Designed alpha-helical peptides of the TRI family with a general sequence Ac-G(LKALEEK)(4)G-CONH(2) were used as model systems for the study of metal-protein interactions. Variants containing cysteine residues in positions 12 (TRI L12C) and 16 (TRI L16C) were used for the metal binding studies. Cd(II) binding was investigated, and the results were compared with previous and current work on Hg(II) and As(III) binding. The metal peptide assemblies were studied with the use of UV, CD, EXAFS, (113)Cd NMR, and (111m)Cd perturbed angular correlation spectroscopy. The metalated peptide aggregates exhibited pH-dependent behavior. At high pH values, Cd(II) was bound to the three sulfurs of the three-stranded alpha-helical coiled coils. A mixture of two species was observed, including Cd(II) in a trigonal planar geometry. The complexes have UV bands at 231 nm (20 600 M(-1) cm(-1)) for TRI L12C and 232 nm (22 600 M(-1) cm(-1)) for TRI L16C, an average Cd-S bond length of 2.49 A for both cases, and a (113)Cd NMR chemical shift at 619 ppm (Cd(II)(TRI L12C)(3)(-)) or 625 ppm (Cd(II)(TRI-L16C)(3)(-)). Nuclear quadrupole interactions show that two different Cd species are present for both peptides. One species with omega(0) = 0.45 rad/ns and low eta is attributed to a trigonal planar Cd-(Cys)(3) site. The other, with a smaller omega(0), is attributed to a four-coordinate Cd(Cys)(3)(H(2)O) species. At low pH, no metal binding was observed. Hg(II) binding to TRI L12C was also found to be pH dependent, and a 3:1 sulfur-to-mercury(II) species was observed at pH 9.4. These metal peptide complexes provide insight into heavy metal binding and metalloregulatory proteins such as MerR or CadC.

Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.

No abstract

An important objective of de novo protein design is the preparation of metalloproteins, as many natural systems contain metals that play crucial roles for the function and/or structural integrity of the biopolymer. [1,2] Metalloproteins catalyze some of the most important processes in nature, from energy generation and transduction to complex chemical transformations. At the same time, metals in excess can be deleterious to cells, and some ions are purely toxic, with no known beneficial effects (e.g., Hg II or Pb II ). Ideally, we would hope to be able to use an approach based on first principles to create both known metallocenters and novel sites, which may lead to exciting new catalytic transformations. However, the design of novel metalloproteins is a challenging and complex task, especially if the aim is to prepare asymmetric metal environments.Numerous metalloprotein systems have been designed over the past 15 years, typically through the use of unassociated peptides that assemble into three-stranded coiled coils or helix-loop-helix motifs that form antiparallel fourstranded bundles. In terms of metal-ion binding, these systems have been functionalized with heme [3,4] and nonheme mononuclear [5] and binuclear centers. [6,7] It is often difficult to prepare nonsymmetrical metal sites through these strategies owing to the symmetry of the systems, which rely on homooligomerization. Thus, the preparation of a single polypeptide chain capable of controlling a metal-coordination environment is a key objective.Previously, we designed soft, thiol-rich metal-binding sites involving cysteine and/or penicillamine as the ligating amino acid residues into the interior of parallel, three-stranded ahelical coiled coils. [8,9] These systems have served as hallmarks for understanding the metallobiochemistry of different heavy metals, such as Cd II , Hg II , As III , and Pb II . [8][9][10][11] We have shown how to control the geometry and coordination number of metals such as Cd II and Hg II at the protein interior and how to fine-tune the physical properties of the metals, which led to site-selective molecular recognition of Cd II . [12][13][14] Although these homotrimeric assemblies have been very useful, the production of heterotrimeric systems in which metal environments could be fine-tuned controllably or a hydrogen bond could be introduced site-specifically has been elusive. [15] Therefore, we chose an alternative strategy to satisfy this objective and used a single polypeptide chain instead of multiple self-associating peptides.Existing designed heteromeric helical bundles and coiled coils show energetic preferences of several kcal mol À1 for the desired heteromeric versus homomeric assemblies. [16,17] However, the energy gap between a hetero-and homomeric assembly often depends critically on ionic strength, the pH value, and other environmental parameters. Moreover, the objective of many studies in de novo protein design is to make the metal ion adopt an energetically suboptimal coordination geometry, and the degree t...

It isn't natural: TRI peptides can selectively control the coordination number of a metal center by changing only one of the amino acids in the primary sequence. Replacement of the cysteine residue with penicillamine leads to a three‐coordinate complex CdIIS3, whereas substitution of alanine for leucine gives four‐coordinate CdS3O (see scheme).

The SmtB/ArsR family of prokaryotic metalloregulators are winged-helix transcriptional repressors that collectively provide resistance to a wide range of both biologically required and toxic heavy-metal ions. CmtR is a recently described Cd(II)/Pb(II) regulator expressed in Mycobacterium tuberculosis that is structurally distinct from the well-characterized SmtB/ArsR Cd(II)/Pb(II) sensor, Staphylococcus aureus plasmid pI258-encoded CadC. From functional analyses and a multiple sequence alignment of CmtR paralogs, M. tuberculosis CmtR is proposed to bind Pb(II) and Cd(II) via coordination by Cys57, Cys61, and Cys102 [Cavet et al. (2003) J. Biol. Chem. 278, 44560-44566]. We establish here that both wild-type and C102S CmtR are homodimers and bind Cd(II) and Pb(II) via formation of cysteine thiolate-rich coordination bonds. UV-vis optical spectroscopy, (113)Cd NMR spectroscopy (delta = 480 ppm), and (111m)Cd perturbed angular correlation (PAC) spectroscopy suggest two or three thiolate donors in the wild-type protein. Cys57 and Cys61 anchor the coordination complex, while Cys102 plays only an accessory role in stabilizing the metal chelate in the free protein because C102S CmtR binds Cd(II) and Zn(II) with only approximately 10-20-fold lower affinity relative to wild-type CmtR but approximately 100-1000-fold lower for Pb(II). Quantitative investigation of CmtR-cmt O/P binding equilibria using fluorescence anisotropy, however, reveals that Cys102 functions as a key allosteric metal ligand, because substitution of Cys102 abrogates disassembly of oligomeric CmtR-cmt O/P oligomeric complexes. The implications of these findings on the evolution of distinct metal-sensing sites in a family of homologous proteins are discussed.

CdII has been used as a probe of zinc metalloenzymes and proteins because of the spectroscopic silence of ZnII. One of the most commonly used spectroscopic techniques is 113Cd NMR; however, in recent years 111mCd Perturbed Angular Correlation spectroscopy (111mCd PAC) has also been shown to provide useful structural, speciation and dynamics information on CdII complexes and biomolecules. In this article, we show how the joint use of 113Cd NMR and 111mCd PAC spectroscopies can provide detailed information about the CdII environment in thiolate-rich proteins. Specifically we show that the 113Cd NMR chemical shifts observed for CdII in the designed TRI series (TRI = Ac-G-(LKALEEK)4G-NH2) of peptides vary depending on the proportion of trigonal planar CdS3 and pseudotetrahedral CdS3O species present in the equilibrium mixture. PAC spectra are able to quantify these mixtures. When one compares the chemical shift range for these peptides (from δ = 570 to 700 ppm), it is observed that CdS3 species have δ 675–700 ppm, CdS3O complexes fall in the range δ 570–600 ppm and mixtures of these forms fall linearly between these extremes. If one then determines the pKa2 values for CdII complexation [pKa2 is for the reaction Cd[(peptide–H)2(peptide)]+→Cd-(peptide)3− + 2H+ and compares these to the observed chemical shift for the Cd(peptide)3− complexes, one finds that there is also a direct linear correlation. Thus, by determining the chemical shift value of these species, one can directly assess the metal-binding affinity of the construct. This illustrates how proteins may be able to fine tune metal-binding affinity by destabilizing one metallospecies with respect to another. More important, these studies demonstrate that one may have a broad 113Cd NMR chemical shift range for a chemical species (e.g., CdS3O) which is not necessarily a reflection of the structural diversity within such a four-coordinate species, but rather a consequence of a fast exchange equilibrium between two related species (e.g., CdS3O and CdS3). This could lead to reinterpretation of the assignments of cadmium–protein complexes and may impact the application of CdII as a probe of ZnII sites in biology.

The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.