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Related Concept Videos

Structural Protein Function01:56

Structural Protein Function

Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity.  In bones and teeth, it mineralizes to form...
Structural Protein Function01:56

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Structural proteins are a category of proteins responsible for functions ranging from cell shape and movement to providing support to major structures such as bones, cartilage, hair, and muscles. This group includes proteins such as collagen, actin, myosin, and keratin.
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The cytoskeleton is a complex dynamic structure performing varied functions based on cellular requirements. The adaptability of the individual filaments in the cytoskeleton determines their ability to perform various functions within the cell. It can undergo rapid reorganization during processes like cell division or remain stable for several hours as in the interphase. The adaptability of these filaments depends on stringent regulatory mechanisms. The microfilament and microtubules of the...
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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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Bacterial cells were initially considered simple, randomly organized structures lacking a cytoskeleton. However, the discovery of cytoskeleton homologs in bacteria led to the change of this opinion. Bacterial cytoskeletal filaments regulate the cell shape, cell polarity, cell division, and partitioning of plasmids during cell division. It was later discovered that bacterial cytoskeletal proteins, mainly actin and tubulin homologs, are diverse compared to their eukaryotic counterparts. On the...
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Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

Ballast: a ball-based algorithm for structural motifs.

Lu He1, Fabio Vandin, Gopal Pandurangan

  • 1Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|February 7, 2013
PubMed
Summary
This summary is machine-generated.

Ballast is a new algorithm for finding structural motifs in proteins. This method efficiently identifies protein structural motifs, aiding in predicting protein function and designing new protein variants.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein structure analysis

Background:

  • Structural motifs reveal local sequence-structure-function relationships in proteins.
  • Predicting protein function and guiding protein engineering relies on motif identification.
  • Existing computational methods for motif finding face challenges in efficiency and theoretical grounding.

Purpose of the Study:

  • To introduce Ballast, a novel and efficient algorithm for matching structural motifs to protein structures.
  • To leverage local geometric and chemical constraints for improved motif-finding efficiency.
  • To provide a general and effective approach for structural motif discovery.

Main Methods:

  • Ballast (ball-based algorithm for structural motifs) utilizes composition and local geometry of motifs.
  • It effectively filters candidate matches by exploiting geometric and chemical properties.
  • The algorithm integrates strengths from previous motif-finding methodologies.

Main Results:

  • Ballast demonstrates efficient and effective identification of structural motifs across diverse problems.
  • The method provides good matches for motif-finding tasks.
  • Theoretical insights into Ballast's performance and effectiveness are presented.

Conclusions:

  • Ballast offers a simple, general, and efficient solution for structural motif matching.
  • The algorithm's ability to support generic similarity measures enhances its utility.
  • Ballast serves as a robust foundation for developing advanced motif-finding algorithms.