Nonstandard Amino Acids in Conformational Design of Peptides. Helical Structures in Crystals of 5-10 Residue Peptides Containing Dipropylglycine and Dibutylglycine

1994 ◽  
Vol 116 (23) ◽  
pp. 10355-10361 ◽  
Author(s):  
Isabella L. Karle ◽  
R. Balaji Rao ◽  
Sudhanand Prasad ◽  
Ramesh Kaul ◽  
P. Balaram
Keyword(s):  
Amino Acids ◽  
Helical Structures

scholarly journals Helical structures of l-Leu-based peptides having chiral six-membered ring amino acids

Tetrahedron ◽  
2016 ◽  
Vol 72 (22) ◽  
pp. 3124-3131 ◽  
Author(s):  
Tomohiro Umeno ◽  
Atsushi Ueda ◽  
Makoto Oba ◽  
Mitsunobu Doi ◽  
Takayuki Hirata ◽  
...  
Keyword(s):  
Amino Acids ◽  
Membered Ring ◽  
Helical Structures

scholarly journals The cDNA-deduced amino acid sequence for trichohyalin, a differentiation marker in the hair follicle, contains a 23 amino acid repeat.

1990 ◽  
Vol 110 (2) ◽  
pp. 427-436 ◽  
Author(s):  
M J Fietz ◽  
R B Presland ◽  
G E Rogers
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Intermediate Filament ◽  
Tandem Repeats ◽  
Single Copy ◽  
Hair Follicles ◽  
Helical Structures ◽  
Differentiation Marker ◽  
Carboxy Terminal

Trichohyalin is a highly expressed protein within the inner root sheath of hair follicles and is similar, or identical, to a protein present in the hair medulla. In situ hybridization studies have shown that trichohyalin is a very early differentiation marker in both tissues and that in each case the trichohyalin mRNA is expressed from the same single copy gene. A partial cDNA clone for sheep trichohyalin has been isolated and represents approximately 40% of the full-length trichohyalin mRNA. The carboxy-terminal 458 amino acids of trichohyalin are encoded, and the first 429 amino acids consist of full- or partial-length tandem repeats of a 23 amino acid sequence. These repeats are characterized by a high proportion of charged amino acids. Secondary structure analyses predict that the majority of the encoded protein could form alpha-helical structures that might form filamentous aggregates of intermediate filament dimensions, even though the heptad motif obligatory for the intermediate filament structure itself is absent. The alternative structural role of trichohyalin could be as an intermediate filament-associated protein, as proposed from other evidence.

Supramolecular secondary helical structures in solid-state N-protected amino acids

Nanoscale ◽  
2020 ◽  
Vol 12 (40) ◽  
pp. 20610-20620
Author(s):  
Zhaohui Zong ◽  
Aiyou Hao ◽  
Pengyao Xing
Keyword(s):  
Amino Acids ◽  
Solid State ◽  
Secondary Structure ◽  
Helical Structures

Helix is an important secondary structure in proteins and polypeptides, which, however, has rarely been recognized in amino acids or their simple derivatives.

Cyclic α,α-Disubstituted α-Amino Acids with Menthone in Their Side-Chains Linked through an Acetal Moiety and Helical Structures of Their Peptides

2016 ◽  
Vol 2016 (17) ◽  
pp. 2988-2998 ◽  
Author(s):  
Kaori Furukawa ◽  
Makoto Oba ◽  
George Ouma Opiyo ◽  
Mitsunobu Doi ◽  
Masakazu Tanaka
Keyword(s):  
Amino Acids ◽  
Side Chains ◽  
Helical Structures

scholarly journals Design, synthesis, and structural characterization of helix-forming aliphatic homo-δ-peptides based on conformational restriction due to the structural characteristics of cyclopropane

2021 ◽  
Author(s):  
Mizuki Watanabe ◽  
Makoto Nagata ◽  
Ryohei Doi ◽  
Mai Uemura ◽  
Nanase Ochiai ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Amino Acid ◽  
Structural Analysis ◽  
Magnetic Resonance ◽  
Structural Characteristics ◽  
Helical Structure ◽  
Resonance Spectroscopy ◽  
Helical Structures ◽  
Nuclear Magnetic

Considerable effort has been directed toward developing artificial peptide-based oligomers that fold into a specific secondary structure, i.e., peptide foldamers. To date, however, detailed structural analysis of crystals of δ-peptide foldamers consisting of aliphatic δ-amino acids, which have a more extended carbon backbone compared with well-studied β- and γ-amino acids, have not been reported. We rationally designed aliphatic homo-δ-peptide foldamers forming a stable helical structure utilizing a chiral cyclopropane δ-amino acid as a monomer unit whose conformation was tightly restricted by the structural characteristics of cyclopropane depending on its stereochemistry. We stereoselectively synthesized the cyclopropane δ-amino acid monomer and prepared its various homo-oligomers. Structural analysis of the homo-δ-peptides using nuclear magnetic resonance, circular dichroism, and infrared spectroscopy revealed that they form a stable 14-helical structure in solution. Furthermore, the effective conformational regulation of the backbone due to the characteristics of cyclopropane allowed us to achieve X-ray crystallographic analysis of the homo-δ-peptides, showing their common right-handed 14-helical structures. The helical structures were consistent with both those predicted by theoretical calculations and those obtained based on nuclear magnetic resonance spectroscopy in solution. A critical point is that the helical structures of these δ-peptides are theoretically predictable by calculations. To our knowledge, this is the first example of aliphatic homo-δ-peptide foldamers forming a stable helical structure both in solution and in crystal.

Dissecting mechanism of coupled folding and binding of an intrinsically disordered protein by chemical synthesis of conformationally constrained analogues

2017 ◽  
Vol 53 (53) ◽  
pp. 7369-7372 ◽  
Author(s):  
Boris Schmidtgall ◽  
Olivier Chaloin ◽  
Valentin Bauer ◽  
Manuela Sumyk ◽  
Catherine Birck ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Synthesis ◽  
Intrinsically Disordered Protein ◽  
Helical Structures ◽  
Activation Domain ◽  
Conformationally Constrained ◽  
Intrinsically Disordered ◽  
Disordered Protein

Non-canonical α-methyl amino acids were incorporated at various sites in the sequence of intrinsically disordered activation domain from the p160 transcriptional co-activator (ACTR) to facilitate the formation of α-helical structures.

scholarly journals Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

2021 ◽  
Vol 16 (2) ◽  
pp. 244-255
Author(s):  
I.V. Likhachev ◽  
V.S. Bystrov
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Self Assembly ◽  
Software Package ◽  
Molecular Structures ◽  
Dynamics Simulation ◽  
Hierarchical Level ◽  
Initial Structure ◽  
Helical Structures ◽  
Final Structure

Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.

scholarly journals Mapping of the VP40-Binding Regions of the Nucleoprotein of Ebola Virus

2007 ◽  
Vol 81 (7) ◽  
pp. 3554-3562 ◽  
Author(s):  
Takeshi Noda ◽  
Shinji Watanabe ◽  
Hiroshi Sagara ◽  
Yoshihiro Kawaoka
Keyword(s):  
Amino Acids ◽  
Mammalian Cells ◽  
Matrix Protein ◽  
Ebola Virus ◽  
Virus Assembly ◽  
Helical Structures ◽  
Antiviral Compounds ◽  
C Terminus ◽  
The Matrix ◽  
Ebola Virus Infection

ABSTRACT Expression of Ebola virus nucleoprotein (NP) in mammalian cells leads to the formation of helical structures, which serve as a scaffold for the nucleocapsid. We recently found that NP binding with the matrix protein VP40 is important for nucleocapsid incorporation into virions (T. Noda, H. Ebihara, Y. Muramoto, K. Fujii, A. Takada, H. Sagara, J. H. Kim, H. Kida, H. Feldmann, and Y. Kawaoka, PLoS Pathog. 2:e99, 2006). To identify the region(s) on the NP molecule required for VP40 binding, we examined the interaction of a series of NP deletion mutants with VP40 biochemically and ultrastructurally. We found that both termini of NP (amino acids 2 to 150 and 601 to 739) are essential for its interaction with VP40 and for its incorporation into virus-like particles (VLPs). We also found that the C terminus of NP is important for nucleocapsid incorporation into virions. Of interest is that the formation of NP helices, which involves the N-terminal 450 amino acids of NP, is dispensable for NP incorporation into VLPs. These findings enhance our understanding of Ebola virus assembly and in so doing move us closer to the identification of targets for the development of antiviral compounds to combat Ebola virus infection.

Mechanical Properties of Biopolymer Chains

1992 ◽  
Vol 292 ◽  
Author(s):  
Ruth Pachter ◽  
Peter D. Haaland ◽  
Robert L. Crane ◽  
W. Wade Adams
Keyword(s):  
Mechanical Properties ◽  
Amino Acids ◽  
Hydrogen Bonding ◽  
Molecular Hydrogen ◽  
Mechanical Response ◽  
Amide Bond ◽  
Pivotal Role ◽  
Helical Structures ◽  
Naturally Occurring

AbstractMolecular simulations that predict the molecular mechanical response of alpha-helical biopolymers with a reinforcing intra-molecular hydrogen bonding network, viz,, a ‘spring-like’ behavior, are presented in this study. Mechanical properties of extended biopolymer strands based on naturally occurring amino acids, namely poly(L-A1a) and for comparison poly(LGlu), versus synthetic PPTA containing an amide bond, are compared to those assuming alpha-helical structures. Thus, the pivotal role of such motifs in biological systems utilizing superior compressive mechanical properties can be inferred.

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