Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Mechanical Protein Functions

Mechanical Protein Functions

Proteins perform many mechanical functions in a cell. These proteins can be classified into two general categories- proteins that generate mechanical forces and proteins that are subjected to mechanical forces. Proteins providing mechanical support to the structure of the cell, such as keratin, are subjected to mechanical force, whereas proteins involved in cell movement and transport of molecules across cell membranes, such as an ion pump, are examples of generating mechanical force.

Derivatives of Simple Functions

Derivatives of Simple Functions

Derivatives quantify the rate of change of a function and can be interpreted geometrically as the slope of a straight line or the slope of a tangent line to a curve at a given point. In the context of a roller coaster, the derivative of the function describing the track’s horizontal position provides a mathematical description of how steep the path is at any location along the ride.Constant and Linear PathsA horizontal segment of a roller coaster can be modeled by a constant function,...

Structural Protein Function

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...

Structural Protein Function

Structural Protein Function

Phosphate Buffer

Phosphate Buffer

The phosphate buffer system is a critical biological mechanism for maintaining pH stability in the body. This system operates primarily through two components: sodium dihydrogen phosphate (NaH2PO4), which acts as a weak acid, and sodium hydrogen phosphate (Na2HPO4), which serves as a weak base.
Sodium dihydrogen phosphate does not fully dissociate in neutral or acidic solutions. When a strong base, such as sodium hydroxide (NaOH), is introduced into the solution, sodium dihydrogen phosphate...

Performing a Simple Data Analysis using MS-Excel Function

Performing a Simple Data Analysis using MS-Excel Function

Microsoft Excel offers a suite of functions and tools ideal for statistical analysis, making it accessible to students and researchers. This article outlines fundamental Excel functions pivotal for data analysis.
SUM: This function calculates the total sum of a range of values. It's the foundation for aggregating data, essential for determining overall trends and totals in datasets.
AVERAGE: It computes the mean value of a given set of numbers, providing a quick insight into the central...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Regulatory landscape of widespread stop codon readthrough in <i>Drosophila</i>.

bioRxiv : the preprint server for biology·2026

Same author

Controlling metal-carbonate phase, form, and function through de novo protein design.

bioRxiv : the preprint server for biology·2026

Same author

Programmed synthesis of mesoporous protein crystals in cellular reactors.

Nature nanotechnology·2026

Same author

Generative design of programmable asymmetric β-barrel nanopores.

bioRxiv : the preprint server for biology·2026

Same author

Author Correction: De novo design of quasisymmetric two-component protein cages.

Nature·2026

Same author

De novo design of RNA pseudoknots with deep learning.

bioRxiv : the preprint server for biology·2026

Same journal

Tau protein as a regulator of mitochondrial function and dynamics.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

A scalable, dividing cell model for the robust propagation and quantification of human sporadic Creutzfeldt-Jakob disease prions.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Epigenetic regulation of mesenchymal BMP signaling directs postnatal organ innervation.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Single-shot wide-field biochemical imaging at 1 kHz frame rate.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

Morphogenesis and topological evolution of a frustrated nematic liquid crystal under confinement.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same journal

B cell-intrinsic CXCR3 drives efficient generation of ectopic pulmonary germinal center responses to influenza A virus infection.

Proceedings of the National Academy of Sciences of the United States of America·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 1, 2026

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Published on: July 26, 2019

Simple yet functional phosphate-loop proteins.

Maria Luisa Romero Romero¹, Fan Yang^2,3, Yu-Ru Lin⁴

¹Department of Biomolecular Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel.

Proceedings of the National Academy of Sciences of the United States of America

|December 4, 2018

Summary

This summary is machine-generated.

The ancient phosphate-binding loop (P-loop) motif can function independently in simple proteins. These de novo designed proteins avidly bind polynucleotides, demonstrating the P-loop

Keywords:

RNA binding protein Walker-A conformational diversity de novo protein design protein evolution

More Related Videos

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Related Experiment Videos

Last Updated: Feb 1, 2026

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Identification of Inositol Phosphate or Phosphoinositide Interacting Proteins by Affinity Chromatography Coupled to Western Blot or Mass Spectrometry

Published on: July 26, 2019

Identification of Functional Protein Regions Through Chimeric Protein Construction

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

Biochemistry and Molecular Biology
Protein Design and Engineering
Evolutionary Biology

Background:

Phosphate-binding loops (P-loops), particularly the Walker-A motif, are crucial for NTPase enzyme function in binding and transferring phosphate groups.
Modern NTPase activity relies on complex active sites with numerous residues, raising questions about the minimal requirements for P-loop function.
The evolutionary origins of enzyme function are often linked to simple, essential motifs.

Purpose of the Study:

To investigate whether simple motifs like P-loops can confer function in a simplified protein context.
To computationally design and experimentally validate de novo proteins incorporating an ancestral P-loop motif.
To determine the binding properties and potential functions of these simplified P-loop proteins.

Main Methods:

Phylogenetic analysis to derive a sequence logo of the ancestral Walker-A P-loop element.
Computational design of de novo β-α repeat proteins incorporating the ancestral P-loop motif.
Biochemical characterization of designed proteins, including binding assays for ATP and polynucleotides (RNA, DNA).

Main Results:

Soluble and stable de novo proteins containing the P-loop motif were successfully designed and produced.
These proteins exhibited magnesium-independent ATP binding, differing from modern P-loop NTPases.
The designed proteins showed avid binding to RNA and single-strand DNA, which was abolished by mutations in key P-loop residues.
Structural plasticity and quaternary structure polymorphism, including oligomerization, were identified as facilitators of avid polynucleotide binding.

Conclusions:

The Walker-A P-loop motif can be successfully implemented in small, simple β-α repeat proteins.
These de novo proteins primarily function as polynucleotide binding motifs, independent of complex NTPase machinery.
The study provides insights into the potential ancestral functions of P-loops and the principles of de novo protein design.