ChemInform Abstract: SIDE-CHAIN CONFORMATIONAL CHANGES OF SOME AMINO ACIDS AND DIPEPTIDES HAVING AROMATIC SIDE CHAINS INDUCED BY COMPLEXATION WITH CYCLOAMYLOSES

1982 ◽  
Vol 13 (11) ◽  
Author(s):  
Y. INOUE ◽  
T. OKUDA ◽  
Y. MIYATA
Keyword(s):  
Amino Acids ◽  
Conformational Changes ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Side Chains

scholarly journals Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

2021 ◽  
Author(s):  
Pär Söderhjelm ◽  
Mandar Kulkarni
Keyword(s):  
Free Energy ◽  
Trypsin Inhibitor ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Residues ◽  
Basic Pancreatic Trypsin Inhibitor ◽  
Pancreatic Trypsin Inhibitor ◽  
Energy Surfaces ◽  
Aromatic Side Chains

Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180° around the Cβ-Cγ axis (χ2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that χ2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed χ1 (N−Cχα) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

Effect of thenardite on the direct detection of aromatic amino acids: implications for the search for life in the solar system

2009 ◽  
Vol 8 (4) ◽  
pp. 291-300 ◽  
Author(s):  
C. Doc Richardson ◽  
Nancy W. Hinman ◽  
Jill R. Scott
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Amino Acid ◽  
Aromatic Amino Acids ◽  
Laser Desorption ◽  
Ionization Mechanism ◽  
Side Chains ◽  
Ion Cyclotron Resonance ◽  
Laser Desorption Mass Spectrometry ◽  
Aromatic Side Chains

AbstractWith the discovery of Na-sulphate minerals on Mars and Europa, recent studies using these minerals have focused on their ability to assist in the detection of bio/organic signatures. This study further investigates the ability of thenardite (Na2SO4) to effectively facilitate the ionization and identification of aromatic amino acids (phenylalanine, tyrosine and tryptophan) using a technique called geomatrix-assisted laser desorption/ionization in conjunction with a Fourier transform ion cyclotron resonance mass spectrometry. This technique is based on the ability of a mineral host to facilitate desorption and ionization of bio/organic molecules for detection. Spectra obtained from each aromatic amino acid alone and in combination with thenardite show differences in ionization mechanism and fragmentation patterns. These differences are due to chemical and structural differences between the aromatic side chains of their respective amino acid. Tyrosine and tryptophan when combined with thenardite were observed to undergo cation-attachment ([M+Na]+), due to the high alkali ion affinity of their aromatic side chains. In addition, substitution of the carboxyl group hydrogen by sodium led to formation of [M-H+Na]Na+ peaks. In contrast, phenylalanine mixed with thenardite showed no evidence of Na+ attachment. Understanding how co-deposition of amino acids with thenardite can affect the observed mass spectra is important for future exploration missions that are likely to use laser desorption mass spectrometry to search for bio/organic compounds in extraterrestrial environments.

How can the aromatic side-chains modulate the conductance of the gramicidin channel? A new approach using non-coded amino acids

2009 ◽  
Vol 38 (3) ◽  
pp. 218-228 ◽  
Author(s):  
PASCAL DAUMAS ◽  
DRISS BENAMAR ◽  
FRÉDÉRIC HEITZ ◽  
LAURENT RANJALAHY-RASOLOARIJAO ◽  
RADOUANE MOUDEN ◽  
...  
Keyword(s):  
Amino Acids ◽  
Side Chains ◽  
New Approach ◽  
Gramicidin Channel ◽  
Aromatic Side Chains

scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

A phase transition from monoclinicC2 withZ′ = 1 to triclinicP1 withZ′ = 4 for the quasiracemateL-2-aminobutyric acid–D-methionine (1/1)

2016 ◽  
Vol 72 (7) ◽  
pp. 536-543 ◽  
Author(s):  
Carl Henrik Görbitz ◽  
David S. Wragg ◽  
Ingrid Marie Bergh Bakke ◽  
Christian Fleischer ◽  
Gaute Grønnevik ◽  
...  
Keyword(s):  
Phase Transition ◽  
Amino Acids ◽  
Room Temperature ◽  
Aminobutyric Acid ◽  
Side Chain ◽  
Side Chains ◽  
Significant Difference ◽  
Hydrophobic Amino Acids ◽  
Chain Conformations ◽  
Triclinic Form

Racemates of hydrophobic amino acids with linear side chains are known to undergo a unique series of solid-state phase transitions that involve sliding of molecular bilayers upon heating or cooling. Recently, this behaviour was shown to extend also to quasiracemates of two different amino acids with opposite handedness [Görbitz & Karen (2015).J. Phys. Chem. B,119, 4975–4984]. Previous investigations are here extended to an L-2-aminobutyric acid–D-methionine (1/1) co-crystal, C4H9NO2·C5H11NO2S. The significant difference in size between the –CH2CH3and –CH2CH2SCH3side chains leads to extensive disorder at room temperature, which is essentially resolved after a phase transition at 229 K to an unprecedented triclinic form where all four D-methionine molecules in the asymmetric unit have different side-chain conformations and all three side-chain rotamers are used for the four partner L-2-aminobutyric acid molecules.

scholarly journals Unexpected Trends in the Hydrophobicity of Fluorinated Amino Acids Reflect Competing Changes in Polarity and Conformation

2018 ◽  
Author(s):  
João R. Robalo ◽  
Ana Vila Verde
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Side Chain ◽  
Side Chains ◽  
Hydration Free Energy ◽  
Crossover Point ◽  
Fluorinated Amino Acids ◽  
Road Map ◽  
Alkyl Side Chains ◽  
The Impact

<div><div><div><p>Fluorination can dramatically improve the thermal and proteolytic stability of proteins and their enzymatic activity. Key to the impact of fluorination on protein properties is the hydrophobicity of fluorinated amino acids. We use molecular dynamics simulations, together with a new fixed-charge, atomistic force field, to quantify the changes in hydration free energy for amino acids with alkyl side chains and with 1 to 6 –CH to –CF side chain substitutions. Fluorination changes the hydration free energy by 1.5 to +2 kcal mol<sup>-</sup>1, but the number of fluorines is a poor predictor of hydrophobicity. Changes in hydration free energy reflect two main contributions: i) fluorination alters side chain-water interactions; we identify a crossover point from hydrophilic to hydrophobic fluoromethyl groups which may be used to estimate the hydrophobicity of fluorinated alkyl side-chains; ii) fluorination alters the number of backbone-water hydrogen bonds via changes in the relative side chain-backbone conformation. Our results offer a road map to mechanistically understand how fluorination alters hydrophobicity of (bio)polymers.</p></div></div></div>

The role of aromatic side chains on the supramolecular hydrogelation of naphthalimide/dipeptide conjugates

2018 ◽  
Vol 42 (6) ◽  
pp. 4443-4449 ◽  
Author(s):  
Shu-Min Hsu ◽  
Rajan Deepan Chakravarthy ◽  
Hsun Cheng ◽  
Fang-Yi Wu ◽  
Tsung-Sheng Lai ◽  
...  
Keyword(s):  
Amino Acid ◽  
Side Chain ◽  
Side Chains ◽  
Amino Acid Side Chain ◽  
Aromatic Side Chains

This study demonstrates the influence of an amino-acid side chain of NI-dipeptides on supramolecular hydrogelation and biocompatibility.

Sign in / Sign up

Export Citation Format

Share Document