scholarly journals A computational study of Trishomocubane amino acid dipeptide

2004 ◽  
Author(s):  
◽  
Poomani Penny Govender
Keyword(s):  
Amino Acid ◽  
Computational Study ◽  
Building Blocks ◽  
Conformational Space ◽  
Basis Set ◽  
Peptide Design ◽  
Helical Structures ◽  
Hartree Fock ◽  
C Terminus ◽  
Acetyl Group

4-amino-(D3)-trishomocubane-4-carboxylic acid (tris-amino acid) is a constrained a-amino acid residue that exhibits peculiar conformational characteristics. The aim of the present study is to provide a deeper understanding of these features, which can be used as a guide when chOOSing@shomocubane as suitable building blocks for peptide design. The Ca carbon of@ishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methyl amide group on its C-terminus. This study involved a complete exploration of the conformational profile of (Yishomocubane using computational techniques.The parm94 parametization of the AMBER oio forc@eld was used to explore the conformational space of the peptide,Q)\xEFshomocubane. The Ramachandran maps computed at the molecular mechanics level' with the parm94 forc@\xEFeld parameters compared reasonably with the corresponding maps computed at the Hartree Fock (HF) level, using the 6-31G* basis set. The results of this study revealed that the conformational profile of the @ishomocubane peptide can be characterized by four low energy regions, viz., C7ax, C7eq, 310 and al helical structures.

scholarly journals Homochirality May Not Be a Prerequisite for Protein Structure and Function: A Computational Model Investigation of Prebiotic Peptides

2020 ◽  
Author(s):  
Jianxun Shen ◽  
Pauline M. Schwartz ◽  
Carl Barratt
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Hierarchical Cluster ◽  
Building Blocks ◽  
Beta Sheets ◽  
Folding Energy ◽  
Primitive Earth ◽  
C Terminus ◽  
Significant Difference ◽  
Prebiotic Amino Acids

On the primitive Earth, both L- and D-amino acids would have been present. However, only L-amino acids are essential blocks to construct proteins in modern life. To study the relative stability of homochiral and heterochiral peptides, a variety of computational methods were employed. 10 prebiotic amino acids (Gly, Ala, Asp, Glu, Ile, Leu, Pro, Ser, Thr, and Val) were previously determined by multiple previous meteorite, spark discharge, and hydrothermal vent studies. We focused on what had been reported as primary early Earth polypeptide analogs: 1ARK, 1PPT, 1ZFI, and 2LZE. Tripeptide composed of only Asp, Ser, and Val exemplified that different positions (i.e., N-terminus, C-terminus, and middle) made a difference in minimal folding energy of peptides, while the classification of amino acid (hydrophobic, acidic, or hydroxylic) did not show significant difference. Hierarchical cluster analysis for dipeptides with all possible combinations of the proposed 10 prebiotic amino acids and their D-amino acid substituted derivatives generated five clusters. Prebiotic polypeptides were built up to test the significance of molecular fluctuations, secondary structure occupancies, and folding energy differences based on these clusters. Most interestingly, among 129 residues, mutation sensitivity profiles presented that the ratio of more stable to less stable to equally stable D-amino acids was about 1:1:1. In conclusion, some combinations of a mixture of L- and D-amino acids can act as essential building blocks of life. Peptides with α-helices, long β-sheets, and long loops are usually less sensitive to D-amino acid replacements in comparison to short β-sheets.

How to fragment a polypeptide? An ab initio computational study of pair interactions between amino acids and ligand-amino acids in proteins

2011 ◽  
Vol 76 (5) ◽  
pp. 605-618
Author(s):  
Vojtěch Klusák ◽  
Petr Dobeš ◽  
Jiří Černý ◽  
Jiří Vondrášek
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Ab Initio ◽  
Building Blocks ◽  
Basis Set ◽  
Single Amino Acid ◽  
Amino Acid Side Chain ◽  
Protein Chain ◽  
The Stability ◽  
Dispersion Term

To determine reasonably which amino acid side chain contributes significantly to the stability of a protein or to the stability of a protein–ligand complex is not a straightforward task. We suggest a partial but systematic solution of the problem by a specific fragmentation of a protein chain into blocks of single amino acid side chains with their corresponding backbone part. For such systems of building blocks, we have calculated the stabilisation/interaction energies by means of correlated ab initio calculations. We have shown that a reasonable way to treat an amino-acid residue composing the protein is to break the homonuclear C–C bond between the Cα atom and the C(O) carboxyl carbon. The reference data obtained by the RI-MP2 method with the cc-pVDZ basis set were compared with RIDFT, RIDFT augmented by the dispersion term, SCC-DFTB-D and Hartree–Fock calculations. The results clearly show the failure of those methods lacking an appropriate treatment of the correlation energy. The DFT methods augmented by the empirical dispersion term on the other hand describe the interaction in good agreement with the reference method.

scholarly journals Modern diversification of the amino acid repertoire driven by oxygen

2017 ◽  
Vol 115 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Matthias Granold ◽  
Parvana Hajieva ◽  
Monica Ioana Toşa ◽  
Florin-Dan Irimie ◽  
Bernd Moosmann
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactivity ◽  
Protein Biosynthesis ◽  
Building Blocks ◽  
Peroxyl Radicals ◽  
Basis Set ◽  
Universal Genetic Code ◽  
Amino Acid Properties

All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7–13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO–LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialized redox cofactors in the late amino acids tryptophan and selenocysteine. We show that the arising prediction of a higher reactivity of the more recently added amino acids is correct as regards various free radicals, particularly oxygen-derived peroxyl radicals. Moreover, we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code.

Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error

2019 ◽  
Vol 60 (1) ◽  
pp. 20-31
Author(s):  
A. El Guerdaoui ◽  
R. Tijar ◽  
M. Bourjila ◽  
B. El Merbouh ◽  
R. D. El Bouzaidi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Conformational Space ◽  
Basis Set ◽  
Basis Set Superposition Error ◽  
Space Analysis

Computation of the Hartree-Fock Exchange by the Tensor-Structured Methods

2010 ◽  
Vol 10 (2) ◽  
pp. 204-218 ◽  
Author(s):  
V. Khoromskaia
Keyword(s):  
Building Blocks ◽  
Basis Set ◽  
Low Rank ◽  
Convolution Product ◽  
Large Molecules ◽  
Hartree Fock ◽  
Rank Tensor ◽  
Coulomb Matrix ◽  
The One ◽  
Algebraic Optimization

AbstractWe propose a novel numerical method for fast and accurate evaluation of the exchange part of the Fock operator in the Hartree-Fock equation which is a (nonlocal) integral operator. Usually, this challenging computational problem is solved by analytical evaluation of two-electron integrals using the “analytically separable” Galerkin basis functions, like Gaussians. Instead, we employ the agglomerated “grey-box” numerical computation of the corresponding six-dimensional integrals in the tensor-structured format which does not require analytical separability of the basis set. The point of our method is a low-rank tensor representation of arising functions and operators on an n×n×n Cartesian grid and the implementation of the corresponding multi-linear algebraic operations in the tensor product format. Linear scaling of the tensor operations, including the 3D convolution product, with respect to the one-dimension grid size n enables computations on huge 3D Cartesian grids thus providing the required high accuracy. The presented algorithm for evaluation of the exchange operator and a recent tensor method for the computation of the Coulomb matrix are the main building blocks in the numerical solution of the Hartree-Fock equation by the tensor-structured methods. These methods provide a new tool for algebraic optimization of the Galerkin basis in the case of large molecules.

Electron Dynamics of Solvated Ti(OH)4

2014 ◽  
Vol 1647 ◽  
Author(s):  
Dayton J. Vogel ◽  
Dmitri S. Kilin
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Geometry Optimization ◽  
Building Blocks ◽  
Basis Set ◽  
Synthesis Methods ◽  
Electron Dynamics ◽  
Relaxation Rates ◽  
Electron Hole ◽  
Ambient Temperatures

ABSTRACTIncreasing interest in the photocatalytic activity of TiO2 has led to considerations of using TiO2 nanoparticles in energy generation. In order to better understand the electron-hole relaxation of nano scale TiO2 structures, it is important to start with an understanding of TiO2 synthesis building blocks. The solvated titanium (IV) ion is a precursor found in synthesis methods of colloidal TiO2 nanostructures. This simplest test compound may reflect some common basic electronic features for larger structures composed of Ti(IV) coordinated with oxygen. For this computational study, a model of Ti(OH)4 with tetrahedral coordination was created. To simulate the electronic properties of a solution of Ti(IV), the model was surrounded with 27 H2O molecules. The model was explored by means of standard density functional theory (DFT) molecular dynamics (MD) followed by nonadiabatic electron dynamics computed with Reduced Density Matrix approach combined with “on-the-fly coupling”. Results were generated with Vienna ab initio Simulation Package (VASP) using the Perdew-Burke-Ernzerhof (PBE) functional, plane wave basis set, and projector augmented wave (PAW) potentials. The absorption spectra, MD, and electron-hole relaxation rates are presented for the Ti(OH)4 model at various ambient temperatures. The electron-hole relaxation rates show a non-linear dependence on temperature and were found to be near the same order of magnitude as electron-hole relaxation rates in bulk TiO2 calculations. A video of the geometry optimization can be found online.[1]

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

Axially Chiral Bis(α-amino Acid)s and Their Deamino Analogues. Synthesis and Configurational Assignment

1998 ◽  
Vol 63 (2) ◽  
pp. 211-221 ◽  
Author(s):  
Miloš Tichý ◽  
Luděk Ridvan ◽  
Miloš Buděšínský ◽  
Jiří Závada ◽  
Jaroslav Podlaha ◽  
...  
Keyword(s):  
Amino Acid ◽  
Nmr Spectra ◽  
Building Blocks ◽  
X Ray Diffraction ◽  
Amino Groups ◽  
X Ray ◽  
Configurational Assignment ◽  
Symmetry Properties ◽  
Axially Chiral ◽  
Polymeric Structures

The axially chiral bis(α-amino acid)s cis-2 and trans-2 as possible building blocks for polymeric structures of novel type of helicity were prepared. Their configuration has been determined by NMR spectroscopy and, in the case of the trans-isomer, confirmed by single-crystal X-ray diffraction. Analogous pair of stereoisomeric diacids cis-3 and trans-3, devoid of the amino groups, was also prepared and their configuration assigned. The observed differences in the NMR spectra of cis- and trans-isomers of 2 and 3 are discussed from the viewpoint of their different symmetry properties.

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