ions and requires the least amount of substance. The other investigated methods provided additional information on structural properties of the formed complexes; however either they required too much pseudopeptide ligand or were not applicable for all transition metal ions used in this study.

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“…1,2,6,13 In this study, our attention is focused on the interaction between the oligopeptide of three amino acid residues (GlyGly-His) and metal ion without solvent effect. (The response of the Gly-Gly-His modified electrode to Cu 2+ ion was measured as a current in the solution experiment of Fisher et al.…”

mentioning

confidence: 99%

“…Several experimental techniques have been applied to present of specific interactions in metal ion-peptide complexes. [1][2][3][4][5][6][7][8] Conformations of metal ion binding to peptides may have a critical impact on the peptide folding processes and peptide biological functions. Among metal ions, Cu 2+ and Ni 2+ have been widely studied and seem to have most interesting chemistry.…”

mentioning

confidence: 99%

“…10,11 Several groups reported the interactions between the special oligopeptides of three or four amino acid residues and metal ion because those oligopeptides are principally capable of providing the saturated (four electron donor atoms) equatorial binding site. 1,2,6,13 In this study, our attention is focused on the interaction between the oligopeptide of three amino acid residues (GlyGly-His) and metal ion without solvent effect. (The response of the Gly-Gly-His modified electrode to Cu 2+ ion was measured as a current in the solution experiment of Fisher et al.…”

mentioning

confidence: 99%

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Ab initio Calculations for Exploring Metal Ion-(Gly-Gly-His) Complexes

Kim

2005

Bulletin of the Korean Chemical Society

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The specific interactions in metal ion-peptide systems have been studied in many research groups. It is known that the coordinated metal ions play a significant role in the biological action of peptide. Several experimental techniques have been applied to present of specific interactions in metal ion-peptide complexes. Theoretical approaches about metal-oligopeptide structure and metal-ligand coordination geometry have been also performed by molecular dynamics simulations and ab initio calculations.9-13 Studies have focused on the structural data of metal ion-ligand complexes. Four-coordination geometries were mainly discussed because they are most frequently encountered in the metal-binding sites of metalloproteins. Two-and six-coordination geometries were also considered.10,11 Several groups reported the interactions between the special oligopeptides of three or four amino acid residues and metal ion because those oligopeptides are principally capable of providing the saturated (four electron donor atoms) equatorial binding site. 1,2,6,13 In this study, our attention is focused on the interaction between the oligopeptide of three amino acid residues (GlyGly-His) and metal ion without solvent effect. (The response of the Gly-Gly-His modified electrode to Cu 2+ ion was measured as a current in the solution experiment of Fisher et al..2 ) The interaction between Gly-Gly-His and metal ion is studied by optimized structures and stabilization energies in ab initio calculations. Ab initio calculations are performed with 6-31G(d) and 6-311+G(d,p) basis sets to determine optimized structures and stabilization energies. Density functional theory(DFT) at B3LYP level is carried out using Gaussian98 14 series of program. The optimized structures and the stabilization energies between Gly-Gly-His and metal ions (Ca

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Cited by 18 publications

References 9 publications

Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions

Understanding the α‐helix to coil transition in polypeptides using network rigidity: Predicting heat and cold denaturation in mixed solvent conditions

Estimation of pseudopeptide metal ion complexation tendencies by special MS methods, HPCE and circular dichroism

Ab initio Calculations for Exploring Metal Ion-(Gly-Gly-His) Complexes

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