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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Generation of Straight or Branched Actin Filaments01:14

Generation of Straight or Branched Actin Filaments

The straight or branched structure formation of actin filaments is controlled by nucleating proteins such as the formins and Arp2/3 complex. Formin-mediated assembly results in straight filaments, whereas Arp2/3 protein complex-mediated assembly results in branched actin filaments.
Arp2/3 Complex
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Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
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Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Calmodulin-dependent Signaling01:16

Calmodulin-dependent Signaling

Calmodulin (CaM) is a calcium-binding protein in eukaryotes that controls various calcium-regulated cellular processes. It has four calcium-binding sites that bind calcium to form the calcium-calmodulin ( Ca2+-CaM) complex. GPCR stimulation increases the calcium levels in the cells that bind to CaM and induces a conformational change.
The Ca2+-CaM complex does not have enzymatic activity by itself. Instead, the complex binds downstream target proteins, including membrane proteins or enzymes,...
Structure of Cadherins01:25

Structure of Cadherins

The cadherins were one of the first cell adhesion molecules discovered; the term “cadherins”   is based on their calcium-dependent adhering properties. The first cadherins discovered on the epithelial, neuronal, and placental cells were named E-cadherin, P-cadherin, and N-cadherin, respectively. These classical cadherins share sequence and structural similarities. Other cadherins, including those involved in cell signaling, are grouped into non-classical cadherins. This diversity of cadherins...
Catenins01:23

Catenins

Catenins are characterized by multiple binding domains and dynamic structures that allow them to function as linker proteins in cell junction complexes. All catenins, except α-catenin, contain a characteristic protein sequence called the armadillo repeat and are therefore also called armadillo proteins.
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Related Experiment Video

Updated: Jul 10, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Sequence motifs determine structure and Ca++-binding by EF-hand proteins.

H H Rashidi1, M Bauer, J Patterson

  • 1Department of Biology, University of California, San Diego, La Jolla 92093, USA.

Journal of Molecular Microbiology and Biotechnology
|August 15, 2000
PubMed
Summary

This study introduces a novel method using multiple sequence motifs to predict protein structures and functions. This approach enhances understanding of calcium-binding proteins and aids in drug design.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure and function prediction is crucial for biological sciences and drug design.
  • EF-hand motifs are key calcium-binding domains in proteins.
  • Existing methods may lack precision for proteins with multiple EF-hand domains.

Purpose of the Study:

  • To present a new sequence description approach for EF-hand motifs with multiple domains.
  • To enable precise insight into the structural and functional properties of EF-hand superfamily proteins.
  • To develop a robust tool for predicting properties of novel proteins.

Main Methods:

  • Utilized three regular expressions (signatures) to describe EF-hand motifs.
  • Defined specific interrelationships between sequence motifs for neighboring EF-hands.
  • Focused on conserved phenylalanine residues within motifs and their spatial separation (57+/-10 amino acids).

Main Results:

  • The new approach provides precise predictions of structural and functional properties.
  • Identified close interaction between conserved phenylalanine residues in tertiary structure.
  • Demonstrated that changes in conserved residues impair calcium-binding ability.

Conclusions:

  • The described method using multiple sequence motifs and their interrelationships is a highly specific and robust tool.
  • This approach significantly improves the prediction of structural and functional characteristics of EF-hand proteins.
  • Enhancements in protein modeling through this method will benefit drug design and biological research.