Charge-Separated Fmoc-Peptide β-Sheets: Sequence-Secondary Structure Relationship for Arranging Charged Side Chains on Both Sides

2014 ◽  
Vol 3 (11) ◽  
pp. 1182-1188 ◽  
Author(s):  
Toru Nakayama ◽  
Taro Sakuraba ◽  
Shunsuke Tomita ◽  
Akira Kaneko ◽  
Eisuke Takai ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Side Chains ◽  
Structure Relationship ◽  
Β Sheets

Electronic Transport via Homopeptides: The Role of Side Chains and Secondary Structure

2015 ◽  
Vol 137 (30) ◽  
pp. 9617-9626 ◽  
Author(s):  
Lior Sepunaru ◽  
Sivan Refaely-Abramson ◽  
Robert Lovrinčić ◽  
Yulian Gavrilov ◽  
Piyush Agrawal ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Electronic Transport ◽  
Side Chains

scholarly journals BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy

2020 ◽  
pp. 175-189
Author(s):  
András Micsonai ◽  
Éva Bulyáki ◽  
József Kardos
Keyword(s):  
Circular Dichroism ◽  
Secondary Structure ◽  
Classical Method ◽  
Cd Spectroscopy ◽  
Protein Fold ◽  
Cd Spectra ◽  
Secondary Structure Analysis ◽  
Β Sheets ◽  
Α Helix ◽  
Circular Dichroïsm

Abstract Far-UV circular dichroism (CD) spectroscopy is a classical method for the study of the secondary structure of polypeptides in solution. It has been the general view that the α-helix content can be estimated accurately from the CD spectra. However, the technique was less reliable to estimate the β-sheet contents as a consequence of the structural variety of the β-sheets, which is reflected in a large spectral diversity of the CD spectra of proteins containing this secondary structure component. By taking into account the parallel or antiparallel orientation and the twist of the β-sheets, the Beta Structure Selection (BeStSel) method provides an improved β-structure determination and its performance is more accurate for any of the secondary structure types compared to previous CD spectrum analysis algorithms. Moreover, BeStSel provides extra information on the orientation and twist of the β-sheets which is sufficient for the prediction of the protein fold. The advantage of CD spectroscopy is that it is a fast and inexpensive technique with easy data processing which can be used in a wide protein concentration range and under various buffer conditions. It is especially useful when the atomic resolution structure is not available, such as the case of protein aggregates, membrane proteins or natively disordered chains, for studying conformational transitions, testing the effect of the environmental conditions on the protein structure, for verifying the correct fold of recombinant proteins in every scientific fields working on proteins from basic protein science to biotechnology and pharmaceutical industry. Here, we provide a brief step-by-step guide to record the CD spectra of proteins and their analysis with the BeStSel method.

NMR structure of bucandin, a neurotoxin from the venom of the Malayan krait (Bungarus candidus)

2001 ◽  
Vol 360 (3) ◽  
pp. 539-548 ◽  
Author(s):  
Allan M. TORRES ◽  
R. Manjunatha KINI ◽  
Nirthanan SELVANAYAGAM ◽  
Philip W. KUCHEL
Keyword(s):  
Solution Structure ◽  
Pharmacological Action ◽  
Nmr Structure ◽  
Side Chains ◽  
X Ray ◽  
Nmr Study ◽  
C Terminus ◽  
Mean Structure ◽  
Β Sheets ◽  
Β Sheet

A high-resolution solution structure of bucandin, a neurotoxin from Malayan krait (Bungarus candidus), was determined by 1H-NMR spectroscopy and molecular dynamics. The average backbone root-mean-square deviation for the 20 calculated structures and the mean structure is 0.47 Å (1 Å = 0.1nm) for all residues and 0.24 Å for the well-defined region that spans residues 23–58. Secondary-structural elements include two antiparallel β-sheets characterized by two and four strands. According to recent X-ray analysis, bucandin adopts a typical three-finger loop motif and yet it has some peculiar characteristics that set it apart from other common α-neurotoxins. The presence of a fourth strand in the second antiparallel β-sheet had not been observed before in three-finger toxins, and this feature was well represented in the NMR structure. Although the overall fold of the NMR structure is similar to that of the X-ray crystal structure, there are significant differences between the two structures that have implications for the pharmacological action of the toxin. These include the extent of the β-sheets, the conformation of the region spanning residues 42–49 and the orientation of some side chains. In comparison with the X-ray structure, the NMR structure shows that the hydrophobic side chains of Trp27 and Trp36 are stacked together and are orientated towards the tip of the middle loop. The NMR study also showed that the two-stranded β-sheet incorporated in the first loop, as defined by residues 1–22, and the C-terminus from Asn59, is probably flexible relative to the rest of the molecule. On the basis of the dispositions of the hydrophobic and hydrophilic side chains, the structure of bucandin is clearly different from those of cytotoxins.

scholarly journals Prion Interaction with Normal Protein in Topological Changing Secondary Structure to Aggregation

2020 ◽  
Vol 9 (2) ◽  
pp. 53
Author(s):  
Yao Yao
Keyword(s):  
Hydrogen Bond ◽  
Secondary Structure ◽  
Amyloid Fibril ◽  
Double Helix ◽  
Β Amyloid ◽  
Structural Analogy ◽  
Β Sheets ◽  
Α Helix ◽  
Dna Double Helix ◽  
Β Sheet

<p>Prion is a protein smaller than virus and it infects host in the absence of nucleic acid. The secondary structure of protein folds incorrectly from α-helices to β-sheets through breaking and re-formation of hydrogen bond. Structural analogy of α-helix and DNA double helix and comparing differences between α-helix and β-sheet show prion's infectivity and propagation. Aggregates of dimers and polymers generate β-amyloid fibril in Alzheimer's disease.</p>

Hydration of amino acid side chains: dependence on secondary structure

1992 ◽  
Vol 5 (8) ◽  
pp. 717-728 ◽  
Author(s):  
Adrian S. Morris ◽  
Narmada Thanki ◽  
Julia M. Goodfellow
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Side Chains ◽  
Amino Acid Side Chains

Solid state assembly of cyclic α-peptoids

CrystEngComm ◽  
2014 ◽  
Vol 16 (18) ◽  
pp. 3667-3687 ◽  
Author(s):  
Consiglia Tedesco ◽  
Loredana Erra ◽  
Irene Izzo ◽  
Francesco De Riccardis
Keyword(s):  
Solid State ◽  
Secondary Structure ◽  
Hydrogen Bonds ◽  
Side Chains ◽  
Beta Sheet ◽  
Face To Face

In cyclic alpha-peptoids, inter-annular CH⋯OC hydrogen bonds provide face to face or side by side arrangement of macrocycles mimicking the beta-sheet secondary structure in proteins. Side chains may promote the formation of peptoid nanotubes, acting as pillars among neighbouring macrocycles.

scholarly journals ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation

2020 ◽  
Vol 76 (3) ◽  
pp. 193-208 ◽  
Author(s):  
Ana Medina ◽  
Josep Triviño ◽  
Rafael J. Borges ◽  
Claudia Millán ◽  
Isabel Usón ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Alternative Model ◽  
Main Chain ◽  
Search Model ◽  
Molecular Replacement ◽  
Graphical Interface ◽  
Target Structure ◽  
Geometrical Properties ◽  
Β Sheets ◽  
Structure Annotation

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

scholarly journals Features of the Secondary Structure of BSA – Containing Protein Complexes, Isolated from Milk of High Temperature Processing

2021 ◽  
Vol 7 (2) ◽  
pp. 020307
Author(s):  
Ivan Shatalov ◽  
Aleksandrina Shatalova ◽  
Lyudmila Plotnikova ◽  
Aleksandr Shleikin
Keyword(s):  
Secondary Structure ◽  
Protein Complexes ◽  
Component Composition ◽  
Powdered Milk ◽  
Dry Milk ◽  
Random Structures ◽  
Simultaneous Decrease ◽  
Β Sheets ◽  
Α Helix ◽  
Sterilized Milk

Present paper describes features of the component composition in the secondary structure of BSA–containing protein complexes isolated from ultra-pasteurized (UHT), sterilized (SHT) and powdered (DRY) milk. We have found β – sheets to present in all complexes investigated. However, the smallest number of such components have been revealed in samples derived from sterilized milk with less β – sheets in 1621–1626 cm–1 region. The composition study of the complexes originated from UHT milk has shown random coils to be the rarest in them. When considering the structure of the complexes isolated from powdered milk, the α – 310 – heliсes were more characteristic for such samples, then the α – helix. Moreover, during spray–drying, the number of random structures increase with a simultaneous decrease in the number of β – sheets, whereas in UHT – and SHT – processing the number of random structures is inversely proportional to the number of α – helices.

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