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The structure of BCL-w with a bound BID-BH3 peptide is determined using NMR spectroscopy and molecular docking. The interactions of BCL-w and the BID-BH3 peptide complex with dodecylphosphocholine micelles are characterized and demonstrated that the conformational change of BCL-w upon lipid binding occurs at the same time as the release and unfolding of the BH3 peptide.

Bacteriocins produced by latic acid bacteria are potent antimicrobial compounds that are active against closely related bacteria. The NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2) is reported.

Changes in conformation in the PBX homeodomain and C-terminal extension after binding DNA and HOX-derived YPWM peptides are discussed. The structure of the free PBX homeodomain was found using NMR spectroscopy. PBX is in the PBC family of proteins with its homologues Drosophilia extradenticle and Caenorhabditis elegans ceh-20. They are in the three amino acid loop extension superclass of homeodomains.

The synthesis of (+/-)-acetomycin has been achieved in five steps by the acetylation of lactone and the stereoselective methylation of beta-keto ester using 1,3-dithinenium tetrafluoroborate thereby providing a model for five membered ring enolates alkylation. Lactones are obtained when R1 and R2 are alkyl groups. The formation of the contrasteric alkylation product is based on the specific conformation of the starting enolates.

An approach is described for studying the cooperativity of rapid protein folding with a combination of differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR) relaxation dispersion experiments and an analysis of the temperature dependence of amide [super 1]H and [super 15]N chemical shifts. The results have shown the coexistence of distinct folded and unfolded forms, has established that folding of PBX homeodomain (PBX-HD) is cooperative and have shown the potential of combining calorimetry with NMR dynamics experiments to dissect mechanisms of protein folding.

The nuclear magnetic resonance solution structure of type IIa immunity protein, PisI, a 98-amino acid protein which is a group B immunity protein conferring immunity against piscicolin 126 (PisA) is reported. PisI, similar to ImB2, EntA-im, and PedB is observed to fold into a globular protein in aqueous solution and contains an antiparallel four-helix bundle.

The BCL-[x.sub.L] dimers are prepared by heating concentrated protein over 50 degree Celsius and the heat-induced mechanism of dimerization is done through [alpha]-helix swapping. The results have shown that the temperature can also induce three-dimensional domain swapping in BCL-2 family proteins

Multidimensional NMR studies on subtilosin A, a bacteriocin from Bacillus subtilis, are carried out to determine the complete primary and three-dimensional solution structure of peptide. Results depicted a cyclized peptide backbone with three cross-links formed between the sulfurs of Cys13, Cys 7, and Cys4 and the alpha-positions of Phe22, Thr28 and Phe31 that are showing L form of stereochemistry.

A new method to reduce dehydro side chains and reductively desulfurize lanthionine bridges found in lantibiotics, using nickel boride in the presence of deuterium gas, is reported. The application f a deuterating variant of the process, using NaBD (sub 4) in deuterated solvent, to lantibiotics leads to lanthionne desulfurization with the concomitant incorporation of a single deuterium atom at each of the residues participating in the sulfur bridge.

The complete primary and three-dimensional solution structure of Subtilosin A is determined. The solution structure is determined using isotopic labeling and multidimensional NMR studies.

ABSTRACT Formation of stable secondary structures by oligomers that mimic natural peptides is a key asset for enhanced biological response. Here we show that oligomeric β3-hexapeptides synthesized from l-aspartic acid monomers (β3-peptides 1, 5a, and 6) or homologated β3-amino acids (β3-peptide 2), fold into similar stable 14-helical secondary structures in solution, except that the former form right-handed 14-helix and the later form left-handed 14-helix. β3-Peptides from l-Asp monomers contain an additional amide bond in the side chains that provides opportunities for more hydrogen bonding. However, based on the NMR solution structures, we found that β3-peptide from l-Asp monomers ( 1) and from homologated amino acids ( 2) form similar structures with no additional side-chain interactions. These results suggest that the β3-peptides derived from l-Asp are promising peptide-mimetics that can be readily synthesized using l-Asp monomers as well as the right-handed 14-helical conformation of these β3-peptides (such as 1 and 6) may prove beneficial in the design of mimics for right-handed α-helix of α-peptides. © 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 102: 359-367, 2014. [ABSTRACT FROM AUTHOR]

Abstract: β-Peptides made from L-aspartic acid monomers form a new class of β3-peptides. Here we report the first three-dimensional NMR solution structure of a β3-hexapeptide (1) from L-aspartic acid monomers in 2,2,2-trifluoroethanol (TFE). We show that 1 forms a right-handed 14-helical structure in TFE. α-peptides from naturally occurring L-amino acids adopt a right-handed α-helix whereas β3-peptides formed from β3-amino acids derived from naturally occurring L-amino acids form left-handed 14-helices. The right-handed 14-helical conformation of 1 is a better mimic of α-peptide conformations. Using the NMR structure of 1 in TFE, we further study the conformation of 1 in water, as well as two similar β3-peptides (2 and 3) in water and TFE by molecular dynamics (MD) simulations. NMR and MD results suggest loss of secondary structure of 1 in water and show that it forms a fully extended structure. 2 and 3 contain residues with oppositely charged side chains that engage in salt-bridge interactions and dramatically stabilize the 14-helical conformation in aqueous media. [Copyright &y& Elsevier]

The dimerization of anti-apoptotic BCL-XL by three-dimensional domain swapping has recently been discovered at alkaline pH; however, the high energetic barrier between the dimer and monomer forms of BCL-XL prevents them from interconverting at room temperature and neutral pH. Here, we demonstrate that BCL-XL dimers can be easily prepared by heating concentrated protein above 50 °C. The 38 κDa BCL-XL dimer was fully characterized by multi-resonance nuclear magnetic resonance (NMR) spectroscopy, and the mechanism of dimerization by α-helix swapping was confirmed. Dimerization strongly affects the NMR signals from the turn between helices α5 and α6 of BCL-XL and a portion of the long loop between helices α1 and α2. Measurements of residual dipolar couplings demonstrate that the solution structure of the BCL-XL dimer is very close to the crystal structure. Dimer formation does not prevent tight binding of ligands to the hydrophobic cleft of BCL-xL; however, binding of a BID BH3—peptide or a polyphenol drug, gossypol, to BCL-XL significantly slowed monomer—dimer interconversion and is an example of the control of BCL protein oligomerization by ligand binding. [ABSTRACT FROM AUTHOR]

Bacteriocins produced by lactic acid bacteria are potent antimicrobial compounds which are active against closely related bacteria. Producer strains are protected against the effects of their cognate bacteriocins by immunity proteins that are located on the same genetic locus and are coexpressed with the gene encoding the bacteriocin. Several structures are available for class IIa bacteriocins; however, to date, no structures are available for the corresponding immunity proteins. We report here the NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2). ImB2 folds into a globular domain in aqueous solution which contains an antiparallel four-helix bundle. Extensive packing by hydrophobic side chains in adjacent helices forms the core of the protein. The C-terminus, containing a fifth helix and an extended strand, is held against the four-helix bundle by hydrophobic interactions with helices 3 and 4. Most of the charged and polar residues in the protein face the solvent. Helix 3 is well-defined to residue 55, and a stretch of nascent helix followed by an unstructured loop joins it to helix 4. No interaction is observed between ImB2 and either carnobacteriocin B2 (CbnB2) or its precursor. Protection from the action of CbnB2 is only observed when ImB2 is expressed within the cell. The loop between helices 3 and 4, and a hydrophobic pocket which it partially masks, may be important for interaction with membrane receptors responsible for sensitivity to class IIa bacteriocins. [ABSTRACT FROM AUTHOR]

Protein disulfide isomerase (PDI) participates in protein folding and catalyses formation of disulfide bonds. The b′ domain of human PDI contributes to binding unfolded proteins; its structure is stabilized by the b domain. Here, we report NMR chemical shift assignments for the bb′ fragment. [ABSTRACT FROM AUTHOR]