Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of proteins based only on knowledge of their amino acid sequence. The secondary structure of proteins is determined by the pattern of hydrogen bonding. A large number of servers and tools are used to predict the secondary structure analysis.. Protein secondary structure refers to the local conformation proteins polypeptide backbone. There are two regular secondary structure states, α-helix (H) and β-strand (E), and one irregular secondary structure type, the coil region (C). Sander developed a secondary structure assignment method Dictionary of Secondary Structure of Proteins (DSSP)3, which automatically assigns secondary structure into eight states (H, E, B, T, S, L, G, and I) according to hydrogen-bonding patterns. These eight states are often further simplified into three states of helix, sheet and coil. The most widely used convention is that helix is designated as G, ...
Earlier chapters introduced alpha-helices and beta-sheets ( Secondary Structure), and some common motifs composed of 2 or 3 of these elements (Supersecondary Structure). Tertiary structure describes the folding of the polypeptide chain to orientate the different secondary structure elements in a particular arrangement. The previous chapter offered a description of certain types of domains, such as globular, membrane-spanning, and fibrous. As helices and sheets are units of secondary structure, so the domain is the unit of tertiary structure. In multi-domain proteins, tertiary structure includes the arrangement of domains relative to each other as well as that of the chain within each domain. There is a blurred distinction between supersecondary structure and tertiary structure. The introduction of the term supersecondary structure was necessary when it became clear that certain arrangements of two or three secondary structures are present in many different protein structures, even with ...
This paper describes a Bayesian learning based approach to protein secondary structure prediction. Four secondary structure types are considered, including
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
A powerful tool used to monitor secondary structure is circular dichroism (CD), which is the differential absorbance of left and right circularly polarized light. Since proteins consist of chiral amino acids, they are CD active and exhibit distinct CD spectra that are sensitive to the proteins secondary structure. This spectra can provide a qualitative snapshot of the protein structure or the secondary structure composition of a protein can be estimated from the far UV CD spectrum using a number of algorithms, several of which are made available in Olis GlobalWorks software.. Protein secondary structure can also be used to monitor protein folding and unfolding. An equilibrium study consists of collection of CD spectra as a function of increasing temperature or chemical denaturant. As the protein unfolds, the CD spectrum reflects this. Fitting data at a single wavelength or the full spectral scans during this denaturation process provides thermodynamic information such as the melting temperature ...
Activation helix orientation of estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations
Quanta will calculate hydrogen bonds and then analyze the secondary structure in its Protein Design Module, but it seems like a rather large investment if all you want to do is determine the secondary structure......... ........Tom Branham ...
Diatoms and sponges use proteins, long chain polyamines, and other biomolecules to assemble silica structures of controlled morphology. Investigated here are biosilicification peptides. Under mild conditions, these peptides produce silica nanoparticles from solutions of silicic acid, whereas harsh methods are currently employed to produce these nanoparticles commercially. Biomimetic precipitation studies have shown that LKα14 (Ac-LKKLLKLLKKLLKL- C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, co-precipitates with silica to form nanospheres. Previous work con- firmed the α-helical secondary structure in both the neat and silica-complexed states of the peptide and suggested that the tetrameric bundles of peptide that are known to form in solution persisted in the silica-complexed form. To further investigate the peptide aggregation, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how the ...
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Designed peptides that fold autonomously to specific conformations in aqueous solution are useful for elucidating protein secondary structural preferences. For example, autonomously folding model systems have been essential for establishing the relationship between alpha-helix length and alpha-helix stability, which would be impossible to probe with alpha-helices embedded in folded proteins. Here, we use designed peptides to examine the effect of strand length on antiparallel beta-sheet stability. alpha-Helices become more stable as they grow longer. Our data show that a two-stranded beta-sheet (beta-hairpin) becomes more stable when the strands are lengthened from five to seven residues, but that further strand lengthening to nine residues does not lead to further beta-hairpin stabilization for several extension sequences examined. (In one case, all-threonine extension, there may be an additional stabilization on strand lengthening from seven to nine residues.) These results suggest that there may be
The following is a list of how-to and tutorial content that matched your search term. ProgrammableWebs how-to content comes from two sources; full-blown tutorials that we publish ourselves and other highly relevant tutorials that we find elsewhere on the Web. This list represents on combination of both tutorial types and if you go to ProgrammableWebs API University, youll not only be able to find more, they are organized based on your role (API providers or developers who consumes APIs). If you know of a tutorial that would be of interest to the ProgrammableWeb community, wed like to know about it. Be sure to check our guidelines for making contributions to ProgrammableWeb ...
article{1e7da19b-137f-4fcf-9f74-7f6d6b4d2ece, abstract = {The loop region of chymotrypsin inhibitor 2 from barley has been employed as a scaffold for testing the intrinsic propensity of a peptide fragment to form a secondary structure. The helix formation of the nine amino acid residue segment Lys-Gln- Ala-Val- Asp- Asn- Ala-Tyr-Ala of helix E from subtilisin Carlsberg has been studied by the construction of a hybrid consisting of chymotrypsin inhibitor 2 (CI2) where part of the active loop has been replaced by the nonapeptide. An expression system for a truncated form of C12 where the 19 structureless residues of the N-terminus have been removed and Leu20 replaced,br/,,br, by methionyl was constructed from the entire 83-residue wild-type C12 gene by polymerase chain reaction,br/,,br, methodology. The gene encoding the hybrid was constructed from the truncated inhibitor gene. The stability of the truncated inhibitor and of the hybrid toward guanidinium chloride denaturation was examined. From ...
jay ananth wrote: , I need one help from u... , , search for best tools for the following : , 1.Secondary Structure prediction in RNA , 2.Protein Secondary Structure Prediction. , 3.Prediction of disordered regions in proteins.. , 4.Case Std on Structure-function relationships in proteins , 5.Prediction of transmembrane regions in proteins , 6.Characterization of antigenecity in polypeptides- epitope mapping , , , , Are you looking for computational tools to do the above ? Can you be more specific ? Autodock, Gromacs are some of the tools that you can use for protein structure prediction. -- Deepan http://codeshepherd.com/ http://codeshepherd.blogspot.com/ http://sudoku-solver.net/ ...
In recent years, the nuclear receptors (NR) dynamics have been studied extensively by various approaches. However, the transition path of helix 12 (H12) to an agonist or an antagonist conformation and the exchange pathway between these states is not clear yet. A number of accelerated molecular dynamics (aMD)
Motivation: Transmembrane beta-barrels exist in the outer membrane of gram-negative bacteria as well as in chloroplast and mitochondria. They are often involved in transport processes and are promising antimicrobial drug targets. Structures of only a few beta-barrel protein families are known. Therefore, a method that could automatically generate such models would be valuable. The symmetrical arrangement of the barrels suggests that an approach based on idealized geometries may be successful. Results: Here, we present tobmodel; a method for generating 3D models of beta-barrel transmembrane proteins. First, alternative topologies are obtained from the BOCTOPUS topology predictor. Thereafter, several 3D models are constructed by using different angles of the beta-sheets. Finally, the best model is selected based on agreement with a novel predictor, ZPRED3, which predicts the distance from the center of the membrane for each residue, i.e. the Z-coordinate. The Z-coordinate prediction has an average ...
The DSSP program works by calculating the most likely secondary structure assignment given the 3D structure of a protein. It does this by reading the position of the atoms in a protein (the ATOM records in a PDB file) followed by calculation of the H-bond energy between all atoms. The best two H-bonds for each atom are then used to determine the most likely class of secondary structure for each residue in the protein.. This means you do need to have a full and valid 3D structure for a protein to be able to calculate the secondary structure. Theres no magic in DSSP, so e.g. it cannot guess the secondary structure for a mutated protein for which you dont have the 3D structure ...
Many proteins are organized into several units. A structural domain is an element of the proteins overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Many domains are not unique to the protein products of one gene or one gene family but instead appear in a variety of proteins. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to; for example, the calcium-binding domain of calmodulin. Because they are self-stabilizing, domains can be swapped by genetic engineering between one protein and another to make chimeras. A motif in this sense refers to a small specific combination of secondary structural elements (such as helix-turn-helix). These elements are often called supersecondary structures. Fold refers to a global type of arrangement, like helix-bundle or beta-barrel. Structure motifs usually consist of just a few elements, e.g. the helix-turn-helix has just ...
Secondary structure prediction and consensus sequence of PelD and PleD. A. Secondary structure predication was made using the web-based ProteinPredict program h
This study demonstrates the feasibility of creating structurally complex and catalytically active enzymes by assembling randomized modules that are constructed from a limited set of building blocks and biased toward helical secondary structure by binary patterning. The binary distribution of hydrophilic/hydrophobic residues is inherent in the genetic code (NAN/NTN), and our results support suggestions (9, 26, 27) that modern enzymes could have evolved from primitive precursors constructed from a relatively small number of polar and nonpolar amino acids. There is, nevertheless, a low probability of finding catalysts, even when both position and identity of all critical active site residues are determined in advance. This finding contrasts with the ease of obtaining folded helical proteins through binary patterning (9), underscoring the exacting demands that catalysis places on protein design.. Extrapolating from our data and from modest sequence constraints on interhelical turns (23, 28-30), we ...
Beta sheets parallel, In parallel beta sheets, the adjacent polypeptide chains run in the same direction. Typically parallel beta sheets are large structures that usually consist of at least five strands. Parallel beta sheets usually have hydrophobic residues on both sides of the sheet.
C. E. N. T. E. R. F. O. R. I. N. T. E. G. R. A. T. I. V. E. B. I. O. I. N. F. O. R. M. A. T. I. C. S. V. U. Lecture 14 Secondary Structure Prediction. Bioinformatics Center IBIVU. Protein structure . Linus Pauling (1951). Slideshow 80412 by LeeJohn
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure ...
Lee, C., L. Kalmar, B. Xue, P. Tompa, G. W. Daughdrill, V. N. Uversky, and K-H. Han, Contribution of proline to the pre-structuring tendency of transient helical secondary structure elements in intrinsically disordered proteins., Biochim Biophys Acta, vol. 1840, issue 3, pp. 993-1003, 2014 Mar. ...
Secondary structure of proteins refers to local and repetitive conformations, such as α‐helices and β‐strands, which occur in protein structures
Synonyms for alpha-helix, alpha-helix in Free Thesaurus. Antonyms for alpha-helix, alpha-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for alpha-helix, alpha-helix?
View Notes - Bio 1A Lect 2 Quiz from BIO 1A at Berkeley. Bio 1A Lect 2 Quiz 50% adenine aldose alpha alpha-helix amino Amino acids antiparallel beta beta-pleated sheets blood flow carbonyl cell
Its not true that the Ramachandran plot will determine the secondary structure of an amino acid. Ramachandran plots show the sterically allowed phi/psi angles of an amino acid. As such nearly all non-glycine amino acids are in alpha/beta spaces. Random coil segments of structure consist mostly of alpha and beta conformation amino acids in nonsense ...
As evidenced by a buried core of hydrophobic residues within globular proteins, hydrophobicity provides essential insights into the folding structure of pr
6. Helix Propensities of Amino Acid Residues via Thioester Exchange. Fisher, B. F.; Hong, S.H.; Gellman, S.H. J. Am. Chem. Soc. DOI: 10.1021/jacs.7b07930. 5. Detection and analysis of chimeric tertiary structures by backbone thioester exchange: Packing of an alpha helix against an alpha/beta-peptide helix, Price, J. L.;Hadley,E. B.;Steinkruger,J. D. and Gellman,S. H., Angew.Chem.Int.Ed Engl., 2010, 49, 368-371.. 4. Preferred Side-chain Constellations at Antiparallel Coiled-coil Interfaces, E. B. Hadley, O. D. Testa, D. N. Woolfson and S. H. Gellman Proc. Natl. Acad. Sci. USA 2008, 105, 530.. 3. An Antiparallel α-Helical Coiled-Coil Model System for Rapid Assessment of Side Chain Recognition at the Hydrophobic Interface, E. B. Hadley an d S. H. Gellman J. Am. Chem. Soc. 2006, 128, 16444.. 2. Thermodynamic Analysis of β-Sheet Secondary Structure Via Backbone Thioester Exchange, E. B. Hadley, A. M. Witek, F. Friere, A. J. Peoples and S. H. Gellman Angew. Chem. Int. Ed. 2007, 46, ...
Two hypotheses have been proposed for the role of turns in protein folding. In one view, turns play a critical role in folding by bringing together and fostering interactions between regular secondary structure elements. This view is supported by mutagenesis studies indicating a critical role for particular residues in the turns of some proteins. Also, nonnative isomers of X-Pro peptide bonds in turns can completely block the conformational folding of some proteins. In the opposing view, turns play a passive role in folding. This view is supported by the poor amino-acid conservation observed in most turns. Also, non-native isomers of many X-Pro peptide bonds in turns have little or no effect on folding. ...
Lyu, P C; Wemmer, D E; Zhou, H X et al. (1993) Capping interactions in isolated alpha helices: position-dependent substitution effects and structure of a serine-capped peptide helix. Biochemistry 32:421-5 ...
On Sun, 13 May 2007, Rolf Kalbermatter wrote: , Changelog , include/winsvc.h , Fix names of structure elements to match PSDK [...] , diff --git a/include/winsvc.h b/include/winsvc.h , index 7a29e8f..af56d29 100644 , --- a/include/winsvc.h , +++ b/include/winsvc.h , @@ -196,13 +196,13 @@ DECL_WINELIB_TYPE_AW(LPENUM_SERVICE_STATUS) , typedef struct _ENUM_SERVICE_STATUS_PROCESSA { , LPSTR lpServiceName; , LPSTR lpDisplayName; , - SERVICE_STATUS_PROCESS ServiceStatusProcess; , + SERVICE_STATUS_PROCESS ServiceStatus; , } ENUM_SERVICE_STATUS_PROCESSA, *LPENUM_SERVICE_STATUS_PROCESSA; [..] This patch is wrong. This field is really called ServiceStatusProcess in the PSDK. -- Francois Gouget ,fgouget at free.fr, http://fgouget.free.fr/ You can have my guns when you pry them from my kids cold, dead hands ...
Scientists have identified where a four-stranded version of DNA exists within the genome of human cells, and suggest that it may hold a key to developing new, targeted therapies for cancer.
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for alpha-helix). {{ pdb }} {{ chain }} ...
Chord diagram. The backbone chain is represented by a circle. Chords (arcs) connect those residues that are in contact. Structure elements can be removed from the above chord diagram by clicking on their symbols. In case of proteins for which it is possible to identify the secondary structure, symbols are given in the Stride classification (e.g. AH stands for alpha-helix). {{ pdb }} {{ chain }} ...
The amino-terminal extremity of the human immunodeficiency virus type 1 transmembrane protein (gp41) is thought to play a pivotal role in the fusion of virus membranes with the plasma membrane of the target cell and in syncytium formation. Peptides with sequences taken from the human immunodeficiency virus type 1 gp41 fusogenic (synthetic peptides SPwt and SP-2) and nonfusogenic (SP-3 and SP-4) glycoproteins adopt mainly a beta-sheet conformation in the absence of lipid, as determined by attenuated total reflection Fourier transform infrared spectroscopy, and after interaction with large unilamellar liposomes, the beta-sheet is partly converted into an alpha-helical conformation. Peptides SPwt and SP-2 but not SP-3 or SP-4 were able to promote lipid mixing as assessed by fluorescence energy transfer assay and dye leakage in a vesicle leakage assay. By using polarized attenuated total reflection Fourier transform infrared spectroscopy, SPwt and SP-2 were found to adopt an oblique orientation in ...
Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The Chou-Fasman algorithm, one of the earliest methods, has been successfully applied to the prediction. However, this method has its limitations due to low accuracy, unreliable parameters, and over prediction. Thanks to the recent development in protein folding type-specific structure propensities and wavelet transformation, the shortcomings in Chou-Fasman method are able to be overcome. We improved Chou-Fasman method in three aspects. (a) Replace the nucleation regions with extreme values of coefficients calculated by the continuous wavelet transform. (b) Substitute the original secondary structure conformational parameters with folding type-specific secondary structure propensities. (c) Modify Chou-Fasman rules. The CB396 data set was tested by using improved Chou-Fasman method and three indices: Q3
in Journal of Protein Chemistry (1994), 13(1), 77-88. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 ... [more ▼]. Peptides corresponding to lipid binding domains of Apo B-100 were synthesized, purified, and incubated with dimyristoylphosphatidylcholine (DMPC) liposomes. The secondary structure of the apo B-100 peptide-lipid complexes was evaluated by attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR). Those peptides belonging to the hydrophobic core domain of apo B-100 when associated with phospholipids were rich in beta sheet structure; a predominant alpha helical conformation was shown to be associated with one peptide located in a surface region of apo B-100. IR dichroic spectra revealed, in the case of the core peptides, that the beta sheet component is the only oriented structure with respect to the ...
In this chapter we provide a survey of protein secondary and supersecondary structure prediction using methods from machine learning. Our focus is on machine learning methods applicable to β-hairpin and β-sheet prediction, but we also discuss methods for more general supersecondary structure prediction. We provide background on the secondary and supersecondary structures that we discuss, the features used to describe them, and the basic theory behind the machine learning methods used. We survey the machine learning methods available for secondary and supersecondary structure prediction and compare them where possible.. ...
In this study, hierarchical cluster analysis (HCA) and principal component analysis (PCA) were used to classify blends produced from diesel S500 and different kinds of biodiesel produced by the TDSP methodology. The different kinds of biodiesel studied in this work were produced from three raw materials: soybean oil, waste cooking oil and hydrogenated vegetable oil. Methylic and ethylic routes were employed for the production of biodiesel. HCA and PCA were performed on the data from attenuated total reflectance Fourier transform infrared spectroscopy, showing the separation of the blends into groups according to biodiesel content present in the blends and to the kind of biodiesel used to form the mixtures ...
LmrP is an electrogenic H(+)/drug antiporter that extrudes a broad spectrum of antibiotics. Five carboxylic residues are implicated in drug binding (Asp142 and Glu327) and proton motive force-mediated restructuring (Asp68, Asp128 and Asp235). ATR-FTIR (Attenuated Total Reflection - Fourier Transform Infrared) and tryptophan quenching experiments revealed that phosphatidylethanolamine (PE) is required to generate the structural intermediates induced by ionization of carboxylic residues. Surprisingly, no ionization-induced conformational changes were detectable in the absence of PE, suggesting either that carboxylic acid residues do not ionize or that ionization does not lead to any conformational change. The mean pKa of carboxylic residues evaluated by ATR-FTIR spectroscopy was 6.5 for LmrP reconstituted in PE liposomes, whereas the pKa calculated in the absence of PE was 4.6. Considering that 16 of the 19 carboxylic residues are located in the extramembrane loops, the pKa values obtained in the ...
TY - JOUR. T1 - Proton nuclear magnetic resonance assignments and secondary structure determination of the Co1E1 rop (rom) protein. AU - Eberle, W.. AU - Klaus, W.. AU - Cesareni, G.. AU - Sander, C.. AU - Rosch, P.. PY - 1990. Y1 - 1990. N2 - The complete resonance assignment of the Co1E1 rop (rom) protein at pH 2.3 was obtained by two-dimensional (2D) proton nuclear magnetic resonance spectroscopy (1H NMR) at 500 and 600 MHz using through-bond and through-space connectivities. Sequential assignments and elements of regular secondary structure were deduced by analysis of nuclear Overhauser enhancement spectroscopy (NOESY) experiments and 3J(HNα) coupling constants. One 7.2-kDa monomer of the homodimer consists of two antiparallel helices connected by a hairpin loop at residue 31. The C-terminal peptide consisting of amino acids 59-63 shows no stable conformation. The dimer forms a four-helix bundle with opposite polarization of neighboring elements in agreement with the X-ray structure.. AB - ...
TY - JOUR. T1 - Salivary molecular spectroscopy. T2 - a sustainable, rapid and non-invasive monitoring tool for diabetes mellitus during insulin treatment. AU - Caixeta, Douglas C.. AU - Aguiar, Emília M. G.. AU - Cardoso-Sousa, Léia. AU - Coelho, Líris M. D.. AU - Oliveira, Stephanie W.. AU - Espindola, Foued S.. AU - Raniero, Leandro. AU - Crosara, Karla T. B.. AU - Baker, Matthew J.. AU - Siqueira, Walter L.. AU - Sabino-Silva, Robinson. PY - 2020/3/17. Y1 - 2020/3/17. N2 - Monitoring of blood glucose is an invasive, painful and costly practice in diabetes. Consequently, the search for a more cost-effective (reagent-free), non-invasive and specific diabetes monitoring method is of great interest. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used in diagnosis of several diseases, however, applications in the monitoring of diabetic treatment are just beginning to emerge. Here, we used ATR-FTIR spectroscopy to evaluate saliva of non-diabetic (ND), ...
Abstract This paper proposes a direct and efficient method to discriminate between counterfeit and authentic Cialis and Viagra samples by combining attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy with multivariate techniques. The chemical profile of 53 commercial samples (Viagra®, Cialis®) and 104 counterfeit samples (Viagra and Cialis) from distinct seizures were obtained from ATR-FTIR…. [...] ...
Looking for online definition of alpha helix conformation in the Medical Dictionary? alpha helix conformation explanation free. What is alpha helix conformation? Meaning of alpha helix conformation medical term. What does alpha helix conformation mean?
TY - JOUR. T1 - Interhelical interactions in the gp41 core. T2 - Implications for activation of HIV-1 membrane fusion. AU - Wang, Shilong. AU - York, Joanne. AU - Shu, Wei. AU - Stoller, Marisa O.. AU - Nunberg, Jack H.. AU - Lu, Min. PY - 2002/6/11. Y1 - 2002/6/11. N2 - The human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein complex (gp120-gp41) promotes viral entry by mediating the fusion of viral and cellular membranes. Formation of a stable trimer-of-hairpins structure in the gp41 ectodomain brings the two membranes into proximity, leading to membrane fusion. The core of this hairpin structure is a six-helix bundle in which three carboxyl-terminal outer helices pack against an inner trimeric coiled coil. Here we investigate the role of these conserved interhelical interactions on the structure and function of both the envelope glycoprotein and the gp41 core. We have replaced each of the eight amino acids at the buried face of the carboxyl-terminal helix with a representative ...
Research Corridor has published a new research study titled Circular Dichroism Spectroscopy Market - Growth, Share, Opportunities, Competitive Analysis and Forecast, 2017 - 2025. The Circular Dichroism Spectroscopy Market report studies current as well as future aspects of the Circular Dichroism Spectroscopy Market based upon factors such as market dynamics, key ongoing trends and segmentation analysis. Apart from the above elements, the Circular Dichroism Spectroscopy Market research report provides a 360-degree view of the Lipstick Packing industry with geographic segmentation, statistical forecast and the competitive landscape.. Browse the complete report at http://www.researchcorridor.com/circular-dichroism-spectroscopy-market/. Geographically, the Circular Dichroism Spectroscopy Market report comprises dedicated sections centering on the regional market revenue and trends. The Circular Dichroism Spectroscopy Market has been segmented on the basis of geographic regions into North America, ...
Transmembrane helix-helix interactions may have at least two major functions: 1) intramolecular helix-helix interactions would serve to stabilize the tertiary structure of the protein in the membrane bilayer, and 2) helix-helix interactions between two or more integral membrane proteins appear to regulate ligand-initiated response systems. X-Ray crystallography of the α1-subunit of Na/K-ATPase (Figure 6) indicates that 5 of the 10 helices (M4, M5, M6, M7 and M8) lie largely within the core of the α1-subunit, whereas the remaining 5 helices (M1, M2, M3 M9 and M10)) are on the periphery. Computer-generated projections of each helix (Figure 7) indicate that helices within the core are disordered whereas peripheral helices are largely ordered. This suggests that the disordered helices contribute to and/or maintain the tertiary structure of the α1-subunit, whereas the peripheral ordered helices are available for interaction with ordered helices of neighboring integral membrane proteins.. In our ...
The model six-residue linear peptide AAGDYY-NH2 from TEM-1 beta -lactamase inhibitor protein and BLIP was predicted to adopt a beta -turn conformation and synthesized in order to elucidate the mechanism of beta -turn formation and stability. Its structural preferences in solution were comprehensively characterized using CD (circular dichroism), FT-IR and H-1-NMR spectroscopy. The set of observed short- and medium-range NOEs, the restrained molecular dynamics simulation, CD and FT-IR spectroscopy were consistent with the formation of beta -turn in solution by the model peptide. The results implicate beta -turn playing an important role in the process of protein folding. ...
To maintain genome integrity, segmented double-stranded RNA viruses of the Reoviridae family must accurately select and package a complete set of up to a dozen distinct genomic RNAs. It is thought that the high fidelity segmented genome assembly involves multiple sequence-specific RNA-RNA interactions between single-stranded RNA segment precursors. These are mediated by virus-encoded non-structural proteins with RNA chaperone-like activities, such as rotavirus (RV) NSP2 and avian reovirus sigma NS. Here, we compared the abilities of NSP2 and sigma NS to mediate sequence-specific interactions between RV genomic segment precursors. Despite their similar activities, NSP2 successfully promotes inter-segment association, while sigma NS fails to do so. To understand the mechanisms underlying such selectivity in promoting inter-molecular duplex formation, we compared RNA-binding and helix-unwinding activities of both proteins. We demonstrate that octameric NSP2 binds structured RNAs with high affinity, ...
CiteSeerX - Document Details (Isaac Councill, Lee Giles, Pradeep Teregowda): Prediction of trans-membrane helices continues to be a difficult task with a few prediction methods clearly taking the lead; none of these is clearly best on all accounts. Recently, we have carefully set up protocols for benchmarking the most relevant aspects of prediction accuracy and have applied it to|30 prediction methods. Here, we present the extension of that analysis to the level of an automatic web server evaluating new methods
The great majority of helical membrane proteins are inserted co-translationally into the ER membrane through a continuous ribosome-translocon channel. The efficiency of membrane insertion depends on transmembrane (TM) helix amino acid composition, the helix length and the position of the amino acids within the helix. In this work, we conducted a computational analysis of the composition and location of amino acids in transmembrane helices found in membrane proteins of known structure to obtain an extensive set of designed polypeptide segments with naturally occurring amino acid distributions. Then, using an in vitro translation system in the presence of biological membranes, we experimentally validated our predictions by analyzing its membrane integration capacity. Coupled with known strategies to control membrane protein topology, these findings may pave the way to de novo membrane protein design. PubMed: 26987712. Doi: 10.1038/srep23397.. ...
The cpssp package ------------------------------------------------------------------------------ This package is released under the LaTeX Project Public License v1.3c or later (see http://www.latex-project.org/lppl.txt). The cpssp package allows you to draw a two-dimensional representation of a proteins secondary structure in LaTeX. Besides, it is possible to graphically compare protein secondary structure predictions. One can both compare predictions from a single program for several protein sequences (which have been aligned using any appropriate algorithm) and predictions from several programs for a single protein sequence. Installation: Run cpssp.ins through LaTeX and follow the instructions. -- Wolfgang Skala June 6th, 2009 ...
For the current problem we define a neural network with one input layer, one hidden layer and one output layer. The input layer encodes a sliding window in each input amino acid sequence, and a prediction is made on the structural state of the central residue in the window. We choose a window of size 17 based on the statistical correlation found between the secondary structure of a given residue position and the eight residues on either side of the prediction point [2]. Each window position is encoded using a binary array of size 20, having one element for each amino acid type. In each group of 20 inputs, the element corresponding to the amino acid type in the given position is set to 1, while all other inputs are set to 0. Thus, the input layer consists of R = 17x20 input units, i.e. 17 groups of 20 inputs each.. In the following code, we first determine for each protein sequence all the possible subsequences corresponding to a sliding window of size W by creating a Hankel matrix, where the ith ...
An alpha helix (α-helix) is a twisted part of a protein. It is one of the two most common parts of the secondary structure, or shape, of a protein. The other is the beta sheet. An alpha helix is created by alternating groups of atoms. There is a carbonyl group, created by a carbon atom double bonded to an oxygen atom, and an amine group, created by a nitrogen atom bonded to a hydrogen atom. Each section containing one of each of these groups is called a residue, a general term for a small part of a molecule. Each amine group forms a hydrogen bond with the carbonyl group four residues earlier. A prion is a protein that causes disease by changing the shape of another protein. It does this by changing some of the alpha helices, which are more common in normal cells, to beta sheets, which are more common in prions. The alpha helix consists of 3.6 residues per turn. All hydrogen bonds face in the same direction. If two or more alpha helices come together, they become a tertiary structure. (Ex. Five ...
Synonyms for a-helix in Free Thesaurus. Antonyms for a-helix. 15 synonyms for helix: spiral, twist, curl, loop, coil, corkscrew, gyre, curlicue, volute, spiral, coil, volute, whorl, spiral, genus Helix. What are synonyms for a-helix?
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a plug (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013). ...
Secondary structure formation of FRA16B DNA following denaturation and re-annealing (reduplexing) reaction. (A) Gel electrophoresis analysis of re-annealed FRA1
This presentation is designed as an aid in teaching material on the secondary structures of proteins. Buttons are intended for the instructors use and are labeled with key words only. Movies are timed so as to allow for explanations between the movements and views of the molecule. To obtain the greatest benefit from the presentation, it is helpful to become fully familiar with the buttons ...
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins.
Circular Dichroism (CD) analysis from SGS - meet regulatory requirements with class-leading CD spectroscopic analysis, alpha helix beta sheet analysis, and secondary and tertiary structure analysis. Learn more.
The mechanism of beta-sheet formation remains a fundamental issue in our understanding of the protein folding process, but is hampered by the often encountered kinetic competition between folding and aggregation. The role of local versus nonlocal interactions has been probed traditionally by mutagenesis of both turn and strand residues. Recently, rigid organic molecules that impose a correct chain reversal have been introduced in several small peptides to isolate the importance of the long-range interactions. Here, we present the incorporation of a well-studied beta-turn mimic, designated as the dibenzofuran-based (DBF) amino acid, in the B1 domain of streptococcal protein G (B1G), and compare our results with those obtained upon insertion of the same mimic into the N-terminal beta-hairpin of B1G (O Melnyk et al., 1998, Lett Pept Sci 5:147-150). The DBF-B1G domain conserves the structure and the functional and thermodynamical properties of the native protein, whereas the modified peptide does ...
A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Torque force may be applied by the ribosome co-translationally, and when accompanied by simultaneous restriction of the rotational mobility of the distal part of the growing chain, the resulting tension in the protein backbone would facilitate the formation of local secondary structure and direct the folding process. Our model of the early stages of protein folding in vivo postulates that the free motion of both terminal regions of the protein during its synthesis and maturation is restricted. The long-known but
Major Professor: Dr. Tim Cross. Structure determination of M. Tuberculosis small helical membrane proteins in lipid by solid state nuclear magnetic resonance. ...
A regular stress test helps to assess coronary blockages by monitoring EKG changes during treadmill exercise protocols. Although helpful in making a diagnosis, a regular stress test lacks the sensitivity and specificity of nuclear stress tests.. For more information on regular stress tests, please visit our Heart Center.. ...
Many different proteins aggregate into amyloid fibrils characterized by cross-beta structure. beta-strands contributed by distinct protein molecules are generally found in a parallel in-register alignment. Here, we describe the web server for a novel algorithm, prediction of amyloid structure aggreg …
The surface of beta-sheet proteins contains amphiphilic regions which may provide clues about protein folding.s profile, publications, research topics, and co-authors
These three amino acids perform a proton relay reaction to transfer electrons between substrate and cofactor. 3α-HSD is capable of running the reaction both ways, either oxidizing or reducing the substrate and cofactor depending on the state of the testosterone. Tyr55 acts as acid, and donates a proton to the steroid--,Tyr55 forms a hydrogen bond to Lys84 for stabilization--,Lys84 forms a salt link to Asp50 for further stability. In Dr. Bantas protein, this reaction must only be run so that the sugar will be oxidized and the cofactor, reduced. The transfer of electrons from cofactor to circuit is already fairly efficient, but the key to an efficient reaction is in transferring the electron from substrate to cofactor. This is where the catalytic triad is extremely important. Dark Grey highlights the beta barrel and helix structure. The barrel consists of eight parallel beta strands and eight anti-parallel alpha helices. The bottom is sealed by two antiparallel beta strands (6-10 and 13-18). ...
Online resource for oligonucleotide and primer design, calculting melting temperature, secondary structure determination, PCR resource and primer databases
The secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids. Secondary structure was predicted by using the programs PSIPRED and ALB. The residues predicted as helical are marked by H by PSIPRED and by H and & by ALB, and those predicted as -structural are marked by E by PSIPRED and by S and B by ALB ...
1qkx: Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II region of the Ramachandran plot.
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The level of protein structure in which combinations of secondary protein structures (ALPHA HELICES; BETA SHEETS; loop regions, and AMINO ACID MOTIFS) pack together to form folded shapes. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. . ...
Regarding the secondary structure of proteins, I know that there are 3 main types. The beta sheet formation is made up of beta strands stabilized by hydrogen bonds to form an anti parallel or a parallel structure. I learned that these beta strands are a zigzag sequence of amino acids, but what traits of beta strands differentiate it from the primary structure? Or are the beta strands just primary structures that link together to make beta sheets?. ...
The publication AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 10000 of the best publications in CiteWeb. Also in the category Chemistry it is included to the Top 1000. Additionally, the publicaiton AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. is placed in the Top 1000 among other scientific works published in 1996 ...
1EM7: Structure of a protein G helix variant suggests the importance of helix propensity and helix dipole interactions in protein design.
GCE CIE Biology - In this article we will explain the primary structure, secondary structure, tertiary structure and quaternary structure of proteins, and also describe the four ma
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Alpha helix   A common motif in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled conformation, resembling a spring,
The pG1 pseudoGTPase domain adopts a small GTPase fold, with a central 6-stranded beta-sheet surrounded by four alpha-helices. The conserved GTPase motifs from the pG1 pseudoGTPase domain, which is not a nucleotide- binding domain ...
1JTN: Crystal Structures of a T4-lysozyme Duplication-extension Mutant Demonstrate that the Highly Conserved beta-Sheet Region has Low Intrinsic Folding Propensity
Vilayanur Ramachandran tells us what brain damage can reveal about the connection between celebral tissue and the mind, using three startling delusions as examples.