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1.
The role of phosphorylation in stabilizing the N‐termini of α‐helices is examined using computer simulations of model peptides. The models comprise either a phosphorylated or unphosphorylated serine at the helix N‐terminus, followed by nine alanines. Monte Carlo/stochastic Dynamics simulations were performed on the model helices. The simulations revealed a distinct stabilization of the helical conformation at the N‐terminus after phosphorylation. The stabilization was attributable to favorable electrostatic interactions between the phosphate and the helix backbone. However, direct helix capping by the phosphorylated sidechain was not observed. The results of the calculations are consistent with experimental evidence on the stabilization of helices by phosphates and other anions. © 1999 John Wiley & Sons, Inc. Biopoly 49: 225–233, 1999 相似文献
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Tori B. Dunlap Jessime M. Kirk Emily A. Pena Meghan S. Yoder Trevor P. Creamer 《Proteins》2013,81(4):607-612
In this work, we have examined contributions to the thermodynamics of calmodulin (CaM) binding from the intrinsic propensity for target peptides to adopt an α‐helical conformation. CaM target sequences are thought to commonly reside in disordered regions within proteins. Using the ability of TFE to induce α‐helical structure as a proxy, the six peptides studied range from having almost no propensity to adopt α‐helical structure through to a very high propensity. This despite all six peptides having similar CaM‐binding affinities. Our data indicate there is some correlation between the deduced propensities and the thermodynamics of CaM binding. This finding implies that molecular recognition features, such as CaM target sequences, may possess a broad range of propensities to adopt local structure. Given that these peptides bind to CaM with similar affinities, the data suggest that having a higher propensity to adopt α‐helical structure does not necessarily result in tighter binding, and that the mechanism of CaM binding is very dependent on the nature of the substrate sequence. Proteins 2013. © 2012 Wiley Periodicals, Inc. 相似文献
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Wenhui Xi Elliott K. Vanderford Qinxin Liao Ulrich H. E. Hansmann 《Protein science : a publication of the Protein Society》2019,28(11):1973-1981
We consider the effect of lauric acid on the stability of various fibril‐like assemblies of Aβ peptides. For this purpose, we have performed molecular dynamics simulations of these assemblies either in complex with lauric acid or without presence of the ligand. While we do not observe a stabilizing effect on Aβ40‐fibrils, we find that addition of lauric acid strengthens the stability of fibrils built from the triple‐stranded S‐shaped Aβ42‐peptides considered to be more toxic. Or results may help to understand how the specifics of the brain‐environment modulate amyloid formation and propagation. 相似文献
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Abdollah Mosleh Anna Heintz Ki‐Taek Lim Jin‐Woo Kim Robert Beitle 《Biotechnology progress》2017,33(3):654-657
This research investigated the use of single‐walled carbon nanotubes (SWNTs) as an additive to increase the permeability of a bacterial cell wall. Recombinant Escherichia coli BL21 (DE3) that expressed β‐lactamase were exposed to SWNTs under various levels of concentration and agitation. Activity of β‐lactamase in the culture fluid and transmission electron microscopy (TEM) were used to determine the amount of released protein, and visually examine the permeability enhancement of the cells. It was found that β‐lactamase release in the culture fluid occurred in a dose‐dependent manner with treatment by SWNTs and was also dependent on agitation rate. Based on TEM, this treatment successfully caused an increase in permeability without significant damage to the cell wall. Consequently, SWNTs can be used as an enhancement agent to cause the release of intracellular proteins. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:654–657, 2017 相似文献
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Self‐assembly of PAs composed of palmitic acid and several repeated heptad peptide sequences, C15H31CO‐(IEEYTKK)n‐NH2 (n = 1–4, represented by PA1–PA4), was investigated systematically. The secondary structures of the PAs were characterized by CD. PA3 and PA4 (n = 3 and 4, respectively) showed an α‐helical structure, whereas PA1 and PA2 (n = 1 and 2, respectively) did not display an α‐helical conformations under the tested conditions. The morphology of the self‐assembled peptides in aqueous medium was studied by transmission electron microscopy. As the number of heptad repeats in the PAs increased, the nanostructure of the self‐assembled peptides changed from nanofibers to nanovesicles. Changes of the secondary structures and the self‐assembly morphologies of PA3 and PA4 in aqueous medium with various cations were also studied. The critical micelle concentrations were determined using a pyrene fluorescence probe. In conclusion, this method may be used to design new peptide nanomaterials. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
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β‐strand interactions at the domain interface critical for the stability of human lens γD‐crystallin
Payel Das Jonathan A. King Ruhong Zhou 《Protein science : a publication of the Protein Society》2010,19(1):131-140
Human age‐onset cataracts are believed to be caused by the aggregation of partially unfolded or covalently damaged lens crystallin proteins; however, the exact molecular mechanism remains largely unknown. We have used microseconds of molecular dynamics simulations with explicit solvent to investigate the unfolding process of human lens γD‐crystallin protein and its isolated domains. A partially unfolded folding intermediate of γD‐crystallin is detected in simulations with its C‐terminal domain (C‐td) folded and N‐terminal domain (N‐td) unstructured, in excellent agreement with biochemical experiments. Our simulations strongly indicate that the stability and the folding mechanism of the N‐td are regulated by the interdomain interactions, consistent with experimental observations. A hydrophobic folding core was identified within the C‐td that is comprised of a and b strands from the Greek key motif 4, the one near the domain interface. Detailed analyses reveal a surprising non‐native surface salt‐bridge between Glu135 and Arg142 located at the end of the ab folded hairpin turn playing a critical role in stabilizing the folding core. On the other hand, an in silico single E135A substitution that disrupts this non‐native Glu135‐Arg142 salt‐bridge causes significant destabilization to the folding core of the isolated C‐td, which, in turn, induces unfolding of the N‐td interface. These findings indicate that certain highly conserved charged residues, that is, Glu135 and Arg142, of γD‐crystallin are crucial for stabilizing its hydrophobic domain interface in native conformation, and disruption of charges on the γD‐crystallin surface might lead to unfolding and subsequent aggregation. 相似文献
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Madhusudana M. B. Reddy Krishnayan Basuroy Subrayashastry Aravinda Padmanabhan Balaram 《Journal of peptide science》2016,22(8):504-510
The solid‐state conformations of two αγ hybrid peptides Boc‐[Aib‐γ4(R)Ile]4‐OMe 1 and Boc‐[Aib‐γ4(R)Ile]5‐OMe 2 are described. Peptides 1 and 2 adopt C12‐helical conformations in crystals. The structure of octapeptide 1 is stabilized by six intramolecular 4 → 1 hydrogen bonds, forming 12 atom C12 motifs. The structure of peptide 2 reveals the formation of eight successive C12 hydrogen‐bonded turns. Average backbone dihedral angles for αγ C12 helices are peptide 1 , Aib; φ (°) = ?57.2 ± 0.8, ψ (°) = ?44.5 ± 4.7; γ4(R)Ile; φ (°) = ?127.3 ± 7.3, θ1 (°) = 58.5 ± 12.1, θ2 (°) = 67.6 ± 10.1, ψ (°) = ?126.2 ± 16.1; peptide 2 , Aib; φ (°) = ?58.8 ± 5.1, ψ (°) = ?40.3 ± 5.5; ψ4(R)Ile; φ (°) = ?123.9 ± 2.7, θ1 (°) = 53.3 θ 4.9, θ 2 (°) = 61.2 ± 1.6, ψ (°) = ?121.8 ± 5.1. The tendency of γ4‐substituted residues to adopt gauche–gauche conformations about the Cα–Cβ and Cβ–Cγ bonds facilitates helical folding. The αγ C12 helix is a backbone expanded analog of α peptide 310 helix. The hydrogen bond parameters for α peptide 310 and α‐helices are compared with those for αγ hybrid C12 helix. Copyright © 2016 European Peptide Society and John Wiley & Sons. 相似文献
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Diego Caballero Jukka Määttä Alice Qinhua Zhou Maria Sammalkorpi Corey S. O'Hern Lynne Regan 《Protein science : a publication of the Protein Society》2014,23(7):970-980
A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an α-helix, β-sheet, or other backbone dihedral angle (-ψ) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for α-helical structures, while experiments on small peptides observe that β-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model for Ala dipeptide mimetics that includes steric interactions between nonbonded atoms and bond length and angle constraints with the goal of evaluating the role of steric interactions in determining protein backbone conformational preferences. We find four key results. For the hard-sphere MD simulations, we show that (1) β-sheet structures are roughly three and half times more probable than α-helical structures, (2) transitions between α-helix and β-sheet structures only occur when the backbone bond angle τ (N–Cα–C) is greater than 110°, and (3) the probability distribution of τ for Ala conformations in the “bridge” region of-ψ space is shifted to larger angles compared to other regions. In contrast, (4) the distributions obtained from Amber and CHARMM MD simulations in the bridge regions are broader and have increased τ compared to those for hard sphere simulations and from high-resolution protein crystal structures. Our results emphasize the importance of hard-sphere interactions and local stereochemical constraints that yield strong correlations between -ψ conformations and τ. 相似文献
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Much effort has been invested in seeking to understand the thermodynamic basis of helix stability in both peptides and proteins. Recently, several groups have measured the helix-forming propensities of individual residues (Lyu, P. C., Liff, M. I., Marky, L. A., Kallenbach, N. R. Science 250:669–673, 1990; O'Neil, K. T., DeGrado, W. F. Science 250:646–651, 1990; Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., Baldwin, R. L. Nature (London) 344:268–270, 1990). Using Monte Carlo computer simulations, we tested the hypothesis that these differences in measured helix-forming propensity are due primarily to loss of side chain conformational entropy upon helix formation (Creamer, T. P., Rose, G. D. Proc. Natl. Acad. Sci. U.S.A. 89:5937–5941, 1992). Our previous study employed a rigid helix backbone, which is here generalized to a completely flexible helix model in order to ensure that earlier results were not a methodological artifact. Using this flexible model, side chain rotamer distributions and entropy losses are calculated and shown to agree with those obtained earlier. We note that the side chain conformational entropy calculated for Trp in our previous study was in error; a corrected value is presented. Extending earlier work, calculated entropy losses are found to correlate strongly with recent helix propensity scales derived from substitutions made within protein helices (Horovitz, A., Matthews, J. M., Fersht, A. R. J. Mol. Biol. 227:560–568, 1992; Blaber, M., Zhang, X.-J., Matthews, B. M. Science 260:1637–1640, 1993). In contrast, little correlation is found between these helix propensity scales and the accessible surface area buried upon formation of a model polyalanyl α-helix. Taken in sum, our results indicate that loss of side chain entropy is a major determinant of the helix-forming tendency of residues in both peptide and protein helices. © 1994 Wiley-Liss, Inc. 相似文献
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Luisa Ronga Pasquale Palladino Gabriella Saviano Teodorico Tancredi Ettore Benedetti Raffaele Ragone Filomena Rossi 《Journal of peptide science》2008,14(10):1096-1102
The 173–195 segment corresponding to the helix 2 of the globular PrP domain is a good candidate to be one of the several ‘spots’ of intrinsic structural flexibility, which might induce local destabilization and concur to protein transformation, leading to aggregation‐prone conformations. Here, we report CD and NMR studies on the α2‐helix‐derived peptide of maximal length (hPrP[180–195]) that is able to exhibit a regular structure different from the prevalently random arrangement of other α2‐helix‐derived peptides. This peptide, which has previously been shown to be affected by buffer composition via the ion charge density dependence typical of Hofmeister effects, corresponds to the C‐terminal sequence of the PrPC full‐length α2‐helix and includes the highly conserved threonine‐rich 188–195 segment. At neutral pH, its conformation is dominated by β‐type contributions, which only very strong environmental modifications are able to modify. On TFE addition, an increase of α‐helical content can be observed, but a fully helical conformation is only obtained in neat TFE. However, linking of the 173–179 segment, as occurring in wild‐type and mutant peptides corresponding to the full‐length α2‐helix, perturbs these intrinsic structural propensities in a manner that depends on whether the environment is water or TFE. Overall, these results confirm that the 180–195 parental region in hPrPC makes a strong contribution to the chameleon conformational behavior of the segment corresponding to the full‐length α2‐helix, and could play a role in determining structural rearrangements of the entire globular domain. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd. 相似文献
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Workalemahu M. Berhanu Ulrich H. E. Hansmann 《Protein science : a publication of the Protein Society》2012,21(12):1837-1848
Recent mutagenesis studies using the hydrophobic segment of Aβ suggest that aromatic π‐stacking interactions may not be critical for fibril formation. We have tested this conjecture by probing the effect of Leu, Ile, and Ala mutation of the aromatic Phe residues at positions 19 and 20, on the double‐layer hexametric chains of Aβ fragment Aβ16–22 using explicit solvent all‐atom molecular dynamics. As these simulations rely on the accuracy of the utilized force fields, we first evaluated the dynamic and stability dependence on various force fields of small amyloid aggregates. These initial investigations led us to choose AMBER99SB‐ILDN as force field in multiple long molecular dynamics simulations of 100 ns that probe the stability of the wild‐type and mutants oligomers. Single‐point and double‐point mutants confirm that size and hydrophobicity are key for the aggregation and stability of the hydrophobic core region (Aβ16–22). This suggests as a venue for designing Aβ aggregation inhibitors the substitution of residues (especially, Phe 19 and 20) in the hydrophobic region (Aβ16–22) with natural and non‐natural amino acids of similar size and hydrophobicity. 相似文献
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In this work, we report the ab initio folding of three different extended helical peptides namely 2khk, N36, and C34 through conventional molecular dynamics simulation at room temperature using implicit solvation model. Employing adaptive hydrogen bond specific charge (AHBC) scheme to account for the polarization effect of hydrogen bonds established during the simulation, the effective folding of the three extended helices were observed with best backbone RMSDs in comparison to the experimental structures over the helical region determined to be 1.30 Å for 2khk, 0.73 Å for N36 and 0.72 Å for C34. In this study, 2khk will be used as a benchmark case serving as a means to compare the ability of polarized (AHBC) and nonpolarized force field in the folding of an extended helix. Analyses conducted revealed the ability of the AHBC scheme in effectively folding the extended helix by promoting helix growth through the stabilization of backbone hydrogen bonds upon formation during the folding process. Similar observations were also noted when AHBC scheme was employed during the folding of C34 and N36. However, under Amber03 force field, helical structures formed during the folding of 2khk was not accompanied by stabilization thus highlighting the importance of electrostatic polarization in the folding of helical structures. Proteins 2013. © 2013 Wiley Periodicals, Inc. 相似文献
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Dan Zabetakis Lisa C. Shriver‐Lake Mark A. Olson Ellen R. Goldman George P. Anderson 《Protein science : a publication of the Protein Society》2019,28(10):1909-1912
Recently Bekker et al. [Bekker G‐J et al. Protein Sci. 2019;28:429–438.] described a computational strategy of applying molecular‐dynamics simulations to estimate the relative stabilities of single‐domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single‐domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti‐cholera toxin single domain antibody selected from a naïve library which has relatively low thermal stability, reflected by a melting point of 48°C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7°C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a usefulin silico approach to protein stabilization. 相似文献
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Jérôme Le Nours Leonardo De Maria Ditte Welner Christel T. Jørgensen Lars L. H. Christensen Torben V. Borchert Sine Larsen Leila Lo Leggio 《Proteins》2009,75(4):977-989
Microbial β‐1,4‐galactanases are glycoside hydrolases belonging to family 53, which degrade galactan and arabinogalactan side chains in the hairy regions of pectin, a major plant cell wall component. They belong to the larger clan GH‐A of glycoside hydrolases, which cover many different poly‐ and oligosaccharidase specificities. Crystallographic complexes of Bacillus licheniformis β‐1,4‐galactanase and its inactive nucleophile mutant have been obtained with methyl‐β(1→4)‐galactotetraoside, providing, for the first time, information on substrate binding to the aglycone side of the β‐1,4‐galactanase substrate binding groove. Using the experimentally determined subsites as a starting point, a β(1→4)‐galactononaose was built into the structure and subjected to molecular dynamics simulations giving further insight into the residues involved in the binding of the polysaccharide from subsite ?4 to +5. In particular, this analysis newly identified a conserved β‐turn, which contributes to subsites ?2 to +3. This β‐turn is unique to family 53 β‐1,4‐galactanases among all clan GH‐A families that have been structurally characterized and thus might be a structural signature for endo‐β‐1,4‐galactanase specificity. Proteins 2009. © 2008 Wiley‐Liss, Inc. 相似文献
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Gert‐Jan Bekker Benson Ma Narutoshi Kamiya 《Protein science : a publication of the Protein Society》2019,28(2):429-438
Single‐domain antibodies (sdAbs) function like regular antibodies, however, consist of only one domain. Because of their low molecular weight, sdAbs have advantages with respect to production and delivery to their targets and for applications such as antibody drugs and biosensors. Thus, sdAbs with high thermal stability are required. In this work, we chose seven sdAbs, which have a wide range of melting temperature (Tm) values and known structures. We applied molecular dynamics (MD) simulations to estimate their relative stability and compared them with the experimental data. High‐temperature MD simulations at 400 K and 500 K were executed with simulations at 300 K as a control. The fraction of native atomic contacts, Q, measured for the 400 K simulations showed a fairly good correlation with the Tm values. Interestingly, when the residues were classified by their hydrophobicity and size, the Q values of hydrophilic residues exhibited an even better correlation, suggesting that stabilization is correlated with favorable interactions of hydrophilic residues. Measuring the Q value on a per‐residue level enabled us to identify residues that contribute significantly to the instability and thus demonstrating how our analysis can be used in a mutant case study. 相似文献
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Xiaohui Cang Linlin Yang Jing Yang Cheng Luo Mingyue Zheng Kunqian Yu Huaiyu Yang Hualiang Jiang 《Proteins》2014,82(5):760-770
Two 8‐µs all‐atom molecular dynamics simulations have been performed on the two highly homologous G protein‐coupled receptor (GPCR) subtypes, β1‐ and β2‐adrenergic receptors, which were embedded in a lipid bilayer with randomly dispersed cholesterol molecules. During the simulations, cholesterol molecules accumulate to different surface regions of the two receptors, suggesting the subtype specificity of cholesterol–β‐adrenergic receptor interaction and providing some clues to the physiological difference of the two subtypes. Meanwhile, comparison between the two receptors in interacting with cholesterols shed some new light on general determinants of cholesterol binding to GPCRs. Our results indicate that although the concave surface, charged residues and aromatic residues are important, neither of these stabilizing factors is indispensable for a cholesterol interaction site. Different combinations of these factors lead to the diversified binding modes of cholesterol binding to the receptors. Our long‐time simulations, for the first time, revealed the pathway of a cholesterol molecule entering the consensus cholesterol motif (CCM) site, and the binding process of cholesterol to CCM is accompanied by a side chain flipping of the conserved Trp4.50. Moreover, the simulation results suggest that the I‐/V‐/L‐rich region on the extracellular parts of helix 6 might be an alternatively conserved cholesterol‐binding site for the class‐A GPCRs. Proteins 2014; 82:760–770. © 2013 Wiley Periodicals, Inc. 相似文献
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A molecular dynamics investigation of the helical forms adopted by (1→4)‐α‐L ‐guluronan in explicit water environment was carried out. Single chains and duplexes were modeled at 300 K starting both from 21 or 32 helical conformations and in the presence of a neutralizing amount of Ca2+ ions. All systems were allowed full conformational freedom. The initial perfect helices with integral screw symmetries were lost at the very beginning of simulations and two distinct behaviors were observed: At equilibrium the 21 models mostly retained the 21 local helical conformations while exploring the 32 ones the rest of the time. In duplexes the two chains, which behaved similarly, were well extended and slightly twisted. By contrast, the chains in 32 duplex models were dissimilar and explored a much broader conformational space in which 21 and 32 local helical conformations were dominant and equally represented but the 31 and other conformations were also present. The wide variety of conformations revealed in this study is consistent with the general difficulty in obtaining crystals of Ca2+‐guluronate with suitable lateral dimensions for crystallographic studies. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 562–571, 2013. 相似文献