Protein post-translational modifications: In silico prediction tools and molecular modeling.
TLDR
Some of the available online platforms and their contribution in the study of PTMs are summarized and the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods are discussed, providing deeper molecular insights into the biological function of post-translational modified proteins.Abstract:
Post-translational modifications (PTMs) occur in almost all proteins and play an important role in numerous biological processes by significantly affecting proteins' structure and dynamics. Several computational approaches have been developed to study PTMs (e.g., phosphorylation, sumoylation or palmitoylation) showing the importance of these techniques in predicting modified sites that can be further investigated with experimental approaches. In this review, we summarize some of the available online platforms and their contribution in the study of PTMs. Moreover, we discuss the emerging capabilities of molecular modeling and simulation that are able to complement these bioinformatics methods, providing deeper molecular insights into the biological function of post-translational modified proteins.read more
Citations
More filters
Journal ArticleDOI
Post-translational modifications in proteins: resources, tools and prediction methods
TL;DR: In this article, the authors comprehensively reviewed the major online databases and related tools to predict posttranslational modifications (PTMs) and the current challenges of computational methods were reviewed in detail.
Journal ArticleDOI
Functions of the sirtuin deacylase SIRT5 in normal physiology and pathobiology.
Surinder Kumar,David B. Lombard +1 more
TL;DR: The current understanding of functional impacts of SIRT5 on its metabolic targets, and its molecular functions in both normal and pathological conditions is reviewed.
Journal ArticleDOI
Post-translational modifications of Beclin 1 provide multiple strategies for autophagy regulation
TL;DR: An overview of the known post-translational modifications of Beclin 1 that govern its role in autophagy and how these modifications are maintained by input from several upstream signalling pathways is provided.
Journal ArticleDOI
Are Physicochemical Properties Shaping the Allergenic Potency of Plant Allergens
Joana Costa,Caterina Villa,Kitty C.M. Verhoeckx,Tanja Cirkovic-Velickovic,Tanja Cirkovic-Velickovic,Denise Schrama,Paola Roncada,Pedro M. Rodrigues,Cristian Piras,Cristian Piras,Laura Martín-Pedraza,Linda Monaci,Elena Molina,Gabriel Mazzucchelli,Isabel Mafra,Roberta Lupi,Daniel Lozano-Ojalvo,Colette Larré,Julia Klueber,Eva Gelencser,Cristina Bueno-Díaz,Araceli Díaz-Perales,Sara Benedé,Simona L. Bavaro,Simona L. Bavaro,Annette Kuehn,Karin Hoffmann-Sommergruber,Thomas Holzhauser +27 more
TL;DR: The authors' extensive analysis of the available literature revealed that physicochemical characteristics had consistent effects on protein allergenicity for allergens belonging to the same protein family, although it fails to explain the potency of some unstable allergens.
Journal ArticleDOI
An overview of albumin and alpha-1-acid glycoprotein main characteristics: highlighting the roles of amino acids in binding kinetics and molecular interactions
TL;DR: This review summarizes the common knowledge about the structural and molecular characteristics of both ALB and AGP in humans, and about the most involved amino acids in their high-affinity binding pockets, and is useful for the design of new drug entities with high-binding characteristics.
References
More filters
Journal ArticleDOI
Development and testing of a general amber force field.
TL;DR: A general Amber force field for organic molecules is described, designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens.
Journal ArticleDOI
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
Wendy D. Cornell,Piotr Cieplak,Piotr Cieplak,Christopher I. Bayly,Christopher I. Bayly,Ian R. Gould,Ian R. Gould,Kenneth M. Merz,Kenneth M. Merz,David M. Ferguson,David M. Ferguson,David C. Spellmeyer,David C. Spellmeyer,Thomas R. Fox,James W. Caldwell,Peter A. Kollman +15 more
TL;DR: Weiner et al. as mentioned in this paper derived a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases.
Journal ArticleDOI
The language of covalent histone modifications.
Brian D. Strahl,C D Allis +1 more
TL;DR: It is proposed that distinct histone modifications, on one or more tails, act sequentially or in combination to form a ‘histone code’ that is, read by other proteins to bring about distinct downstream events.
Journal ArticleDOI
The Protein Kinase Complement of the Human Genome
TL;DR: The protein kinase complement of the human genome is catalogued using public and proprietary genomic, complementary DNA, and expressed sequence tag sequences to provide a starting point for comprehensive analysis of protein phosphorylation in normal and disease states and a detailed view of the current state of human genome analysis through a focus on one large gene family.
Journal ArticleDOI
Mass spectrometry-based proteomics
Ruedi Aebersold,Matthias Mann +1 more
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.