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Bhatt MR, Ganguly HK, Zondlo NJ. Acyl Capping Group Identity Effects on α-Helicity: On the Importance of Amide·Water Hydrogen Bonds to α-Helix Stability. Biochemistry 2024; 63:1118-1130. [PMID: 38623827 DOI: 10.1021/acs.biochem.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Acyl capping groups stabilize α-helices relative to free N-termini by providing one additional C═Oi···Hi+4-N hydrogen bond. The electronic properties of acyl capping groups might also directly modulate α-helix stability: electron-rich N-terminal acyl groups could stabilize the α-helix by strengthening both i/i + 4 hydrogen bonds and i/i + 1 n → π* interactions. This hypothesis was tested in peptides X-AKAAAAKAAAAKAAGY-NH2, where X = different acyl groups. Surprisingly, the most electron-rich acyl groups (pivaloyl and iso-butyryl) strongly destabilized the α-helix. Moreover, the formyl group induced nearly identical α-helicity to that of the acetyl group, despite being a weaker electron donor for hydrogen bonds and for n → π* interactions. Other acyl groups exhibited intermediate α-helicity. These results indicate that the electronic properties of the acyl carbonyl do not directly determine the α-helicity in peptides in water. In order to understand these effects, DFT calculations were conducted on α-helical peptides. Using implicit solvation, α-helix stability correlated with acyl group electronics, with the pivaloyl group exhibiting closer hydrogen bonds and n → π* interactions, in contrast to the experimental results. However, DFT and MD calculations with explicit water solvation revealed that hydrogen bonding to water was impacted by the sterics of the acyl capping group. Formyl capping groups exhibited the closest water-amide hydrogen bonds, while pivaloyl groups exhibited the longest. In α-helices in the PDB, the highest frequency of close amide-water hydrogen bonds is observed when the N-cap residue is Gly. The combination of experimental and computational results indicates that solvation (hydrogen bonding of water) to the N-terminal amide groups is a central determinant of α-helix stability.
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Affiliation(s)
- Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware Newark, Delaware 19716, United States
| | - Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware Newark, Delaware 19716, United States
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2
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Bhatt MR, Zondlo NJ. Synthesis and conformational preferences of peptides and proteins with cysteine sulfonic acid. Org Biomol Chem 2023; 21:2779-2800. [PMID: 36920119 DOI: 10.1039/d3ob00179b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Cysteine sulfonic acid (Cys-SO3H; cysteic acid) is an oxidative post-translational modification of cysteine, resulting from further oxidation from cysteine sulfinic acid (Cys-SO2H). Cysteine sulfonic acid is considered an irreversible post-translational modification, which serves as a biomarker of oxidative stress that has resulted in oxidative damage to proteins. Cysteine sulfonic acid is anionic, as a sulfonate (Cys-SO3-; cysteate), in the ionization state that is almost exclusively present at physiological pH (pKa ∼ -2). In order to understand protein structural changes that can occur upon oxidation to cysteine sulfonic acid, we analyzed its conformational preferences, using experimental methods, bioinformatics, and DFT-based computational analysis. Cysteine sulfonic acid was incorporated into model peptides for α-helix and polyproline II helix (PPII). Within peptides, oxidation of cysteine to the sulfonic acid proceeds rapidly and efficiently at room temperature in solution with methyltrioxorhenium (MeReO3) and H2O2. Peptides containing cysteine sulfonic acid were also generated on solid phase using trityl-protected cysteine and oxidation with MeReO3 and H2O2. Using methoxybenzyl (Mob)-protected cysteine, solid-phase oxidation with MeReO3 and H2O2 generated the Mob sulfone precursor to Cys-SO2- within fully synthesized peptides. These two solid-phase methods allow the synthesis of peptides containing either Cys-SO3- or Cys-SO2- in a practical manner, with no solution-phase synthesis required. Cys-SO3- had low PPII propensity for PPII propagation, despite promoting a relatively compact conformation in ϕ. In contrast, in a PPII initiation model system, Cys-SO3- promoted PPII relative to neutral Cys, with PPII initiation similar to Cys thiolate but less than Cys-SO2- or Ala. In an α-helix model system, Cys-SO3- promoted α-helix near the N-terminus, due to favorable helix dipole interactions and favorable α-helix capping via a sulfonate-amide side chain-main chain hydrogen bond. Across all peptides, the sulfonate side chain was significantly less ordered than that of the sulfinate. Analysis of Cys-SO3- in the PDB revealed a very strong propensity for local (i/i or i/i + 1) side chain-main chain sulfonate-amide hydrogen bonds for Cys-SO3-, with >80% of Cys-SO3- residues exhibiting these interactions. DFT calculations conducted to explore these conformational preferences indicated that side chain-main chain hydrogen bonds of the sulfonate with the intraresidue amide and/or with the i + 1 amide were favorable. However, hydrogen bonds to water or to amides, as well as interactions with oxophilic metals, were weaker for the sulfonate than the sulfinate, due to lower charge density on the oxygens in the sulfonate.
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Affiliation(s)
- Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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3
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Uncovering Streptomyces-Derived Compounds as Cosmeceuticals for the Development of Improved Skin Photoprotection Products: An In Silico Approach to Explore Multi-Targeted Agents. Sci Pharm 2022. [DOI: 10.3390/scipharm90030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The search for novel photoprotective substances has become a challenge in cosmeceutical research. Streptomyces-derived compounds can serve as a promising source of photoprotective agents to formulate skin photoprotection products, such as sunscreens. This study aimed to identify specialized metabolites with the potential to modulate UV-induced cellular damage in the skin by identifying potential multi-target-directed ligands. Using a combination of ligand- and target-based virtual screening approaches, a public compound library comprising 6524 Streptomyces-derived specialized metabolites was studied for their photoprotective capability. The compounds were initially filtered by safety features and then examined for their ability to interact with key targets in the photodamage pathway by molecular docking. A set of 50 commercially available UV filters was used as the benchmark. The protein–ligand stability of selected Streptomyces-derived compounds was also studied by molecular dynamics (MD) simulations. From the compound library, 1981 compounds were found to meet the safety criteria for topically applied products, such as low skin permeability and low or non-toxicity-alerting substructures. A total of 34 compounds had promising binding scores against crucial targets involved in UV-induced photodamage, such as serotonin-receptor subtype 5-HT2A, platelet-activating factor receptor, IL-1 receptor type 1, epidermal growth factor receptor, and cyclooxygenase-2. Among these compounds, aspergilazine A and phaeochromycin F showed the highest ranked interactions with four of the five targets and triggered complex stabilization over time. Additionally, the predicted UV-absorbing profiles also suggest a UV-filtering effect. Streptomyces is an encouraging biological source of compounds for developing topical products. After in silico protein–ligand interactions, binding mode and stabilization of aspergilazine A and phaeochromycin F led to the discovery of potential candidates as photodamage multi-target inhibitors. Therefore, they can be further explored for the formulation of skin photoprotection products.
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4
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Urmey AR, Zondlo NJ. Structural preferences of cysteine sulfinic acid: The sulfinate engages in multiple local interactions with the peptide backbone. Free Radic Biol Med 2020; 148:96-107. [PMID: 31883974 DOI: 10.1016/j.freeradbiomed.2019.12.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/16/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023]
Abstract
Cysteine sulfinic acid (Cys-SO2-) is a non-enzymatic oxidative post-translational modification (PTM) that has been identified in hundreds of proteins. However, the effects of cysteine sulfination are in most cases poorly understood. Cys-SO2- is structurally distinctive, with long sulfur-carbon and sulfur-oxygen bonds, and with tetrahedral geometry around sulfur due to its lone pair. Cys-SO2- thus has a unique range of potential interactions with the protein backbone which could facilitate protein structural changes. Herein, the structural effects of cysteine oxidation to the sulfinic acid were investigated in model peptides and folded proteins using NMR spectroscopy, circular dichroism, bioinformatics, and computational studies. In the PDB, Cys-SO2- shows a greater preference for α-helix than Cys. In addition, Cys-SO2- is more commonly found in structures with φ > 0, including in multiple types of β-turn. Sulfinate oxygens engage in hydrogen bonds with adjacent (i or i + 1) amide hydrogens. Over half of sulfinates have at least one hydrogen bond with an adjacent amide, and several structures have hydrogen bonds with both adjacent amides. Alternately, sulfur or either oxygen can act as an electron donor for n→π* interactions with the backbone carbonyl of the same residue, as indicated by frequent S⋯CO or O⋯CO distances below the sums of their van der Waals radii in protein structures. In peptides, Cys-SO2- favored α-helical structure at the N-terminus, consistent with helix dipole effects and backbone hydrogen bonds with the sulfinate promoting α-helix. Cys-SO2- has only modestly greater polyproline II helix propensity than Cys-SH, likely due to competition from multiple side chain-backbone interactions. Cys-SO2- stabilizes the i+1 position of a β-turn relative to Cys-SH. Within proteins, the range of side chain-main chain interactions available to Cys-SO2- compared to Cys-SH provides a basis for potential changes in protein structure and function due to cysteine oxidation to the sulfinic acid.
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Affiliation(s)
- Andrew R Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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5
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Huang Y, Soliakov A, Le Brun AP, Macdonald C, Johnson CL, Solovyova AS, Waller H, Moore GR, Lakey JH. Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A. Biochemistry 2019; 58:4882-4892. [PMID: 31686499 PMCID: PMC6899464 DOI: 10.1021/acs.biochem.9b00705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/31/2019] [Indexed: 11/28/2022]
Abstract
Numerous bacterial toxins and other virulence factors use low pH as a trigger to convert from water-soluble to membrane-inserted states. In the case of colicins, the pore-forming domain of colicin A (ColA-P) has been shown both to undergo a clear acidic unfolding transition and to require acidic lipids in the cytoplasmic membrane, whereas its close homologue colicin N shows neither behavior. Compared to that of ColN-P, the ColA-P primary structure reveals the replacement of several uncharged residues with aspartyl residues, which upon replacement with alanine induce an unfolded state at neutral pH. Here we investigate ColA-P's structural requirement for these critical aspartyl residues that are largely situated at the N-termini of α helices. As previously shown in model peptides, the charged carboxylate side chain can act as a stabilizing helix N-Cap group by interacting with free amide hydrogen bond donors. Because this could explain ColA-P destabilization when the aspartyl residues are protonated or replaced with alanyl residues, we test the hypothesis by inserting asparagine, glutamine, and glutamate residues at these sites. We combine urea (fluorescence and circular dichroism) and thermal (circular dichroism and differential scanning calorimetry) denaturation experiments with 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy of ColA-P at different pH values to provide a comprehensive description of the unfolding process and confirm the N-Cap hypothesis. Furthermore, we reveal that, in urea, the single domain ColA-P unfolds in two steps; low pH destabilizes the first step and stabilizes the second.
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Affiliation(s)
- Yan Huang
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- College
of Chemistry and Molecular Sciences, Wuhan
University, Wuhan 430072, People’s Republic of China
| | - Andrei Soliakov
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Anton P. Le Brun
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
- Australian
Centre for Neutron Scattering, Australian
Nuclear Science and Technology Organisation, Kirrawee DC, NSW 2232, Australia
| | - Colin Macdonald
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Christopher L. Johnson
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Alexandra S. Solovyova
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Helen Waller
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
| | - Geoffrey R. Moore
- Department
of Chemistry Centre for Structural & Molecular Biology, School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Jeremy H. Lakey
- Institute
for Cell and Molecular Biosciences, The Medical School, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4HH, U.K.
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6
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7
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Crooks RO, Lathbridge A, Panek AS, Mason JM. Computational Prediction and Design for Creating Iteratively Larger Heterospecific Coiled Coil Sets. Biochemistry 2017; 56:1573-1584. [PMID: 28267310 DOI: 10.1021/acs.biochem.7b00047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A major biochemical goal is the ability to mimic nature in engineering highly specific protein-protein interactions (PPIs). We previously devised a computational interactome screen to identify eight peptides that form four heterospecific dimers despite 32 potential off-targets. To expand the speed and utility of our approach and the PPI toolkit, we have developed new software to derive much larger heterospecific sets (≥24 peptides) while directing against antiparallel off-targets. It works by predicting Tm values for every dimer on the basis of core, electrostatic, and helical propensity components. These guide interaction specificity, allowing heterospecific coiled coil (CC) sets to be incrementally assembled. Prediction accuracy is experimentally validated using circular dichroism and size exclusion chromatography. Thermal denaturation data from a 22-CC training set were used to improve software prediction accuracy and verified using a 136-CC test set consisting of eight predicted heterospecific dimers and 128 off-targets. The resulting software, qCIPA, individually now weighs core a-a' (II/NN/NI) and electrostatic g-e'+1 (EE/EK/KK) components. The expanded data set has resulted in emerging sequence context rules for otherwise energetically equivalent CCs; for example, introducing intrahelical electrostatic charge blocks generated increased stability for designed CCs while concomitantly decreasing the stability of off-target CCs. Coupled with increased prediction accuracy and speed, the approach can be applied to a wide range of downstream chemical and synthetic biology applications, in addition more generally to impose specificity on structurally unrelated PPIs.
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Affiliation(s)
- Richard O Crooks
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Alexander Lathbridge
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Anna S Panek
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
| | - Jody M Mason
- Department of Biology and Biochemistry, University of Bath , Claverton Down, Bath BA2 7AY, U.K
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8
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Fukuda Y, Cheong PL, Lynch J, Brighton C, Frase S, Kargas V, Rampersaud E, Wang Y, Sankaran VG, Yu B, Ney PA, Weiss MJ, Vogel P, Bond PJ, Ford RC, Trent RJ, Schuetz JD. The severity of hereditary porphyria is modulated by the porphyrin exporter and Lan antigen ABCB6. Nat Commun 2016; 7:12353. [PMID: 27507172 PMCID: PMC4987512 DOI: 10.1038/ncomms12353] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/23/2016] [Indexed: 01/10/2023] Open
Abstract
Hereditary porphyrias are caused by mutations in genes that encode haem biosynthetic enzymes with resultant buildup of cytotoxic metabolic porphyrin intermediates. A long-standing open question is why the same causal porphyria mutations exhibit widely variable penetrance and expressivity in different individuals. Here we show that severely affected porphyria patients harbour variant alleles in the ABCB6 gene, also known as Lan, which encodes an ATP-binding cassette (ABC) transporter. Plasma membrane ABCB6 exports a variety of disease-related porphyrins. Functional studies show that most of these ABCB6 variants are expressed poorly and/or have impaired function. Accordingly, homozygous disruption of the Abcb6 gene in mice exacerbates porphyria phenotypes in the Fechm1Pas mouse model, as evidenced by increased porphyrin accumulation, and marked liver injury. Collectively, these studies support ABCB6 role as a genetic modifier of porphyria and suggest that porphyrin-inducing drugs may produce excessive toxicities in individuals with the rare Lan(−) blood type. Accumulation of intermediates of haem biosynthesis, porphyrins, is harmful and usually inherited, but it is unclear how the same mutation may make some individuals more ill than others. Here, the authors show that a porphyrin transporter ABCB6 is a modulator of porphyria, and that patients with functionally defective ABCB6 show more severe symptoms.
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Affiliation(s)
- Yu Fukuda
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Pak Leng Cheong
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John Lynch
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Cheryl Brighton
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Sharon Frase
- Department of Tissue Cell Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Vasileios Kargas
- Department of Structural Biology, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Evadnie Rampersaud
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA.,Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Yao Wang
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Bing Yu
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Paul A Ney
- New York Blood Center, New York, New York 10065, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Peter Vogel
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Peter J Bond
- Bioinformatics Institute, 30 Biopolis Street, Singapore 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Robert C Ford
- Department of Structural Biology, Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Ronald J Trent
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, New South Wales 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - John D Schuetz
- Department of Pharmaceutical Sciences, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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Dannenberg JJ. The importance of cooperative interactions and a solid-state paradigm to proteins: what Peptide chemists can learn from molecular crystals. ACTA ACUST UNITED AC 2016; 72:227-73. [PMID: 16581379 DOI: 10.1016/s0065-3233(05)72009-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Proteins and peptides in solution or in vivo share properties with both liquids and solids. More often than not, they are studied using the liquid paradigm rather than that of a solid. Studies of molecular crystals illustrate how the use of a solid paradigm may change the way that we consider these important molecules. Cooperative interactions, particularly those involving H-bonding, play much more important roles in the solid than in the liquid paradigms, as molecular crystals clearly illustrate. Using the solid rather than the liquid paradigm for proteins and peptides includes these cooperative interactions while application of the liquid paradigm tends to ignore or minimize them. Use of the solid paradigm has important implications for basic principles that are often implied about peptide and protein chemistry, such as the importance of entropy in protein folding and the nature of the hydrophobic effect. Understanding the folded states of peptides and proteins (especially alpha-helices) often requires the solid paradigm, whereas understanding unfolded states does not. Both theoretical and experimental studies of the energetics of protein and peptide folding require comparison to a suitable standard. Our perspective on these energetics depends on the reasonable choice of reference. The use of multiple reference states, particularly that of component amino acids in the gas phase, is proposed.
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Affiliation(s)
- J J Dannenberg
- Department of Chemistry, City University of New York, Hunter College and the Graduate School New York, New York 10021
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10
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Deriving Heterospecific Self-Assembling Protein-Protein Interactions Using a Computational Interactome Screen. J Mol Biol 2015; 428:385-398. [PMID: 26655848 PMCID: PMC4751974 DOI: 10.1016/j.jmb.2015.11.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 11/13/2015] [Accepted: 11/19/2015] [Indexed: 11/21/2022]
Abstract
Interactions between naturally occurring proteins are highly specific, with protein-network imbalances associated with numerous diseases. For designed protein–protein interactions (PPIs), required specificity can be notoriously difficult to engineer. To accelerate this process, we have derived peptides that form heterospecific PPIs when combined. This is achieved using software that generates large virtual libraries of peptide sequences and searches within the resulting interactome for preferentially interacting peptides. To demonstrate feasibility, we have (i) generated 1536 peptide sequences based on the parallel dimeric coiled-coil motif and varied residues known to be important for stability and specificity, (ii) screened the 1,180,416 member interactome for predicted Tm values and (iii) used predicted Tm cutoff points to isolate eight peptides that form four heterospecific PPIs when combined. This required that all 32 hypothetical off-target interactions within the eight-peptide interactome be disfavoured and that the four desired interactions pair correctly. Lastly, we have verified the approach by characterising all 36 pairs within the interactome. In analysing the output, we hypothesised that several sequences are capable of adopting antiparallel orientations. We subsequently improved the software by removing sequences where doing so led to fully complementary electrostatic pairings. Our approach can be used to derive increasingly large and therefore complex sets of heterospecific PPIs with a wide range of potential downstream applications from disease modulation to the design of biomaterials and peptides in synthetic biology. Naturally occurring protein–protein interactions (PPIs) are highly specific. For designed PPIs, however, specificity can be notoriously difficult to engineer. We have computationally screened a vast interactome to derive four heterospecific PPIs. Eight peptides form four heterospecific coiled coils; all 32 off targets are disfavoured. The method can derive larger and increasingly complex sets of heterospecific PPIs
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11
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Abstract
Background Interactions that involve one or more amino acid side chains near the ends of protein helices stabilize helix termini and shape the geometry of the adjacent loops, making a substantial contribution to overall protein structure. Previous work has identified key helix-terminal motifs, such as Asx/ST N-caps, the capping box, and hydrophobic and electrostatic interactions, but important questions remain, including: 1) What loop backbone geometries are favoured by each motif? 2) To what extent are multi-amino acid motifs likely to represent genuine cooperative interactions? 3) Can new motifs be identified in a large, recent dataset using the latest bioinformatics tools? Results Three analytical tools are applied here to answer these questions. First, helix-terminal structures are partitioned by loop backbone geometry using a new 3D clustering algorithm. Next, Cascade Detection, a motif detection algorithm recently published by the author, is applied to each cluster to determine which sequence motifs are overrepresented in each geometry. Finally, the results for each motif are presented in a CapMap, a 3D conformational heatmap that displays the distribution of the motif’s overrepresentation across loop geometries, enabling the rapid isolation and characterization of the associated side chain interaction. This work identifies a library of geometry-specific side chain interactions that provides a new, detailed picture of loop structure near the helix terminus. Highlights include determinations of the favoured loop geometries for the Asx/ST N-cap motifs, capping boxes, “big” boxes, and other hydrophobic, electrostatic, H-bond, and pi stacking interactions, many of which have not been described before. Conclusions This work demonstrates that the combination of structural clustering and motif detection in the sequence space can efficiently identify side chain motifs and map them to the loop geometries which they support. Protein designers should find this study useful, because it identifies side chain interactions which are good candidates for inclusion in synthetic helix-terminal loops with specific desired geometries, since they are used in nature to support these geometries. The techniques described here can also be applied to map side chain interactions associated with other structural components of proteins such as beta and gamma turns. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0671-4) contains supplementary material, which is available to authorized users.
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12
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Baker EG, Bartlett GJ, Crump MP, Sessions RB, Linden N, Faul CFJ, Woolfson DN. Local and macroscopic electrostatic interactions in single α-helices. Nat Chem Biol 2015; 11:221-8. [PMID: 25664692 PMCID: PMC4668598 DOI: 10.1038/nchembio.1739] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/01/2014] [Indexed: 11/09/2022]
Abstract
The noncovalent forces that stabilize protein structures are not fully understood. One way to address this is to study equilibria between unfolded states and α-helices in peptides. Electrostatic forces-which include interactions between side chains, the backbone and side chains, and side chains and the helix macrodipole-are believed to contribute to these equilibria. Here we probe these interactions experimentally using designed peptides. We find that both terminal backbone-side chain and certain side chain-side chain interactions (which include both local effects between proximal charges and interatomic contacts) contribute much more to helix stability than side chain-helix macrodipole electrostatics, which are believed to operate at larger distances. This has implications for current descriptions of helix stability, the understanding of protein folding and the refinement of force fields for biomolecular modeling and simulations. In addition, this study sheds light on the stability of rod-like structures formed by single α-helices, which are common in natural proteins such as non-muscle myosins.
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Affiliation(s)
- Emily G. Baker
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Richard B. Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Noah Linden
- School of Mathematics, University of Bristol, University Walk, Bristol, BS8 1TW, UK
| | - Charl F. J. Faul
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
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13
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Effect of external pulling forces on the length distribution of peptides. Biochim Biophys Acta Gen Subj 2014; 1850:903-910. [PMID: 25261776 DOI: 10.1016/j.bbagen.2014.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 11/20/2022]
Abstract
BACKGROUND The distribution of the length of a polypeptide, or that of the distance between any two of its atoms, is an important property as it can be analytically or numerically estimated for a number of polymer models. Importantly, it is directly measurable through a number of different experimental techniques. Length distributions can be straightforwardly assessed from molecular dynamics simulation; however, true convergence through full accurate coverage of the length range is difficult to achieve. METHODS The application of external constant force combined with the weighted-histogram analysis method (WHAM) is used to enhance sampling of unlikely 'long' or 'short' conformations and obtain the potential of mean force, while also collecting dynamic properties of the chain under variable tension. RESULTS We demonstrate the utility of constant force to enhance the sampling efficiency and obtain experimentally measurable quantities on a series of short peptides, including charge-rich sequences that are known to be highly helical but whose properties are distinct from those of helical peptides undergoing helix-coil transitions. CONCLUSIONS Force-enhanced sampling enhances the range and accuracy of the length-based potential of mean force of the peptide, in particular those sequences that contain increased numbers of charged residues. GENERAL SIGNIFICANCE This approach allows users to simultaneously probe the force-dependent behaviour of peptides directly, enhance the range and accuracy of the length-based PMF of the peptide and also test the convergence of simulations by comparing the overlap of PMF profiles from different constant forces. This article is part of a special issue entitled Recent developments of molecular dynamics.
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Rosenlöw J, Isaksson L, Mayzel M, Lengqvist J, Orekhov VY. Tyrosine phosphorylation within the intrinsically disordered cytosolic domains of the B-cell receptor: an NMR-based structural analysis. PLoS One 2014; 9:e96199. [PMID: 24769851 PMCID: PMC4000212 DOI: 10.1371/journal.pone.0096199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
Intrinsically disordered proteins are found extensively in cell signaling pathways where they often are targets of posttranslational modifications e.g. phosphorylation. Such modifications can sometimes induce or disrupt secondary structure elements present in the modified protein. CD79a and CD79b are membrane-spanning, signal-transducing components of the B-cell receptor. The cytosolic domains of these proteins are intrinsically disordered and each has an immunoreceptor tyrosine-based activation motif (ITAM). When an antigen binds to the receptor, conserved tyrosines located in the ITAMs are phosphorylated which initiate further downstream signaling. Here we use NMR spectroscopy to examine the secondary structure propensity of the cytosolic domains of CD79a and CD79b in vitro before and after phosphorylation. The phosphorylation patterns are identified through analysis of changes of backbone chemical shifts found for the affected tyrosines and neighboring residues. The number of the phosphorylated sites is confirmed by mass spectrometry. The secondary structure propensities are calculated using the method of intrinsic referencing, where the reference random coil chemical shifts are measured for the same protein under denaturing conditions. Our analysis revealed that CD79a and CD79b both have an overall propensity for α-helical structure that is greatest in the C-terminal region of the ITAM. Phosphorylation of CD79a caused a decrease in helical propensity in the C-terminal ITAM region. For CD79b, the opposite was observed and phosphorylation resulted in an increase of helical propensity in the C-terminal part.
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Affiliation(s)
- Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Gothenburg, Sweden
| | - Johan Lengqvist
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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15
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Effects of side chains in helix nucleation differ from helix propagation. Proc Natl Acad Sci U S A 2014; 111:6636-41. [PMID: 24753597 DOI: 10.1073/pnas.1322833111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Helix-coil transition theory connects observable properties of the α-helix to an ensemble of microstates and provides a foundation for analyzing secondary structure formation in proteins. Classical models account for cooperative helix formation in terms of an energetically demanding nucleation event (described by the σ constant) followed by a more facile propagation reaction, with corresponding s constants that are sequence dependent. Extensive studies of folding and unfolding in model peptides have led to the determination of the propagation constants for amino acids. However, the role of individual side chains in helix nucleation has not been separately accessible, so the σ constant is treated as independent of sequence. We describe here a synthetic model that allows the assessment of the role of individual amino acids in helix nucleation. Studies with this model lead to the surprising conclusion that widely accepted scales of helical propensity are not predictive of helix nucleation. Residues known to be helix stabilizers or breakers in propagation have only a tenuous relationship to residues that favor or disfavor helix nucleation.
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16
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Elbaum MB, Zondlo NJ. OGlcNAcylation and phosphorylation have similar structural effects in α-helices: post-translational modifications as inducible start and stop signals in α-helices, with greater structural effects on threonine modification. Biochemistry 2014; 53:2242-60. [PMID: 24641765 PMCID: PMC4004263 DOI: 10.1021/bi500117c] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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OGlcNAcylation
and phosphorylation are the major competing intracellular
post-translational modifications of serine and threonine residues.
The structural effects of both post-translational modifications on
serine and threonine were examined within Baldwin model α-helical
peptides (Ac-AKAAAAKAAAAKAAGY-NH2 or Ac-YGAKAAAAKAAAAKAA-NH2). At the N-terminus of an α-helix, both phosphorylation
and OGlcNAcylation stabilized the α-helix relative to the free
hydroxyls, with a larger induced structure for phosphorylation than
for OGlcNAcylation, for the dianionic phosphate than for the monoanionic
phosphate, and for modifications on threonine than for modifications
on serine. Both phosphoserine and phosphothreonine resulted in peptides
more α-helical than alanine at the N-terminus, with dianionic
phosphothreonine the most α-helix-stabilizing residue here.
In contrast, in the interior of the α-helix, both post-translational
modifications were destabilizing with respect to the α-helix,
with the greatest destabilization seen for threonine OGlcNAcylation
at residue 5 and threonine phosphorylation at residue 10, with peptides
containing either post-translational modification existing as random
coils. At the C-terminus, both OGlcNAcylation and phosphorylation
were destabilizing with respect to the α-helix, though the induced
structural changes were less than in the interior of the α-helix.
In general, the structural effects of modifications on threonine were
greater than the effects on serine, because of both the lower α-helical
propensity of Thr and the more defined induced structures upon modification
of threonine than serine, suggesting threonine residues are particularly
important loci for structural effects of post-translational modifications.
The effects of serine and threonine post-translational modifications
are analogous to the effects of proline on α-helices, with the
effects of phosphothreonine being greater than those of proline throughout
the α-helix. These results provide a basis for understanding
the context-dependent structural effects of these competing protein
post-translational modifications.
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Affiliation(s)
- Michael B Elbaum
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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17
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Brister M, Pandey AK, Bielska AA, Zondlo NJ. OGlcNAcylation and phosphorylation have opposing structural effects in tau: phosphothreonine induces particular conformational order. J Am Chem Soc 2014; 136:3803-16. [PMID: 24559475 PMCID: PMC4004249 DOI: 10.1021/ja407156m] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Indexed: 01/12/2023]
Abstract
Phosphorylation and OGlcNAcylation are dynamic intracellular protein post-translational modifications that frequently are alternatively observed on the same serine and threonine residues. Phosphorylation and OGlcNAcylation commonly occur in natively disordered regions of proteins, and often have opposing functional effects. In the microtubule-associated protein tau, hyperphosphorylation is associated with protein misfolding and aggregation as the neurofibrillary tangles of Alzheimer's disease, whereas OGlcNAcylation stabilizes the soluble form of tau. A series of peptides derived from the proline-rich domain (residues 174-251) of tau was synthesized, with free Ser/Thr hydroxyls, phosphorylated Ser/Thr (pSer/pThr), OGlcNAcylated Ser/Thr, and diethylphosphorylated Ser/Thr. Phosphorylation and OGlcNAcylation were found by CD and NMR to have opposing structural effects on polyproline helix (PPII) formation, with phosphorylation favoring PPII, OGlcNAcylation opposing PPII, and the free hydroxyls intermediate in structure, and with phosphorylation structural effects greater than OGlcNAcylation. For tau196-209, phosphorylation and OGlcNAcylation had similar structural effects, opposing a nascent α-helix. Phosphomimic Glu exhibited PPII-favoring structural effects. Structural changes due to Thr phosphorylation were greater than those of Ser phosphorylation or Glu, with particular conformational restriction as the dianion, with mean (3)JαN = 3.5 Hz (pThr) versus 5.4 Hz (pSer), compared to 7.2, 6.8, and 6.2 Hz for Thr, Ser, and Glu, respectively, values that correlate with the backbone torsion angle ϕ. Dianionic phosphothreonine induced strong phosphothreonine amide protection and downfield amide chemical shifts (δmean = 9.63 ppm), consistent with formation of a stable phosphate-amide hydrogen bond. These data suggest potentially greater structural importance of threonine phosphorylation than serine phosphorylation due to larger induced structural effects.
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Affiliation(s)
| | | | - Agata A. Bielska
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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18
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Theillet FX, Kalmar L, Tompa P, Han KH, Selenko P, Dunker AK, Daughdrill GW, Uversky VN. The alphabet of intrinsic disorder: I. Act like a Pro: On the abundance and roles of proline residues in intrinsically disordered proteins. INTRINSICALLY DISORDERED PROTEINS 2013; 1:e24360. [PMID: 28516008 PMCID: PMC5424786 DOI: 10.4161/idp.24360] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 03/17/2013] [Indexed: 11/19/2022]
Abstract
A significant fraction of every proteome is occupied by biologically active proteins that do not form unique three-dimensional structures. These intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) have essential biological functions and are characterized by extensive structural plasticity. Such structural and functional behavior is encoded in the amino acid sequences of IDPs/IDPRs, which are enriched in disorder-promoting residues and depleted in order-promoting residues. In fact, amino acid residues can be arranged according to their disorder-promoting tendency to form an alphabet of intrinsic disorder that defines the structural complexity and diversity of IDPs/IDPRs. This review is the first in a series of publications dedicated to the roles that different amino acid residues play in defining the phenomenon of protein intrinsic disorder. We start with proline because data suggests that of the 20 common amino acid residues, this one is the most disorder-promoting.
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Affiliation(s)
- Francois-Xavier Theillet
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - Lajos Kalmar
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium
| | - Peter Tompa
- VIB Department of Structural Biology; Vrije Universiteit Brussel; Brussels, Belgium.,Institute of Enzymology; Research Centre for Natural Sciences; Hungarian Academy of Sciences; Budapest, Hungary
| | - Kyou-Hoon Han
- Department of Bioinformatics; University of Science and Technology; Daejeon, Yuseong-gu, Korea.,Biomedical Translational Research Center; Division of Convergent Biomedical Research; Korea Research Institute of Bioscience and Biotechnology; Daejeon, Yuseong-gu, Korea
| | - Philipp Selenko
- In-cell NMR Spectroscopy; Leibniz Institute of Molecular Pharmacology (FMP Berlin); Berlin, Germany
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics; Department of Biochemistry and Molecular Biology; Indiana University School of Medicine; Indianapolis, IN USA
| | - Gary W Daughdrill
- Center for Drug Discovery and Innovation; Department of Cell Biology, Microbiology and Molecular Biology; University of South Florida; Tampa, FL USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; College of Medicine; University of South Florida; Tampa, FL USA.,Institute for Biological Instrumentation; Russian Academy of Sciences; Moscow Region, Russia
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19
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de Sousa MM, Munteanu CR, Pazos A, Fonseca NA, Camacho R, Magalhães AL. Amino acid pair- and triplet-wise groupings in the interior of α-helical segments in proteins. J Theor Biol 2010; 271:136-44. [PMID: 21130100 DOI: 10.1016/j.jtbi.2010.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/03/2010] [Accepted: 11/23/2010] [Indexed: 10/18/2022]
Abstract
A statistical approach has been applied to analyse primary structure patterns at inner positions of α-helices in proteins. A systematic survey was carried out in a recent sample of non-redundant proteins selected from the Protein Data Bank, which were used to analyse α-helix structures for amino acid pairing patterns. Only residues more than three positions apart from both termini of the α-helix were considered as inner. Amino acid pairings i, i+k (k=1, 2, 3, 4, 5), were analysed and the corresponding 20×20 matrices of relative global propensities were constructed. An analysis of (i, i+4, i+8) and (i, i+3, i+4) triplet patterns was also performed. These analysis yielded information on a series of amino acid patterns (pairings and triplets) showing either high or low preference for α-helical motifs and suggested a novel approach to protein alphabet reduction. In addition, it has been shown that the individual amino acid propensities are not enough to define the statistical distribution of these patterns. Global pair propensities also depend on the type of pattern, its composition and orientation in the protein sequence. The data presented should prove useful to obtain and refine useful predictive rules which can further the development and fine-tuning of protein structure prediction algorithms and tools.
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Affiliation(s)
- Miguel M de Sousa
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Cristian R Munteanu
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal; Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Alejandro Pazos
- Computer Science Faculty, University of A Coruña, Campus de Elviña S/N, 15071A Coruña, Spain
| | - Nuno A Fonseca
- CRACS-INESC Porto L.A., R. Campo Alegre 1021/1055, 4169-007 Porto, Portugal
| | - Rui Camacho
- LIAAD-INESC-Porto, DEI and FEUP, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal
| | - A L Magalhães
- REQUIMTE/University of Porto, Faculty of Sciences, R. Campo Alegre 687, 4169-007 Porto, Portugal
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20
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Bhattacharjee N, Biswas P. Position-specific propensities of amino acids in the β-strand. BMC STRUCTURAL BIOLOGY 2010; 10:29. [PMID: 20920153 PMCID: PMC2955036 DOI: 10.1186/1472-6807-10-29] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/28/2010] [Indexed: 11/23/2022]
Abstract
Background Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated. Results The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands. Conclusions The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.
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21
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Ghosh TS, Chaitanya SK, Sankararamakrishnan R. End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1032-41. [PMID: 19770500 DOI: 10.1107/s0907444909027012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 07/09/2009] [Indexed: 11/10/2022]
Abstract
Helix-helix interactions are important for the structure, stability and function of alpha-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples of such helix pairs are found in aquaporin, H(+)/Cl(-) transporter and Bcl-2 proteins. The frequency of the occurrence of such ;end-to-end' (EE) and ;end-to-middle' (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-alpha proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N-N, N-C, C-C, N-MID and C-MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix pairs, residues with large surface area/volume and longer side chains are preferred in the interfacial region.
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Affiliation(s)
- Tarini Shankar Ghosh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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22
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Hong L. A statistical mechanical model for antiparallel β-sheet/coil equilibrium. J Chem Phys 2008; 129:225101. [DOI: 10.1063/1.3028635] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Hong L, Lei J. Statistical mechanical model for helix-sheet-coil transitions in homopolypeptides. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:051904. [PMID: 19113152 DOI: 10.1103/physreve.78.051904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Indexed: 05/27/2023]
Abstract
In this paper, we propose a simple statistical mechanical model to study the conformation transition between the alpha helix, beta sheet, and random coil in homopolypeptides. In our model, five parameters are introduced to obtain the partition function. There are two factors for helical propagation and initiation, which are the same as those used in the Zimm-Bragg model, and three newly introduced parameters for beta structures: the strand propagation factor for residues in beta strands and two correction factors for the initiation effect of the beta strand and beta sheet. Our model shows that the variation of these parameters may induce conformation transition from alpha helix or random coil to beta sheet. The sharpness of the transition depends on the initiation factors.
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Affiliation(s)
- Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing, People's Republic of China, 100084.
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24
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Abraham LC, Zuena E, Perez-Ramirez B, Kaplan DL. Guide to collagen characterization for biomaterial studies. J Biomed Mater Res B Appl Biomater 2008; 87:264-85. [PMID: 18386843 DOI: 10.1002/jbm.b.31078] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah C Abraham
- Departments of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA
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25
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Stewart JM, Lin JC, Andersen NH. Lysine and arginine residues do not increase the helicity of alanine-rich peptide helices. Chem Commun (Camb) 2008:4765-7. [PMID: 18830486 DOI: 10.1039/b807101b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The helix-disfavoring, versus alanine, propagation values of lysine (0.8) and arginine (1.0) residues placed centrally in an (Ala)(9) unit have been measured by (13)C NMR.
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Affiliation(s)
- James M Stewart
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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26
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Fonseca NA, Camacho R, Magalhães AL. Amino acid pairing at the N- and C-termini of helical segments in proteins. Proteins 2008; 70:188-96. [PMID: 17654550 DOI: 10.1002/prot.21525] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A systematic survey was carried out in an unbiased sample of 815 protein chains with a maximum of 20% homology selected from the Protein Data Bank, whose structures were solved at a resolution higher than 1.6 A and with a R-factor lower than 25%. A set of 5556 subsequences with alpha-helix or 3(10)-helix motifs was extracted from the protein chains considered. Global and local propensities were then calculated for all possible amino acid pairs of the type (i, i + 1), (i, i + 2), (i, i + 3), and (i, i + 4), starting at the relevant helical positions N1, N2, N3, C3, C2, C1, and N-int (interior positions), and also at the first nonhelical positions in both termini of the helices, namely, N-cap and C-cap. The statistical analysis of the propensity values has shown that pairing is significantly dependent on the type of the amino acids and on the position of the pair. A few sequences of three and four amino acids were selected and their high prevalence in helices is outlined in this work. The Glu-Lys-Tyr-Pro sequence shows a peculiar distribution in proteins, which may suggest a relevant structural role in alpha-helices when Pro is located at the C-cap position. A bioinformatics tool was developed, which updates automatically and periodically the results and makes them available in a web site.
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Affiliation(s)
- Nuno A Fonseca
- IBMC and LIACC, R. Campo Alegre, 1021/1055, 4169-007 Porto, Portugal
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27
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Bastolla U, Porto M, Ortíz AR. Local interactions in protein folding determined through an inverse folding model. Proteins 2008; 71:278-99. [DOI: 10.1002/prot.21730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Stability and Design of α-Helical Peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008; 83:1-52. [DOI: 10.1016/s0079-6603(08)00601-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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29
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Lawson J, O'Mara ML, Kerr ID. Structure-based interpretation of the mutagenesis database for the nucleotide binding domains of P-glycoprotein. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1778:376-91. [PMID: 18035039 DOI: 10.1016/j.bbamem.2007.10.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 10/12/2007] [Accepted: 10/25/2007] [Indexed: 12/15/2022]
Abstract
P-glycoprotein (P-gp) is the most intensively studied eukaryotic ATP binding cassette (ABC) transporter, due to its involvement in the multidrug resistance phenotype of a number of cancers. In common with most ABC transporters, P-gp is comprised of two transmembrane domains (TMDs) and two nucleotide binding domains (NBD), the latter coupling ATP hydrolysis with substrate transport (efflux in the case of P-gp). Biochemical investigations over the past twenty years have attempted to unlock mechanistic aspects of P-glycoprotein through scanning and site-directed mutagenesis of both the TMDs and the NBDs. Contemporaneously, crystallographers have elucidated the atomic structure of numerous ABC transporter NBDs, as well as the intact structure (i.e. NBDs and TMDs) of a distantly related ABC-exporter Sav1866. Significantly, the structure of P-gp remains unknown, and only low resolution electron microscopy data exists. Within the current manuscript we employ crystallographic data for homologous proteins, and a molecular model for P-gp, to perform a structural interpretation of the existing "mutagenesis database" for P-gp NBDs. Consequently, this will enable testable predictions to be made that will result in further in-roads into our understanding of this clinically important drug pump.
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Affiliation(s)
- J Lawson
- School of Biomedical Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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30
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Couch VA, Cheng N, Nambiar K, Fink W. Structural characterization of alpha-helices of implicitly solvated poly-alanine. J Phys Chem B 2007; 110:3410-9. [PMID: 16494355 DOI: 10.1021/jp055209j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural characteristics of alpha-helices in poly-alanine-based peptides have been investigated via molecular dynamics simulation with the goal of understanding the basic features of peptide simulations within the context of a model system, classical molecular dynamics with generalized Born (GB) solvation, and to shed insight into the formation and stabilization of alpha-helices in short peptides. The effects of peptide length, terminal charges, proline substitution, and temperature on the alpha-helical secondary structure have been studied. The simulations have shown that distinct secondary structure begins to develop in peptides with lengths approaching 10 residues while ambiguous structures occur in shorter peptides. The helical content of peptides with lengths > or =10 amino acids is observed to be nearly constant up to (Ala)(40). Interestingly, terminal charges and proline in the second position from the N-terminus alter the secondary structure locally with little effect on the overall alpha-helical content of the peptide. The free energy profile of helix formation was also investigated. A large increase in free energy accompanying the formation of helices with more than two consecutive hydrogen bonds in the (i, i + 4) pattern was observed while the free energy increases linearly with additional hydrogen bonds. Values for the change in enthalpy and entropy of helix nucleation and propagation are reported. Additionally the results obtained from the GB model are compared to explicit solvent simulations of two synthetic alanine-based peptides.
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Affiliation(s)
- Vernon A Couch
- Department of Chemistry, University of California, Davis, California 95616, USA.
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31
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Mikhonin AV, Asher SA, Bykov SV, Murza A. UV Raman spatially resolved melting dynamics of isotopically labeled polyalanyl peptide: slow alpha-helix melting follows 3(10)-helices and pi-bulges premelting. J Phys Chem B 2007; 111:3280-92. [PMID: 17388440 DOI: 10.1021/jp0654009] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We used UV resonance Raman (UVRR) to examine the spatial dependence of the T-jump secondary structure relaxation of an isotopically labeled 21-residue mainly Ala peptide, AdP. The AdP penultimate Ala residues were perdeuterated, leaving the central residues hydrogenated, to allow separate monitoring of melting of the middle versus the end peptide bonds. For 5 to 30 degrees C T-jumps, the central peptide bonds show a approximately 2-fold slower relaxation time (189 +/- 31 ns) than do the exterior peptide bonds (97 +/- 15 ns). In contrast, for a 20 to 40 degrees C T-jump, the central peptide bond relaxation appears to be faster (56 +/- 6 ns) than that of the penultimate peptide bonds (131 +/- 46 ns). We show that, if the data are modeled as a two-state transition, we find that only exterior peptide bonds show anti-Arrhenius folding behavior; the middle peptide bonds show both normal Arrhenius-like folding and unfolding. This anti-Arrhenius behavior results from the involvement of pi-bulges/helices and 3(10)-helix states in the melting. The unusual temperature dependence of the (un)folding rates of the interior and exterior peptide bonds is due to the different relative (un)folding rates of 3(10)-helices, alpha-helices, and pi-bulges/helices. Pure alpha-helix unfolding rates are approximately 12-fold slower (approximately 1 micros) than that of pi-bulges and 3(10)-helices. In addition, we also find that the alpha-helix is most stable at the AdP N-terminus where eight consecutive Ala occur, whereas the three hydrophilic Arg located in the middle and at the C-terminus destabilize the alpha-helix in these regions and induce defects such as pi-bulges and 3(10)-helices.
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Affiliation(s)
- Aleksandr V Mikhonin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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32
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Davis RB, Lecomte JTJ. A dynamic N-capping motif in cytochrome b5: evidence for a pH-controlled conformational switch. Proteins 2007; 63:336-48. [PMID: 16372350 DOI: 10.1002/prot.20759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Apocytochrome b5 is a marginally stable protein exhibiting under native conditions a slow conformational exchange in its C-terminal region. The affected elements of secondary structure include a 3(10)-helix containing at its N-terminus a histidine Ncap and a subsequent proline. Participation of the neutral histidine side-chain in backbone amide capping lowers the imidazole pKa. To explore the nature of the conformational exchange in the protein and determine whether it is related to cis-trans isomerization of the His-Pro bond, three octapeptides encompassing the helix were synthesized and studied by NMR spectroscopy. One corresponded to the wild-type sequence, the second was the D-histidine epimer, and the third contained an alanine in place of the proline. It was found that the rates of cis-trans interconversion in the proline-containing peptides were slower than the rates of the conformational exchange in the protein. In addition, the wild-type peptide hinted at a predisposition for Ncap formation when in the trans configuration. Analysis of the pH response of the peptides and protein suggested that at pH near neutral, the conformational exchange detected in the protein involved only species with a trans His-Pro bond and could be approximated with a three-state model by which the terminal helix sampled a locally unfolded state. This state, which contained an uncapped histidine with a normal pKa, partitioned into neutral and protonated populations according to pH. The intrinsic conformational bias of the wild-type peptide and the pH-driven equilibria illustrated how a 3(10)-element could serve as a nucleation site for structural rearrangement.
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Affiliation(s)
- Ronald B Davis
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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33
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Iqbalsyah TM, Moutevelis E, Warwicker J, Errington N, Doig AJ. The CXXC motif at the N terminus of an alpha-helical peptide. Protein Sci 2006; 15:1945-50. [PMID: 16877711 PMCID: PMC2242585 DOI: 10.1110/ps.062271506] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
An active site containing a CXXC motif is always found in the thiol-disulphide oxidoreductase superfamily. A survey of crystal structures revealed that the CXXC motif had a very high local propensity (26.3 +/- 6.2) for the N termini of alpha-helices. A helical peptide with the sequence CAAC at the N terminus was synthesized to examine the helix-stabilizing capacity of the CXXC motif. Circular dichroism was used to confirm the helical nature of the peptide and study behavior under titration with various species. With DTT, a redox potential of E(o) = -230 mV was measured, indicating that the isolated peptide is reducing in nature and similar to native human thioredoxin. The pK(a) values of the individual Cys residues could not be separated in the titration of the reduced state, giving a single transition with an apparent pK(a) of 6.74 (+/-0.06). In the oxidized state, the N-terminal pK(a) is 5.96 (+/-0.05). Analysis of results with the modified helix-coil theory indicated that the disulfide bond stabilized the alpha-helical structure by 0.5 kcal/mol. Reducing the disulfide destabilizes the helix by 0.9 kcal/mol.
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Affiliation(s)
- Teuku M Iqbalsyah
- Manchester Interdisciplinary Biocentre, The University of Manchester, UK
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34
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Aydin Z, Altunbasak Y, Borodovsky M. Protein secondary structure prediction for a single-sequence using hidden semi-Markov models. BMC Bioinformatics 2006; 7:178. [PMID: 16571137 PMCID: PMC1479840 DOI: 10.1186/1471-2105-7-178] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2005] [Accepted: 03/30/2006] [Indexed: 11/10/2022] Open
Abstract
Background The accuracy of protein secondary structure prediction has been improving steadily towards the 88% estimated theoretical limit. There are two types of prediction algorithms: Single-sequence prediction algorithms imply that information about other (homologous) proteins is not available, while algorithms of the second type imply that information about homologous proteins is available, and use it intensively. The single-sequence algorithms could make an important contribution to studies of proteins with no detected homologs, however the accuracy of protein secondary structure prediction from a single-sequence is not as high as when the additional evolutionary information is present. Results In this paper, we further refine and extend the hidden semi-Markov model (HSMM) initially considered in the BSPSS algorithm. We introduce an improved residue dependency model by considering the patterns of statistically significant amino acid correlation at structural segment borders. We also derive models that specialize on different sections of the dependency structure and incorporate them into HSMM. In addition, we implement an iterative training method to refine estimates of HSMM parameters. The three-state-per-residue accuracy and other accuracy measures of the new method, IPSSP, are shown to be comparable or better than ones for BSPSS as well as for PSIPRED, tested under the single-sequence condition. Conclusions We have shown that new dependency models and training methods bring further improvements to single-sequence protein secondary structure prediction. The results are obtained under cross-validation conditions using a dataset with no pair of sequences having significant sequence similarity. As new sequences are added to the database it is possible to augment the dependency structure and obtain even higher accuracy. Current and future advances should contribute to the improvement of function prediction for orphan proteins inscrutable to current similarity search methods.
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Affiliation(s)
- Zafer Aydin
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0250, USA
| | - Yucel Altunbasak
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0250, USA
| | - Mark Borodovsky
- School of Biology, the Wallace H. Coulter Department of Biomedical Engineering and the Center for Bioinformatics and Computational Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
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35
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Maity H, Rumbley JN, Englander SW. Functional role of a protein foldon-An Ω-loop foldon controls the alkaline transition in ferricytochrome c. Proteins 2005; 63:349-55. [PMID: 16287119 DOI: 10.1002/prot.20757] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Hydrogen exchange results for cytochrome c and several other proteins show that they are composed of a number of foldon units which continually unfold and refold and account for some functional properties. Previous work showed that one Omega-loop foldon controls the rate of the structural switching and ligand exchange behavior of cytochrome c known as the alkaline transition. The present work tests the role of foldons in the alkaline transition equilibrium. We measured the effects of denaturant and 14 destabilizing mutations. The results show that the ligand exchange equilibrium is controlled by the stability of the same foldon unit implicated before. In addition, the results obtained confirm the epsilon-amino group of Lys79 and Lys73 as the alkaline replacement ligands and bear on the search for a triggering group.
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Affiliation(s)
- Haripada Maity
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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36
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Galea C, Bowman P, Kriwacki RW. Disruption of an intermonomer salt bridge in the p53 tetramerization domain results in an increased propensity to form amyloid fibrils. Protein Sci 2005; 14:2993-3003. [PMID: 16260757 PMCID: PMC2253254 DOI: 10.1110/ps.051622005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We describe in molecular detail how disruption of an intermonomer salt bridge (Arg337-Asp352) leads to partial destabilization of the p53 tetramerization domain and a dramatically increased propensity to form amyloid fibrils. At pH 4.0 and 37 degrees C, a p53 tetramerization domain mutant (p53tet-R337H), associated with adrenocortical carcinoma in children, readily formed amyloid fibrils, while the wild-type (p53tet-wt) did not. We characterized these proteins by equilibrium denaturation, 13C(alpha) secondary chemical shifts, (1H)-15N heteronuclear NOEs, and H/D exchange. Although p53tet-R337H was thermodynamically less stable, NMR data indicated that the two proteins had similar secondary structure and molecular dynamics. NMR derived pK(a) values indicated that at low pH the R337H mutation partially disrupted an intermonomer salt bridge. Backbone H/D exchange results showed that for at least a small population of p53tet-R337H molecules disruption of this salt bridge resulted in partial destabilization of the protein. It is proposed that this decrease in p53tet-R337H stability resulted in an increased propensity to form amyloid fibrils.
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Affiliation(s)
- Charles Galea
- Department of Structural Biology, St. Jude Children's Research Hospital, 332 North Lauderdale Street, Memphis, TN 38105, USA
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37
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Kojima S, Kuriki Y, Yazaki K, Miura KI. Stabilization of the fibrous structure of an α-helix-forming peptide by sequence reversal. Biochem Biophys Res Commun 2005; 331:577-82. [PMID: 15850799 DOI: 10.1016/j.bbrc.2005.03.219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2005] [Indexed: 10/25/2022]
Abstract
The alpha3-peptide, which comprises three repeats of the sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala and forms an amphipathic alpha-helix, is unique among various alpha-helix-forming peptides in that it assembles into fibrous structures that can be observed by transmission electron microscopy. As part of our investigation of the structure-stability relationships of the alpha3-peptide, we synthesized the r3-peptide, whose amino acid sequence is the reverse of that of the alpha3-peptide, and we investigated the effects of sequence reversal on alpha-helix stability and the formation of fibrous structures. Unexpectedly, the r3-peptide formed a more-stable alpha-helix and longer fibers than did the alpha3-peptide. The stability of the r3-peptide helix decreased when the ionic strength of the buffer was increased and when the pH of the buffer was adjusted to 2 or 12. These results suggest that the r3-peptide underwent a "magnet-like" oligomerization and that an increase in the charge-distribution inequality may be the driving force for the formation of fibrous structures.
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Affiliation(s)
- Shuichi Kojima
- Institute for Biomolecular Science, Gakushuin University, Mejiro, Tokyo 171-8588, Japan.
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38
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Wilson CL, Boardman PE, Doig AJ, Hubbard SJ. Improved prediction for N-termini of alpha-helices using empirical information. Proteins 2005; 57:322-30. [PMID: 15340919 DOI: 10.1002/prot.20218] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The prediction of the secondary structure of proteins from their amino acid sequences remains a key component of many approaches to the protein folding problem. The most abundant form of regular secondary structure in proteins is the alpha-helix, in which specific residue preferences exist at the N-terminal locations. Propensities derived from these observed amino acid frequencies in the Protein Data Bank (PDB) database correlate well with experimental free energies measured for residues at different N-terminal positions in alanine-based peptides. We report a novel method to exploit this data to improve protein secondary structure prediction through identification of the correct N-terminal sequences in alpha-helices, based on existing popular methods for secondary structure prediction. With this algorithm, the number of correctly predicted alpha-helix start positions was improved from 30% to 38%, while the overall prediction accuracy (Q3) remained the same, using cross-validated testing. Although the algorithm was developed and tested on multiple sequence alignment-based secondary structure predictions, it was also able to improve the predictions of start locations by methods that use single sequences to make their predictions. Furthermore, the residue frequencies at N-terminal positions of the improved predictions better reflect those seen at the N-terminal positions of alpha-helices in proteins. This has implications for areas such as comparative modeling, where a more accurate prediction of the N-terminal regions of alpha-helices should benefit attempts to model adjacent loop regions. The algorithm is available as a Web tool, located at http://rocky.bms.umist.ac.uk/elephant.
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Affiliation(s)
- Claire L Wilson
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester, United Kingdom
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39
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Lin JC, Barua B, Andersen NH. The helical alanine controversy: an (Ala)6 insertion dramatically increases helicity. J Am Chem Soc 2004; 126:13679-84. [PMID: 15493925 PMCID: PMC3870188 DOI: 10.1021/ja047265o] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Employing chemical shift melts and hydrogen/deuterium exchange NMR techniques, we have determined the stabilization of the Trp-cage miniprotein due to multiple alanine insertions within the N-terminal alpha-helix. Alanine is shown to be uniquely helix-stabilizing and this stabilization is reflected in the global fold stability of the Trp-cage. The associated free energy change per alanine can be utilized to calculate the alanine propagation value. From the Lifson-Roig formulation, the calculated value (wAla = 1.6) is comparable to those obtained for short, solubilized, alanine-rich helices and is much larger than the values obtained by prior host-guest techniques or in N-terminally templated helices and peptides bearing long contiguous strings of alanines with no capping or solubilizing units present.
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Affiliation(s)
- Jasper C. Lin
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Bipasha Barua
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - Niels H. Andersen
- Contribution from the Department of Chemistry, University of Washington, Seattle, Washington 98195
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40
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Abstract
N3 is the third position from the N terminus in the alpha-helix with helical backbone dihedral angles. All 20 amino acids have been placed in the N3 position of a synthetic helical peptide (CH(3)CO-[AAX AAAAKAAAAKAGY]-NH(2)) and the helix content measured by circular dichroism spectroscopy at 273 K. The dependence of peptide helicity on N3 residue identity has been used to determine a free energy scale by analysis with a modified Lifson-Roig helix coil theory that includes a parameter for the N3 energy (n3). The most stabilizing residues at N3 in rank order are Ala, Glu, Met/Ile, Leu, Lys, Ser, Gln, Thr, Tyr, Phe, Asp, His, and Trp. Free energies for the most destabilizing residues (Cys, Gly, Asn, Arg, and Pro) could not be fitted. The results correlate with N1, N2, and helix interior energies and not at all with N-cap preferences. This completes our work on studying the structural and energetic preferences of the amino acids for the N-terminal positions of the alpha-helix. These results can be used to rationally modify protein stability, help design helices, and improve prediction of helix location and stability.
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Affiliation(s)
- Teuku M Iqbalsyah
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology (UMIST), Manchester M60 1QD, UK
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41
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Engel DE, DeGrado WF. Amino acid propensities are position-dependent throughout the length of alpha-helices. J Mol Biol 2004; 337:1195-205. [PMID: 15046987 DOI: 10.1016/j.jmb.2004.02.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Revised: 01/28/2004] [Accepted: 02/04/2004] [Indexed: 11/30/2022]
Abstract
The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix. These position-specific propensities should provide valuable parameters to guide de novo protein design, and should allow more precise prediction of helical topology in natural proteins.
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Affiliation(s)
- Donald E Engel
- Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
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42
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Affiliation(s)
- Norma J Greenfield
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, University of medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
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43
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Signarvic RS, DeGrado WF. De Novo Design of a Molecular Switch: Phosphorylation-dependent Association of Designed Peptides. J Mol Biol 2003; 334:1-12. [PMID: 14596795 DOI: 10.1016/j.jmb.2003.09.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The de novo design of peptides that switch their oligomerization state in response to a chemical stimulus is of interest, both as a tool for understanding the basis of molecular switching as well as development of reagents for the study of signal transduction in cells. The target of the current study is the design of a series of peptides that undergo a transition from an unstructured monomer to a four-helical bundle upon phosphorylation by the enzyme cyclic AMP-dependent protein kinase (PKA). The designed peptides are based on the 20-residue Lac repressor tetramerization domain. Beginning with this structure, we introduced a phosphorylation site near the N terminus. Phosphorylation leads to a 2-4.6 kcal/mol increase in the stability of the tetramer, depending on the design. The most successful switches were designed such that phosphorylation would increase the stability of the individual helices and also relieve an unfavorable electrostatic interaction in the tetramer.
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Affiliation(s)
- Rachel S Signarvic
- Department of Biochemistry and Biophysics, School of Medicine, Stellar-Chance Bldg Room 1010, University of Pennsylvania, 421 Curie Blvd, Philadelphia, PA 19104-6059, USA
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44
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Zhang W, Loughran MG, Kanna SI, Yano K, Ikebukuro K, Yokobayashi Y, Kuroda R, Karube I. Exploration of structural features of monomeric helical peptides designed with a genetic algorithm. Proteins 2003; 53:193-200. [PMID: 14517971 DOI: 10.1002/prot.10509] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A genetic algorithm (GA)-based strategy to dissect the determinants of peptide folding into alpha-helix was developed. The structural information of helical peptides was obtained with respect to patterns of sequence variability. In many previously reported studies the intrinsic alpha-helical propensities of amino acids although sequence-dependent are apparently independent of the amino acid position. In this research, monomeric helical peptides selected from possible sequences produced by a GA-chemical synthesis were analyzed to identify possible influential structural features. These hexadeca-peptides were obtained after four successive generations. A total of 128 synthetic peptides were evaluated via circular dichroism (CD) measurements in aqueous solution, while the mean ellipticity at 222 nm confirmed the monomeric state of the peptides. The results presented here show that our GA-based strategy may be useful in the design of proteins with increased alpha-helix content.
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Affiliation(s)
- Wuming Zhang
- Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
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45
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Koscielska-Kasprzak K, Cierpicki T, Otlewski J. Importance of alpha-helix N-capping motif in stabilization of betabetaalpha fold. Protein Sci 2003; 12:1283-9. [PMID: 12761399 PMCID: PMC2323898 DOI: 10.1110/ps.0301703] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
FSD-1 (full sequence design 1) is a protein folded in a betabetaalpha motif, designed on the basis of the second zinc finger domain of Zif268 by a substitution of its metal coordination site with a hydrophobic core. In this work, we analyzed the possibility of introducing the DNA recognition motif of the template zinc finger (S(13)RSDH(17)) into FSD-1 sequence in order to obtain a small DNA-binding module devoid of cross-link(s) or metal cofactors. The hybrid protein was unfolded, as judged by CD and NMR criteria. To reveal the role of each of the five amino acids, which form the N-capping motif of the alpha-helix, we analyzed conformational and stability properties of eight FSD-1 mutants. We used a shielded methyl group of Leu 18 and a CD signal at 215 nm as a convenient measure of the folded state. Glu 17-->His substitution at the N(3) in S(13)NEKE(17) variant decreased the folded structure content from 90% to 25% (equivalent to 1.8 kcal * mole(-1) destabilization) by disruption of N-capping interactions, and had the most significant effect among single mutants studied here. The N(cap) Asn 14 substitution with Arg considerably decreased stability, reducing structure content from 90% to 40% (1.4 kcal * mole(-1) destabilization) by disruption of a helix-capping hydrogen bond and destabilization of a helix macrodipole. The N(1) Glu 15-->Ser mutation also produced a considerable effect (1.0 kcal * mole(-1) destabilization), again emphasizing the significance of electrostatic interactions in alpha-helix stabilization.
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Affiliation(s)
- Katarzyna Koscielska-Kasprzak
- Laboratory of Protein Engineering, Institute of Biochemistry and Molecular Biology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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46
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Abstract
Amino acids seem to have specific preferences for various locations in alpha-helices. These specific preferences, called singlet local propensity (SLP), have been determined by calculating the preference of occurrence of each amino acid in different positions of the alpha-helix. We have studied the occurrence of amino acids, single or pairs, in different positions, singlet or doublet, of alpha-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 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 alpha-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 alpha-helix is significantly different from the expected frequency of occurrence in that position. The doublet local propensity (DLP) was defined as the preference of occurrences of amino acid pairs in different doublet positions of the alpha-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 identified above, the DLP(O) and DLP(E) values were significantly different. 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 specified 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 specific position of the alpha-helix. These cases have been identified and listed in various tables in this paper. The amount of mutual information carried by the exceptional pairs of amino acids was significantly 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.
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Affiliation(s)
- Bahram Goliaei
- Laboratory of Biophysics and Molecular Biology, Institute of Biochemistry and Biophysics, University of Tehran, Iran.
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47
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Abstract
Peptide helices in solution form a complex mixture of all helix, all coil or, most frequently, central helices with frayed coil ends. In order to interpret experiments on helical peptides and make theoretical predictions on helices, it is therefore essential to use a helix-coil theory that takes account of this equilibrium. The original Zimm-Bragg and Lifson-Roig helix-coil theories have been greatly extended in the last 10 years to include additional interactions. These include preferences for the N-cap, N1, N2, N3 and C-cap positions, capping motifs, helix dipoles, side chain interactions and 3(10)-helix formation. These have been applied to determine energies for these preferences from experimental data and to predict the helix contents of peptides. This review discusses these newly recognised structural features of helices and how they have been included in helix-coil models.
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Affiliation(s)
- Andrew J Doig
- Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK.
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48
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Abstract
The thermally-induced helix-coil transition in polyamino acids is a good model for determining the helix-forming propensities of amino acids but not for the two-state folding/unfolding transition in globular proteins. The equilibrium and kinetic treatments of the helix-coil transition are summarized here together with a description of applications to various types of homopolymers and copolymers. Attention is then focused on the helix-coil transition in poly-L-alanine as an example of a non-polar polyamino acid. To render such a non-polar polymer water soluble, it is necessary to introduce polar amino acids such as lysines, but care must be taken as to the location of such polar residues. If they are attached as end groups, as in a triblock copolymer, they do not perturb the helix-forming tendency of the central poly-L-alanine block significantly, but if they are introduced within the sequence of alanine residues, then the hydration properties of the lysines dominate the behavior of the resulting copolymer, thereby leading to erroneous values of the parameters characterizing the helix-forming tendency of the alanines. Neutral but polar residues, such as glutamines, also exhibit hydration-dominating properties but less so than charged lysines. Some details of the calculations for an alanine/glutamine copolymer are presented here. It is concluded that random copolymers based on a neutral water-soluble host provide reliable information about the helix-forming tendencies of amino acid residues that are introduced as guests among such neutral host residues.
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Affiliation(s)
- Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithica, NY 14853-1301, USA.
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49
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Wilson CL, Hubbard SJ, Doig AJ. A critical assessment of the secondary structure alpha-helices and their termini in proteins. Protein Eng Des Sel 2002; 15:545-54. [PMID: 12200536 DOI: 10.1093/protein/15.7.545] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Secondary structure prediction from amino acid sequence is a key component of protein structure prediction, with current accuracy at approximately 75%. We analysed two state-of-the-art secondary structure prediction methods, PHD and JPRED, comparing predictions with secondary structure assigned by the algorithms DSSP and STRIDE. The specific focus of our study was alpha-helix N-termini, as empirical free energy scales are available for residue preferences at N-terminal positions. Although these prediction methods perform well in general at predicting the alpha-helical locations and length distributions in proteins, they perform less well at predicting the correct helical termini. For example, although most predicted alpha-helices overlap a real alpha-helix (with relatively few completely missed or extra predicted helices), only one-third of JPRED and PHD predictions correctly identify the N-terminus. Analysis of neighbouring N-terminal sequences to predicted helical N-termini shows that the correct N-terminus is often within one or two residues. More importantly, the true N-terminal motif is, on average, more favourable as judged by our experimentally measured free energies. This suggests a simple, but powerful, strategy to improve secondary structure prediction using empirically derived energies to adjust the predicted output to a more favourable N-terminal sequence.
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Affiliation(s)
- Claire L Wilson
- Department of Biomolecular Sciences, UMIST, P.O. Box 88, Manchester M60 1QD, UK
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50
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Petukhov M, Uegaki K, Yumoto N, Serrano L. Amino acid intrinsic alpha-helical propensities III: positional dependence at several positions of C terminus. Protein Sci 2002; 11:766-77. [PMID: 11910021 PMCID: PMC2373540 DOI: 10.1110/ps.2610102] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
In this study, we have analyzed experimentally the helical intrinsic propensities of non-charged and non-aromatic residues at different C-terminal positions (C1, C2, C3) of an Ala-based peptide. The effect was found to be complex, resulting in extra stabilization or destabilization, depending on guest amino acid and position under consideration. Polar (Ser, Thr, Cys, Asn, and Gln) amino acids and Gly were found to have significantly larger helical propensities at several C-terminal positions compared with the alpha-helix center (-1.0 kcal/mole in some cases). Some of the nonpolar residues, especially beta-branched ones (Val and Ile) are significantly more favorable at position C3 (-0.3 to -0.4 kcal/mole), although having minor differences at other C-terminal positions compared with the alpha-helix center. Leu has moderate (-0.1 to -0.2 kcal/mole) stabilization effects at position C2 and C3, whereas being relatively neutral at C1. Finally, Met was found to be unfavorable at C1 and C2 ( +0.2 kcal/mole) and favorable at C3 (-0.2 kcal/mole). Thus, significant differences found between the intrinsic helical propensities at the C-terminal positions and those in the alpha-helix center must be accounted for in helix/coil transition theories and in protein design.
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Affiliation(s)
- Michael Petukhov
- European Molecular Biology Laboratory, Heidelberg, D-69012, Germany
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