A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil

Oakley, Martha G.; Kim, Peter

doi:10.1021/bi981269m

Cited by 183 publications

(202 citation statements)

References 40 publications

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“…These a and d positions are oriented on one side of an alpha helix and, by interacting with the a and d residues of a second alpha helix, form a hydrophobic core that stabilizes the coiled coil. In experiments performed with synthetic coiled coils, introduction of a single polar amino acid within the hydrophobic core can be tolerated and, in fact, influences the orientation assumed by the coiled coil (15,24). We reasoned that introduction of Cys residues within the hydrophobic core of the delta antigen coiled coil may similarly be tolerated, and therefore we individually substituted Cys residues at all a and d positions throughout the delta antigen coiled coil.…”

Section: Resultsmentioning

confidence: 99%

Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

Cornillez-Ty

Lazinski

2003

J Virol

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Hepatitis delta virus expresses two essential proteins, the small and large delta antigens, and both are required for viral propagation. Proper function of each protein depends on the presence of a common amino-terminal multimerization domain. A crystal structure, solved using a peptide fragment that contained residues 12 to 60, depicts the formation of an octameric ring composed of antiparallel coiled-coil dimers. Because this crystal structure was solved for only a fragment of the delta antigens, it is unknown whether octamers actually form in vivo at physiological protein concentrations and in the context of either intact delta antigen. To test the relevance of the octameric structure, we developed a new method to probe coiled-coil structures in vivo. We generated a panel of mutants containing cysteine substitutions at strategic locations within the predicted monomer-monomer interface and the dimer-dimer interface. Since the small delta antigen contains no cysteine residues, treatment of cell extracts with a mild oxidizing reagent was expected to induce disulfide bond formation only when the appropriate pairs of cysteine substitution mutants were coexpressed. We indeed found that, in vivo, both the small and large delta antigens assembled as antiparallel coiled-coil dimers. Likewise, we found that both proteins could assume an octameric quaternary structure in vivo. Finally, during the course of these experiments, we found that unprenylated large delta antigen molecules could be disulfide cross-linked via the sole cysteine residue located within the carboxy terminus. Therefore, in vivo, the C terminus likely provides an additional site of protein-protein interaction for the large delta antigen.

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Section: Resultsmentioning

confidence: 99%

Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

Cornillez-Ty

Lazinski

2003

J Virol

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“…The ground-breaking work of DeGrado and coworkers (17)(18)(19)(20) has led to the development of well packed helix bundle proteins with natural-like sequences and stabilizing interactions. In their work, and pioneering work from other laboratories, a specific fold has been achieved via the formation of tertiary hydrogen bonds (20)(21)(22)(23), crystal contacts (18,24), disulfide bonds (25,26) or favorable charge-charge interactions (19,20,23,24,26,27). Previous work toward simplifying proteins has shown that a native-like Src homology 3 fold can be achieved with chiefly five different residues (although 13 in total) (28), and a four-helix bundle protein can be formed from only nine different residues (29).…”

Section: The Presence Of An Aromatic Ring At the C Terminus Is Requirmentioning

confidence: 99%

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Osa

Bateman

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

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Can unique protein structures arise from a limited set of amino acids present on the prebiotic Earth? To address this question, we have determined the stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala. NMR methods reveal that KIA7 tetramerizes and folds on the millisecond time scale to adopt a four-helix X-bundle structure with a tightly and specifically packed core. Denaturation studies and hydrogen exchange measurements of KIA7 and several variants demonstrate that ridges-into-grooves packing of Ala and Ile side chains and the packing of a C-terminal aromatic group into the hydrophobic core are sufficient to give rise to a rather stable, well folded protein structure, with no favorable electrostatic interactions or tertiary or quaternary hydrogen bonds. Both modern proteins and RNAs can adopt specific structures, but RNAs do so with a limited ''alphabet'' of residues and types of stabilizing interactions. The results reported here show that specific, well folded protein structures can also arise from a highly reduced set of stabilizing interactions and amino acids that are thought to have been present on the prebiotic Earth.four-helix bundle ͉ NMR spectroscopy ͉ protein stability ͉ chemical evolution ͉ protein folding I n the prebiotic Earth, hydrophobic and charged amino acids were thought to have been rather common, whereas polar amino acids were rare (1, 2). Could such a limited set of amino acids have given rise to unique well folded proteins? To gain insight into this question, we have studied the conformational stability and structure of KIA7, a 20-residue polypeptide containing chiefly Lys, Ile, and Ala, plus a -Gly-Gly-Tyr extension for concentration determination, which self-associates to form a well packed, four-helix bundle protein.KIA7 was previously identified from a combinatorial peptide library as having a highly helical structure (as gauged by CD), a well packed hydrophobic core (1-anilino-8-naphthalene sulfonate fluorescence), and a specific tetrameric quaternary structure (analytical ultracentrifugation) (3, 4). The positively charged lysine side chains prevent the formation of higherordered oligomers. Because no tertiary hydrogen bonds, higherorder oligomerization or crystal packing interactions, or favorable electrostatic interactions are present in KIA7, this study constitutes a test of whether or not a specific, unique structure can arise from a highly limited set of stabilizing interactions, namely, the hydrophobic effect and van der Waals interactions.In addition to KIA7, two other members of the KIA series of peptides, KIA5 and KIA10, were studied (Table 1). These peptides are variants of the KIA7 sequence and possess lesser degrees of ordered structure (3). A stabilized KIA7 variant with a disulfide cross-link, CG 3 KIA7, was also examined, and additional peptides truncating the -Gly-Gly-Tyr C-terminal extension, KIA7⌬, or carrying Tyr to Phe, KIA7F, or Tyr to Ile, KIA7I, substitutions were studied to probe the possible stabilizing or struc...

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“…The hydrophobic effect drives the burial of nonpolar residues at the helix-pairing interface and influences geometric details of resulting structures (4). Electrostatic and polar residues at buried or solvent-exposed locations provide additional means to manipulate structural features by stabilization or destabilization (negative design) of key interactions (5)(6)(7)(8).…”

mentioning

confidence: 99%

Toward the development of peptide nanofilaments and nanoropes as smart materials

Wagner

Phillips

Ali

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

118

117

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Protein design studies using coiled coils have illustrated the potential of engineering simple peptides to self-associate into polymers and networks. Although basic aspects of self-assembly in protein systems have been demonstrated, it remains a major challenge to create materials whose large-scale structures are well determined from design of local protein-protein interactions. Here, we show the design and characterization of a helical peptide, which uses phased hydrophobic interactions to drive assembly into nanofilaments and fibrils (''nanoropes''). Using the hydrophobic effect to drive self-assembly circumvents problems of uncontrolled self-assembly seen in previous approaches that used electrostatics as a mode for self-assembly. The nanostructures designed here are characterized by biophysical methods including analytical ultracentrifugation, dynamic light scattering, and circular dichroism to measure their solution properties, and atomic force microscopy to study their behavior on surfaces. Additionally, the assembly of such structures can be predictably regulated by using various environmental factors, such as pH, salt, other molecular crowding reagents, and specifically designed ''capping'' peptides. This ability to regulate self-assembly is a critical feature in creating smart peptide biomaterials.biomaterial ͉ coiled coil ͉ protein design ͉ circular dichroism ͉ atomic force microscopy D esigned proteins are valuable paradigms for engineering at the nanoscale, offering favorable properties such as atomiclevel precision and tight regulation of self-assembly by using a variety of environmental cues (i.e., pH, ionic strength, temperature) (1-3). As one of the most well studied and naturally abundant structural motifs in proteins, coiled coils are particularly suited to protein design. Their basic sequence feature, the heptad repeat, is a seven-residue pattern (abcdefg) n of nonpolar and polar residues that gives rise to amphipathic ␣-helices. The hydrophobic effect drives the burial of nonpolar residues at the helix-pairing interface and influences geometric details of resulting structures (4). Electrostatic and polar residues at buried or solvent-exposed locations provide additional means to manipulate structural features by stabilization or destabilization (negative design) of key interactions (5-8).Recent attempts to design self-assembling protein networks by using coiled coils have focused on simple systems, such as linear and branched fibrils (9-14), planar assemblies (15), and hydrogels (16-18). Specifically, filament formation has been achieved by stabilization of intermediate structures that foster intermolecular coiled-coil interactions (11)(12)(13)(14). Previous studies have reported the design of short helical peptides, which interact via a dimeric coiled-coil motif and are stabilized by a combination of overlapping hydrophobic and electrostatic intermolecular interactions (9, 13, 14). These peptides do indeed self-assemble into filaments; however, these filaments also show evidence of extensive...

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A Buried Polar Interaction Can Direct the Relative Orientation of Helices in a Coiled Coil

Cited by 183 publications

References 40 publications

Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

Determination of the Multimerization State of the Hepatitis Delta Virus Antigens In Vivo

Getting specificity from simplicity in putative proteins from the prebiotic Earth

Toward the development of peptide nanofilaments and nanoropes as smart materials

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