Structure, stability and folding of the α-helix

Doig, Andrew J.; Andrew, Charles D.; Cochran, Duncan A. E.; Hughes, Eleri; Penel, Simon; Sun, Jun; Stapley, Benjamin J.; Clarke, David T.; Jones, Gareth R.

doi:10.1042/bss0680095

Cited by 10 publications

(7 citation statements)

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“…The 116 residue HIV-Rev protein binds to RNA with Kd approximately 1 nM (28). Nociceptin (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) is an agonist at only nM concentrations (25). We also found the helix-constrained compounds to be more stable in human serum than their linear analogues, the latter being typically degraded within 1 h whereas the constrained peptides were stable for >24 h, except for the exocyclic residues, which were cleaved by proteases over several hours.…”

Section: Discussionmentioning

confidence: 79%

“…This relatively low helicity for mimetic 26 versus mimetics 20, 22, and 24 is attributed to the unstructured "triggering" message domain at the N-terminus, as well as accumulation of positive charges on one helix face. Nevertheless, the induction of at least some helix structure in this peptide suggested that it should be more active than nociceptin (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). Function was investigated by nociceptin(1-17) induced intracellular ERK phosphorylation in mouse Neuro-2a neuroblastoma cells (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Downsizing human, bacterial, and viral proteins to short water-stable alpha helices that maintain biological potency

Harrison

Shepherd²,

Hoang³

et al. 2010

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

168

166

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Recombinant proteins are important therapeutics due to potent, highly specific, and nontoxic actions in vivo. However, they are expensive medicines to manufacture, chemically unstable, and difficult to administer with low patient uptake and compliance. Small molecule drugs are cheaper and more bioavailable, but less target-specific in vivo and often have associated side effects. Here we combine some advantages of proteins and small molecules by taking short amino acid sequences that confer potency and selectivity to proteins, and fixing them as small constrained molecules that are chemically and structurally stable and easy to make. Proteins often use short α-helices of just 1-4 helical turns (4-15 amino acids) to interact with biological targets, but peptides this short usually have negligible α-helicity in water. Here we show that short peptides, corresponding to helical epitopes from viral, bacterial, or human proteins, can be strategically fixed in highly α-helical structures in water. These helix-constrained compounds have similar biological potencies as proteins that bear the same helical sequences. Examples are (i) a picomolar inhibitor of Respiratory Syncytial Virus F protein mediated fusion with host cells, (ii) a nanomolar inhibitor of RNA binding to the transporter protein HIV-Rev, (iii) a submicromolar inhibitor of Streptococcus pneumoniae growth induced by quorum sensing pheromone Competence Stimulating Peptide, and (iv) a picomolar agonist of the GPCR pain receptor opioid receptor like receptor ORL-1. This approach can be generally applicable to downsizing helical regions of proteins with broad applications to biology and medicine.helix | inhibitor | structure | mimetic | anti-infective P roteins are key functional components that define life, aging, disease, and death. Their uses in medicine, science, and industry are however limited by their complexity, high costs, chemical instability, and low bioavailability. Consequently, new chemical technology is needed to create simpler, smaller, cheaper, more stable, and bioavailable molecules that can execute or inhibit selected functions of proteins. If generic approaches could be developed to stabilize or recreate new molecular shapes that mimic structural components of proteins (e.g., helices, turns, strands, and combinations), the resulting molecules could potentially be extremely valuable for interrogating biological systems and for exploring prospective applications such as new pharmaceuticals, diagnostics, vaccines, and nanomaterials.Some proteins elicit biological function through a single short α-helical segment (usually 4-15 amino acids in 1-4 helical turns) that interacts with nucleic acids or proteins (1-3). However, short synthetic peptides of this length are usually not thermodynamically stable helices in water and adopt only random structures (4). Techniques developed as generalized strategies for stabilising or mimicking short peptide α-helices have been limited by lack of helical structure in water, by sequence or context dependent helici...

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Section: Discussionmentioning

confidence: 79%

Section: Resultsmentioning

confidence: 99%

Downsizing human, bacterial, and viral proteins to short water-stable alpha helices that maintain biological potency

Harrison

Shepherd²,

Hoang³

et al. 2010

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

168

166

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“…SRCD is especially suited for this type of experiment as it requires only small amounts of material for stopped-flow and kinetic studies, and its sensitivity means it has the potential for making single wavelength measurements over the very short time periods compatible with protein folding processes. 9 However, the ability to detect a whole spectrum simultaneously (using white light) instead of monitoring at single wavelengths will obviously make this an even more exciting tool for investigating protein folding or fast kinetic reactions. Developments in detector technology should make this possible.…”

Section: Technical Developmentsmentioning

confidence: 99%

Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics

2006

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The technique of Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy and its advantages over conventional circular dichroism spectroscopy are described in this tutorial review, as well as recent applications of the technique in structural and functional genomics. Circular dichroism (CD) spectroscopy is a well-established method in biological chemistry and structural biology, but its utility can be limited by the low flux of the light source in the far ultraviolet and vacuum ultraviolet wavelength regions in conventional CD instruments. The development of synchrotron radiation circular dichroism (SRCD), using the intense light of a synchrotron beam, has greatly expanded the utility of the method, especially as a tool for both structural and functional genomics. These applications take advantage of the enhanced features of SRCD relative to conventional CD: the ability to measure lower wavelength data containing more electronic transitions and hence more structural information, the higher signal-to-noise hence requiring smaller samples, the higher intensity enabling measurements in absorbing buffers and in the presence of lipids and detergents, and the ability to do faster measurements enabling high throughput and time-resolved spectroscopy.This article discusses recent developments in SRCD instrumentation, software, sample preparation and methods of analyses, with particular emphasis on their applications to the study of proteins. These advances have led to new applications in structural genomics (SG), including the potential for fold recognition as a means of target selection and the examination of membrane proteins, a class of proteins usually excluded from SG programmes. Other SG uses include detection of macromolecular interactions as a screen for complex formation, and examination of glycoproteins and sugar components. In functional genomics (FG) new applications include screening for ligand binding as a means of identifying function, and examination of structural differences in mutant proteins as a means of gaining insight into function.

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“…The first turn of the α‐helix was also analyzed and good N 2 amino acids such as Gln, Glu, Asp, Asn, Ser, Thr and His were found to hydrogen bond to the back bone of the helix [16]. Recent studies have also shown that different helical positions such as N 1 and N 2 have special effect on α‐helix stability [17–19].…”

Section: Introductionmentioning

confidence: 99%

Exceptional pairs of amino acid neighbors in α‐helices

Goliaei¹,

Minuchehr²

2003

FEBS Letters

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Amino acids seem to have speci¢c preferences for various locations in K K-helices. These speci¢c preferences, called singlet local propensity (SLP), have been determined by calculating the preference of occurrence of each amino acid in di¡er-ent positions of the K K-helix. We have studied the occurrence of amino acids, single or pairs, in di¡erent positions, singlet or doublet, of K K-helices in a database of 343 non-homologous proteins representing a unique superfamily from the SCOP database with a resolution better than 2.5 A î from the Protein Data Bank. The preference of single amino acids for various locations of the helix was shown by the relative entropy of each amino acid with respect to the background. Based on the total relative entropy of all amino acids occurring in a single position, the N cap position was found to be the most selective position in the K K-helix. A rigorous statistical analysis of amino acid pair occurrences showed that there are exceptional pairs for which, the observed frequency of occurrence in various doublet positions of the K K-helix is signi¢cantly di¡erent from the expected frequency of occurrence in that position. The doublet local propensity (DLP) was de¢ned as the preference of occurrences of amino acid pairs in di¡erent doublet positions of the K K-helix. For most amino acid pairs, the observed DLP (DLP O ) was nearly equal to the expected DLP (DLP E ), which is the product of the related SLPs. However, for exceptional pairs of amino acids identi¢ed above, the DLP O and DLP E values were signi¢cantly di¡erent. Based on the relative values of DLP O and DLP E , exceptional amino acid pairs were divided into two categories. Those, for which the DLP O values are higher than DLP E , should have a strong tendency to pair together in the speci¢ed position. For those pairs which the DLP O values are less than DLP E , there exists a hindrance in neighboring of the two amino acids in that speci¢c position of the K K-helix. These cases have been identi¢ed and listed in various tables in this paper. The amount of mutual information carried by the exceptional pairs of amino acids was signi¢cantly higher than the average mutual information carried by other amino acid pairs. The average mutual information conveyed by amino acid pairs in each doublet position was found to be very small but non-zero. ß

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Structure, stability and folding of the α-helix

Cited by 10 publications

References 0 publications

Downsizing human, bacterial, and viral proteins to short water-stable alpha helices that maintain biological potency

Downsizing human, bacterial, and viral proteins to short water-stable alpha helices that maintain biological potency

Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics

Exceptional pairs of amino acid neighbors in α‐helices

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