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Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination.

Woonghee Lee¹, Jaime L Stark, John L Markley

¹National Magnetic Resonance Facility at Madison, and Biochemistry Department, University of Wisconsin-Madison, Madison, WI, 53706, USA, whlee@nmrfam.wisc.edu.

Journal of Biomolecular NMR

|September 6, 2014

Summary

PONDEROSA-C/S is a software suite that enhances protein structure determination using Nuclear Magnetic Resonance (NMR) data. It automates Nuclear Overhauser Effect (NOE) peak picking and structure calculation for faster, more robust results.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Biochemistry
Structural Biology
Computational Biology

Background:

Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures.
Automated methods are needed to accelerate the structure determination process.
Previous software like PONDEROSA has aided NMR-based structure determination.

Purpose of the Study:

To introduce PONDEROSA-C/S, an enhanced software package for semi-automated NMR-based protein structure determination.
To improve upon existing PONDEROSA software with advanced features for structure calculation and refinement.
To demonstrate the utility of PONDEROSA-C/S in solving protein structures rapidly and robustly.

Main Methods:

PONDEROSA-C/S integrates three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer.
Input includes protein sequence, assigned chemical shifts, and Nuclear Overhauser Effect (NOESY) data.
Output comprises assigned NOEs and 3D structural models, with Ponderosa Analyzer for visualization and validation.

Main Results:

PONDEROSA-C/S successfully processed Nuclear Overhauser Effect (NOE) data for protein structure determination.
The software package was tested on four proteins, including those from the Critical Assessment of automated Structure Determination by NMR competition.
Structures were determined rapidly, with results typically returned within 1-2 days.

Conclusions:

PONDEROSA-C/S provides a rapid and robust platform for semi-automated NMR-based protein structure determination.
The enhanced features facilitate improved structure calculation and refinement.
The software is freely available, promoting wider accessibility in structural biology research.