Is Protein Polar Or Nonpolar

Advances in Protein Chemistry and Structural Biology

Steven One thousand. Wise , ... Anthony Due south. Weiss , in Advances in Protein Chemistry and Structural Biological science, 2009

A Elastin Sequence-Based Hydrogels

Dominating over 75% of its content with just four nonpolar amino acids (Gly, Val, Ala, Pro), the amino acid sequence of tropoelastin contains many repeating motifs. Typical examples include sequences such equally VGVPG ( Sandberg et al., 1986) and VPGVG or VGGVG (Li and Daggett, 2002). Synthetic polypeptides taking reward of the intrinsic elasticity provided past these sequences accept been widely studied and have strong potential for tissue engineering applications (Chilkoti et al., 2006). Individual domains of tropoelastin have besides been produced, which take later formed the basis of a minimalist approach to understanding the associates of elastin. Specifically the relationship betwixt structure and mechanical properties of elastin tin be studied using reassembled tropoelastin domains, given that even very short sequences will cocky-get together and can be cross-linked (Bellingham et al., 2001). Soluble elastin sequence-based molecules accept been stabilized through the utilise of chemical cross-linkers including 1-ethyl-3-(iii-dimethylaminopropyl)carbodiimide (EDC) and Northward-hydroxysuccinimide (NHS), glutaraldehyde (GA), bis(sulfosuccinimidyl) suberate (BS3), genipin (GP), pyrroloquinoline quinone (PQQ), and one,6-diisocyanatohexane (HMDI). Cross-linking of these soluble elastins has led to the formation of a diversity of hydrogels. (Mithieux et al., 2009).

Elastin-like polypeptides consisting of VPGXG repeats (where X was Lys every vii or 17 pentapeptides, otherwise V), have been synthesized and chemically cross-linked to produce hydrogels. Gels ranged in stiffness from 0.24 to 3.seven kPa at 7 ˚C and from one.6 to 15 kPa at 37 ˚C depending on protein concentration, lysine content, and molecular weight. Changes in gel backdrop suggest that at low temperatures, these structures are nearly completely elastic (Trabbic-Carlson et al., 2003). Improvements to the mechanical and cell-interactive properties of these polypeptide materials has been achieved past copolymerizing sequence blocks from multiple parts of the elastin sequence, or combining with elements from other proteins. Constructs containing repeating elastin-derived (VPGIG)x repeating sequences, likewise as jail cell-binding domains derived from fibronectin were cross-linked using glutaraldehyde. Tensile properties of cantankerous-linked protein films were establish to be inversely related to the molecular weights of the engineered constructs which varied from 14 to 59 kDa. At the highest cross-link density and everyman molecular weight, the elastic modulus was found to be similar to that of native elastin (Welsh and Tirrell, 2000).

The utilise of recombinant human being elastin polypeptides has demonstrated that equally few as three tropoelastin hydrophobic domains flanking ii cross-linking domains are sufficient to back up a self-assembly process that aligns lysines for cross-linking (Keeley et al., 2002). These sequences comprise sufficient information to self-organize into fibrillar structures and promote the formation of lysine-derived cross-links. When cross-linked with PQQ, these materials had an extensional rubberband modulus of ∼250 kPa, approaching the value ordinarily described for native elastin (300–600 kPa) (Fung, 1993). Sheets could be subjected to extensional strains of ∼100% before breaking. The intrinsic ability of such polypeptides to self-organize into polymer structures not just makes them a useful model for agreement the process of associates of elastin, but also sheds light on the blueprint of self-assembling biomaterials (Bellingham et al., 2003).

Recombinant human elastin polypeptides have besides been cross-linked using GP, impacting on their concrete and mechanical backdrop. The micron-calibration topography of GP hydrogels revealed the presence of heterogeneity compared with PQQ analogs, which were insufficiently uniform. It was also shown that the porosity of the GP hydrogels was much greater. GP-cross-linked sheets likewise exhibited significantly greater tensile strength, with a modulus greater than fourfold higher than similarly produced PQQ scaffolds. The alter in physical characteristics appears to be acquired past a higher cross-link density in the case of GP, probable due to its capacity to class both short- and long-range cross-links (Vieth et al., 2007).

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/S1876162308780015

Protein and Peptide Nanoparticles for Drug Delivery

Andrew P. Jallouk , ... Samuel A. Wickline , in Advances in Protein Chemistry and Structural Biology, 2015

3.ane.3 Hydrophobic CPPs

Hydrophobic CPPs possess a low net accuse and are composed of predominantly nonpolar amino acids. Several hydrophobic CPPs are derived from natural proteins, including α1-antitrypsin ( Rhee & Davis, 2006) and fibroblast growth gene 12 (Nakayama et al., 2011). However, this course includes the fewest CPPs discovered to date and most new hydrophobic CPPs are generated using synthetic peptide libraries (Marks, Placone, Hristova, & Wimley, 2011). This course also includes a number of chemically modified peptides, such equally stapled peptides (Chu et al., 2014), prenylated peptides (Ochocki, Mullen, Wattenberg, & Distefano, 2011), and pepducins (Covic, Gresser, Talavera, Swift, & Kuliopulos, 2002). The use of these constructed modifications to enhance peptide uptake raises exciting prospects for the evolution of cell-penetrating agents based on a broad variety of natural products.

Read total affiliate

URL:

https://www.sciencedirect.com/science/article/pii/S1876162314000613

Electric and Magnetic Fields in Cells and Tissues

J. Gimsa , in Reference Module in Materials Science and Materials Engineering, 2017

Membrane Proteins

Intercalation of proteins in the membrane relies on a microenvironment of specific dielectric properties. Nonpolar amino acids form the protein surface where it is exposed to the lipid concatenation region. Highly polar protein groups as loops and tails of the polypeptide bondage are exposed to aqueous surfaces. They possess a higher degree of molecular liberty suggesting higher permittivities. The peptide bonds of the membrane part of most proteins are very rigid. Their highly restricted mobility results in a depression permittivity. Upwardly to low kHz frequencies, the protein mediated ion transport is also of importance for electric protein properties.

Read full affiliate

URL:

https://www.sciencedirect.com/scientific discipline/article/pii/B9780128035818009826

Elastin

Judith Ann Foster , in Encyclopedia of Biological Chemistry, 2004

Composition and Principal Sequence

Elastin, as whatsoever protein, possesses a unique amino acid composition and a unique sequence of those amino acid residues along the polypeptide chain.

Amino Acid Composition

The soluble form of elastin, sometimes referred to every bit tropoelastin, contains a preponderance of uncharged and nonpolar amino acids. The polypeptide chain contains appropriately 850 amino acids and a molecular mass of 65–72 kDa. The bodily size varies somewhat amid dissimilar species. Glycine (33%), alanine (eighteen%), proline (13%), valine (17%), and leucine (v%) residues stand for 86% of the full amino acids. Prolyl hydroxylase converts 1–2% of the proline residues to hydroxyproline simply it is unclear as to the significance of this cotranslational modification. There are ∼36–38 lysine residues per molecule so the overall accuse of monomer is basic with an isoelectric point over pH 10. Once lysyl oxidase deaminates the epsilon amino grouping of almost lysine residues in the protein, the resulting semialdehydes undergo a series of aldol condensations and Schiff bases to grade the desmosine cross-links. At this stage, the protein is irreversibly insoluble and whatever success in extracting soluble fragments requires cleavage of peptide bonds.

Amino Acid Sequence

Unlike the classical triple repeat of collagen wherein glycine residues occupy every 3rd position of the triplet, elastin does non contain a compatible repeating structure. Instead, elastin contains two wide sequence motifs that accommodate much subdivision. Most lysine residues segregate together with alanine residues to create pairs of lysines separated by two or three alanine residues. These sequences exist within stretches of uncharged, nonpolar amino acid residues such as glycine, valine, and proline. The latter amino acid residues occur together with other nonpolar, hydrophobic, and polar residues, course tri, tetra, penta, and hexa repeats with not a unmarried consistent motif. The carboxy terminal sequence is unique and highly conserved amid different species. It contains the only cysteine residues within the molecule.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B0124437109001915

Elastin

J.A. Foster , in Encyclopedia of Biological Chemistry (2d Edition), 2013

Composition and Primary Sequence

Elastin, as any poly peptide, possesses a unique amino acid composition and a unique sequence of those amino acrid residues forth the polypeptide chain.

Amino Acid Composition

The soluble form of elastin, sometimes referred to every bit tropoelastin, contains a preponderance of uncharged and nonpolar amino acids. The polypeptide concatenation contains approximately 850 amino acids and a molecular mass of 65–72 kDa. The bodily size varies somewhat amid dissimilar species. Glycine (33%), alanine (18%), proline (13%), valine (17%), and leucine (5%) residues represent 86% of the full amino acids. Prolyl hydroxylase converts i–2% of the proline residues to hydroxyproline simply it is unclear as to the significance of this cotranslational modification. There are ~36–38 lysine residues per molecule, and so the overall charge of monomer is basic with an isoelectric point over pH 10. Once lysyl oxidase deaminates the epsilon amino group of most lysine residues in the protein, the resulting semi-aldehydes undergo a series of aldol condensations and Schiff bases to form the desmosine cross-links. At this stage, the protein is irreversibly insoluble and whatever success in extracting soluble fragments requires cleavage of peptide bonds.

Amino Acrid Sequence

Unlike the classical triple repeat of collagen wherein glycine residues occupy every third position of the triplet, elastin does not contain a compatible repeating structure. Instead, elastin contains two wide sequence motifs that accommodate much subdivision. Nearly lysine residues segregate together with alanine residues to create pairs of lysines separated past two or three alanine residues. These sequences be within stretches of uncharged, nonpolar amino acid residues such as glycine, valine, and proline. The latter amino acrid residues occur together with other nonpolar, hydrophobic, and polar residues, form tri, tetra, penta, and hexa repeats with not a single consistent motif. The carboxy terminal sequence is unique and highly conserved amid unlike species. It contains the only cysteine residues inside the molecule.

Read full affiliate

URL:

https://world wide web.sciencedirect.com/science/commodity/pii/B9780123786302001705

Polymers in Biology and Medicine

One thousand.E. Buck , D.A. Tirrell , in Polymer Scientific discipline: A Comprehensive Reference, 2012

9.07.4.1.2 Protein design by binary patterning

Moffet and Hecht ¹¹⁹ developed a general strategy for designing novel proteins by patterning the sequence and arrangement of polar and nonpolar amino acids in the protein sequence. In this approach, the arrangement of polar and nonpolar amino acids is specified, but the identity of each amino acid in the sequence is not, permitting the combinatorial assembly of libraries of de novo proteins. Binary patterning exploits the periodicity inherent in secondary structures and places polar and nonpolar residues in accordance with the desired secondary structure. Figure 10 shows a schematic illustration of this concept. The degeneracy of the genetic lawmaking is harnessed to generate combinatorial libraries of proteins with similar folding patterns only unlike overall sequences. For example, nonpolar and polar residues are encoded past the general codons NTN and NAN, respectively, where N tin be whatsoever of the iv nucleobases. Kamtekar et al. ¹²⁰ reported the starting time apply of a binary patterning strategy to pattern a library of 4-helix bundles. The general pattern of nonpolar and polar residues required to form a helix packet is shown in Figure 10 (b). Despite varying the identity of the amino acids in the sequence, the majority of the proteins generated in this approach folded into four-helix bundles. ¹²⁰ Wei et al. ¹²¹ modified the amino acid sequence of a single protein from the initial combinatorial library, again using concepts of binary patterning, to generate longer proteins that folded into more stable four-helix bundles.

β-Sheet proteins can also be generated by binary patterning. Amphiphilic β-strands have alternating polar and nonpolar amino acids, as shown in Figure 10 (c). Due west et al. ¹²² designed a library of β-sheet proteins using this periodic placement of polar and nonpolar residues. Proteins in the library were composed of 6 β-strands with the periodicity of amino acids shown in Effigy 10 (c). Circular dichroism confirmed the presence of β-sail structures, and the proteins were constitute to gather reversibly into fibril-like aggregates. ¹²² This model for protein design, equally well every bit the ability to generate libraries of proteins designed de novo, opens a myriad of opportunities to develop new poly peptide polymers with predictable folding patterns and new functions.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780444533494002193

Emerging seaweed extraction techniques: Supercritical fluid extraction

Siti Machmudah , ... Motonobu Goto , in Sustainable Seaweed Technologies, 2020

2.ii Proteins

Proteins are big biomolecules, or macromolecules, comprising one or more long chains of amino acid residues. Most of them are constructed of 20 diverse amino acids linked by substituted amide bonds. Ordinarily, proteins take a folded meaty structure, in which nonpolar amino acids residues are located in the interior of molecular and hydrophilic residues located on the molecular surface. The poly peptide's macroalgae content were known to vary from species to species, and the presence of them in macroalgae were also various and can be obtained equally conjugated or simple proteins. Conjugated proteins comprise simple proteins associated with a nonproteinous component whereas simple proteins incorporate only amino acids. Moreover, macroalgae too consist of protein-derived compounds, i.east., peptides or enzymes, too as free amino acids ( Rijpma et al., 2017). Proteins and their derivatives found in macroalgae can exist identified past their cellular location, their diverse structure, and their functions. Near of these components possess antioxidant, anticancer, antiaging, antiinflammatory, and protective activities. The macroalgae proteins are besides employed as moisturizing agents on hair and pare (Samarakoon and Jeon, 2012; Bleakley and Hayes, 2017). Therefore, these proteins may exist effectively utilized in functional cosmedicals and cosmetics (Sekar and Chandramohan, 2008).

Read total chapter

URL:

https://www.sciencedirect.com/science/article/pii/B978012817943700010X

Design and training of biomimetic and bioinspired materials

Five. Leiro , ... C.C. Barrias , in Bioinspired Materials for Medical Applications, 2017

1.iv.ii.3 Peptide amphiphiles

PAs are double character molecules whose self-assembling mechanism resembles that of phospholipids in cell membranes. To pattern a PA, a hydrophobic structural domain—usually in the form of a polymer or alkyl chain, or less frequently, a sequence of nonpolar amino acids—is linked to hydrophilic peptides.

When placed in aqueous environment such amphipathic graphic symbol molecules tend to assemble into supramolecular architectures such as spherical or cylindrical micelles. The power to encapsulate hydrophilic molecules has already been shown by van Hell et al. (2007) who reported the pattern of several PAs, which self-gather into vesicles. In addition to providing a capable carrier environment, these systems also present the reward of allowing a fine control of the properties of the associates surface past judicious selection of composing amino acids. Liang et al. (2014) have shown this versatility past incorporating lysines in the design of a PA molecule to confer pH-responsiveness. The PAs self-assembled into micelle, entrapping DOX, an antineoplastic drug that is released when placed in acidic conditions due to electrostatic repulsions between the protonated lysine molecules. Other successful drug carriers based on PAs have been created (Bulut et al., 2011; Kim et al., 2009; Matson et al., 2012; Webber et al., 2012) and a compilation of carriers based on peptide self-associates is provided on Tabular array ane.1.

Table i.1. List of peptide-based carriers

Peptide sequence/carrier	Secondary structure	Guest/drug	References
Polypeptide chain fragment from protein tetrabrachion (Staphylothermus marinus)	α-Helix/coiled roll	Cisplatin	Eriksson et al. (2009), Stetefeld et al. (2000)
MRGSHHHHHHGSGRLRPQMLREL QRTNAALRDVRELLRQQVKEITRL KNTVRRSRASGKLN	α-Helix/coiled gyre	DNA	More et al. (2014)
(IAALEKE)₂ IAALEKG	α-Helix/coiled coil	Methotrexate	Apostolovic et al. (2011)
[VSSLESK]₂VSKLESKKSKLESKVS KLESKVSSLESK]-NH₂	α-Helix/coiled roll	Doxorubicin	Al-Ahmady et al. (2012)
RADA16 = (RADA)₄	β-Sheet	Phenol ruby-red, bromophenol pyranine, 4-PSA, CBBG	Nagai et al. (2006)
RADAFI ([CH_iiiCONH]-RADARADF(RADA)₂-[CONH₂]) RADAFII ([CH₃CONH]-RADF(RADA)_three-[CONH_two])	β-Canvass	50-Phenylalanine	Zhao et al. (2010)
RADA16 RADA16-DGE: Ac-(RADA)₄GGDGEA-CONH₂ RADA16-PFS:Ac-(RADA)₄GGPFSSTKT-CONH_ii	β-Sheet	Homo recombinant BDNF, βFGF, and VEGF121	Gelain et al. (2006)
RADA16	β-Sheet	Lysozyme, trypsin inhibitor, BSA, and IgG	Koutsopoulos et al. (2009)
ac-(RADA)4-CONH₂ ac-(KLDL)3-CONH₂	β-Canvas	IgG	Koutsopoulos and Zhang (2012)
MAX1: (VK)₄V^DPPT-(KV)₄ MAX8: (VK)₄V^DPPTKVEVKVKV	β-Hairpin	FITC–dextran of different sizes	Branco et al. (2009)
MAX8	β-Hairpin	Curcumin	Altunbas et al. (2011)
PSFCFKFEP	β-Sheet, β-plough	Pyrene	Ruan et al. (2009)
Ac-AAVVLLLWE2-COOH Air conditioning-AAVVLLLWE7-COOH	Peptide amphiphile	Calcein	van Hell et al. (2007)
(5)₆KKGRGDS	Peptide amphiphile	Doxorubicin	Liang et al. (2014)
CH3(CH2)14CONHGTAGLIGQRGDS- COOH	Peptide amphiphile	Cisplatin	Kim et al. (2009)
C16-V₂A_iiEastward_ii	Peptide amphiphile	Dexamethasone	Webber et al. (2012)
C12-VVAGK-Am	Peptide amphiphile	Bcl-2 antisense oligodeoxynucleotide	Bulut et al. (2011)
C16-V2A2E2K(Hydrazide) C16-V2A2K(Hyd)E2 C16-V2K(Hyd)A2E2 C16-K(Hyd)V2A2E2	Peptide amphiphile	Prodan	Matson et al. (2012)

Adapted from Durão, J., Gales, L., 2015. Peptide cocky-assembly for therapeutic applications. Curr. Org. Chem. xix, 1874–1881.

Read full chapter

URL:

https://www.sciencedirect.com/science/article/pii/B9780081007419000012

Proteins in food manufacture

Mahmoud Nasrollahzadeh , ... Nasrin Shafiei , in Biopolymer-Based Metal Nanoparticle Chemistry for Sustainable Applications, 2021

3.3.2 Emulsifying and foaming

Emulsifying and foaming properties are ii pregnant poly peptide functionalities in food products, such as beverages, ice foam, dressings, mousses, whipped toppings, and margarine [seven, 24, 31] . Owing to their amphiphilic nature (presence of polar and nonpolar amino acid residues), proteins human action equally emulsifiers by adsorbing at the interface, coating oil or air droplets, increasing stable films, and stabilizing dispersions. Emulsions (oil-h2o interface) or foams (air-water interface) are prepared by dispersing oil droplets in an aqueous medium or a movie or peel surroundings air cells, respectively. In both examples, the value of the picture depends on prevention of coalescence, flocculation, and sedimentation in emulsions and the downfall of air bubbles in the cream. Protein properties such every bit the hydrophobicity-hydrophilicity ratio and the simplicity of protein folding-unfolding take a substantial consequence on their emulsifying behavior [14]. The future of a protein to be applied as a food emulsifier is related to its amino acid sequence, structure, and properties at colloidal interfaces. Beast-based proteins, peculiarly those derived from eggs and milk, are usually practical to stabilize emulsions and foams [72]. The interfacial structures and backdrop of found-based proteins accept not been considered in details. However, plant proteins commonly course a moderately thicker interfacial layer at oil-water interfaces due to their low molecular size and structural limitation by disulfide cross links [73]. This compound, which is the result of weak protein interactions in which absorption occurs at the interfaces, contributes to the superior stability of emulsions stabilized by diverse plant-based proteins compared with, for example, dairy proteins. For example, soy proteins have been studied more than other plant-based proteins for their emulsification properties [74]. Some plant-based proteins, including those derived from peanut, rice, lentil, potato, and pea, have been evaluated for emulsifying properties [75–79]. In the case of foam properties, the capability of a protein to form stable foams is pregnant for the production of a large number of nutrient products. Even so, proteins derived from egg white, soy, and milk together with gluten and collagen are the almost commonly applied for forming foams in the food industry. Various found-based proteins have been displayed to own skillful foaming properties and contribute to the compatible distribution of good air cells in foods [80]. Proteins perform as foam forming and stabilizing agents in unlike foodstuffs such as baked products, sweets, desserts, and beer. In summary, the perfect cream forming and stabilizing proteins are known by a low molecular weight, loftier surface hydrophobicity, excellent solubility, a small net charge at the pH of the nutrient, and piece of cake denaturability [32].

Read full affiliate

URL:

https://www.sciencedirect.com/science/commodity/pii/B9780323899703000032

Amino Acids, Peptides and Proteins

Paul C. Engel , Francesca Paradisi , in Comprehensive Natural Products Two, 2010

five.03.3.3.iii fifty-Leucine dehydrogenase in labeling of amino acids

There is a continuing demand for amino acids labeled with deuterium, ¹³C or ¹⁵N, in item for multidimensional NMR applications, and the broad specificity of LeuDHs has led to its use in several procedures for making labeled amino acids. Chiriac et al. ³⁹ have recently reported an efficient procedure for ^fifteen North labeling of several nonpolar amino acids using the thermostable LeuDH of Bacillus stearothermophilus and ¹⁵NH₃. Although this conversion runs in the thermodynamically favored management of the reaction, it requires coenzyme recycling to ensure a complete conversion and to this end the authors used GluDH and glucose together with a mutarotase to provide a rapid supply of the glucose anomer used by GluDH ( Scheme viii ).

The Bristol group of Christine Willis, in collaboration with Amersham International, adult a procedure for deuterium (or ¹³C) labeling of nonpolar amino acids. ^xl In the chemical steps, a selectively methyl-labeled oxazolidinone is converted first into a 2-methyl carboxylic acrid and then diffuse by two carbon atoms without racemization to yield an α-keto methyl ester ( Scheme nine ).

In the enzymatic part of the process, a 1-pot conversion was achieved by using Candida lipase (Lip) to hydrolyze the ester and and then LeuDH to catalyze the reductive amination (with or without ¹⁵N labeling). In this instance, the coenzyme recycling was accomplished by calculation FDH and formate. The same grouping used a similar enzymatic strategy to ready labeled l-threonine and l-allothreonine starting from the α-keto methyl ester. ⁴¹

Read full affiliate

URL:

https://www.sciencedirect.com/scientific discipline/article/pii/B9780080453828007000