TITLE

Editorial Hot Topic: Protein Folding & Misfolding (Guest Editor: Carlos Henrique I. Ramos)]

AUTHOR(S)
Ramos, Carlos Henrique I.
PUB. DATE
April 2005
SOURCE
Protein & Peptide Letters;Apr2005, Vol. 12 Issue 3, p211
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
The three-dimensional structure of a protein depends on its amino acid sequence, as do the stability and the folding mechanism. The first milestones in the study of protein folding took place at the beginning of the 20th century: in 1911, Chick and Martin (J. Physiol. 43:1) showed that proteins can be denaturated; in 1931, Wu (Chin. Physiol. 1:219) showed that the process of denaturation involves unfolding; and in 1931, Anson and Mirsky (Phys. Chem. 35:185) showed that the process of unfolding can be reverted. Almost a century later, the convergence of theoretical and experimental work has started to unify the current view of the folding process. This special issue on Protein Folding & Misfolding deals with the biological and physical aspects of this important process. The leading review in this issue, written by Ramos and Ferreira, gives a general view of the field throughout the description of the intermediates, the transition states, the models on protein folding, the biotechnological challenges caused by protein misfolding and aggregation, and the dreadful consequences that misfolding and aggregation can have on conformational diseases. The review by Pereira de Ara�jo, centered on the use of minimalist models to understand the thermodynamics of cooperative protein folding, addresses the importance of the use of computational methods to understand protein folding. Jamin gives an overview on the folding process of one of the best studied models for protein folding, apomyoglobin, with special attention to the characterization of its folding kinetics. The reviews by Spyracopolous, on the use of nuclear magnetic resonance spectroscopy to determine thermodynamic parameters of proteins, and by Correa and Farah, on the use of 5-hydroxytryptophan as a fluorescence probe to monitor structural properties of proteins, emphasize the importance of spectroscopic techniques as tools for the investigation of folding and stability. Differently from well-behaved proteins that are usually stable at several different conditions, some proteins have a strong tendency to aggregate or to form fibrils, which have medical relevance because these proteins are associated with conformational diseases. In her review, Foguel neatly presents the interpretation of current results in the formation of fibrils by transthyretin using high hydrostatic pressure to investigate the aggregate states of this protein. Cordeiro and Silva center their review on the possible causes of the conversion of the prion protein into its infectious form, pointing out the nucleotide interactions as active components in this reaction. Although we find protein folding very complex, it takes place continually inside cells, partly because of the action of chaperones, proteins involved in a complex machinery in keeping other proteins in their folded states. Chaperones are the theme of the review by Borges and Ramos that summarizes the recent findings in this field. Throughout the articles in this special issue, we see that the final picture emerging from protein folding studies is that this process is governed by simplistic principles. While stability depends more on specific inter-atomic contacts between amino acid residues, the mechanism of folding appears to depend more on the global geometry, or topology, of the native structure. The determination of the protein folding principles is opening a new era in which the structural prediction and design of novel protein structures from the corresponding amino acid sequences are becoming possible. However, considerable work still needs to be done so that we can fully understand how the amino acid sequence encodes the characteristics related to the shape of the folding funnel and to the overall topology of the native protein.
ACCESSION #
16677564

 

Related Articles

  • Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display. Pal, Arumay; Bahadur, Ranjit Prasad; Ray, Partha Sarathi; Chakrabarti, Pinak // BMC Bioinformatics;2009, Vol. 10, Special section p1 

    Background: Depending on chemical features residues have preferred locations -- interior or exterior -- in protein structures, which also determine how many other residues are found around them. The close packing of residues is the hallmark of protein interior and protein-protein interaction...

  • A Functional Proteomic Approach to the Identification and Characterization of Protein Composition in Wheat Leaf. Jung-Feng Hsieh; Shui-Tein Chen // Current Proteomics;Dec2008, Vol. 5 Issue 4, p253 

    Proteomics and bioinformatics approach were applied for the analyzing of wheat leaf proteins' composition and function. Wheat proteins were precipitated by ammonium sulfate and analyzed by two-dimensional gel electrophoresis and mass spectrometry. A total of 200 wheat proteins were selected to...

  • WildSpan: mining structured motifs from protein sequences. Chen-Ming Hsu; Chien-Yu Chen; Baw-Jhiune Liu // Algorithms for Molecular Biology;2011, Vol. 6 Issue 1, p6 

    Background: Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually...

  • Analysis of the Human Kinome Using Methods Including Fold Recognition Reveals Two Novel Kinases. Briedis, Kristine M.; Starr, Ayelet; Bourne, Philip E. // PLoS ONE;2008, Vol. 3 Issue 2, p1 

    Background: Protein sequence similarity is a commonly used criterion for inferring the unknown function of a protein from a protein of known function. However, proteins can diverge significantly over time such that sequence similarity is difficult, if not impossible, to find. In some cases, a...

  • APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. O. O'Sullivan; M. Zehnder; D. Higgins; P. Bucher; A. Grosdidier; C. Notredame // Bioinformatics;Jan2009 Supplement, Vol. 19, p215 

    Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple...

  • Combinatorial peptidomics: a generic approach for protein expression profiling. Soloviev, Mikhail; Barry, Richard; Scrivener, Elaine; Terrett, Jonathan // Journal of Nanobiotechnology;2003, Vol. 1, p4 

    Traditional approaches to protein profiling were built around the concept of investigating one protein at a time and have long since reached their limits of throughput. Here we present a completely new approach for comprehensive compositional analysis of complex protein mixtures, capable of...

  • Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources. Mizianty, Marcin J.; Stach, Wojciech; Ke Chen; Kedarisetti, Kanaka Durga; Disfani, Fatemeh Miri; Kurgan, Lukasz // Bioinformatics;Sep2010, Vol. 26 Issue 18, pi489 

    Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from...

  • Information on the secondary structure improves the quality of protein sequence alignment. Litvinov, I. I.; Lobanov, M. Yu.; Mironov, A. A.; Finkelshtein, A. V.; Roytberg, M. A. // Molecular Biology;May2006, Vol. 40 Issue 3, p474 

    The most popular algorithms employed in the pairwise alignment of protein primary structures (Smith-Watermann (SW) algorithm, FASTA, BLAST, etc.) only analyze the amino acid sequence. The SW algorithm is the most accurate, yielding alignments that agree best with superimpositions of the...

  • Early Molecular Evolution. TRIFONOV, EDWARD N. // Israel Journal of Ecology & Evolution;2006, Vol. 52 Issue 3/4, p375 

    Four fundamentally novel, recent developments make a basis for the Theory of Early Molecular Evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1)...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics