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Related Concept Videos

Standard Enthalpy of Formation02:37

Standard Enthalpy of Formation

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Enthalpy changes are typically tabulated for reactions in which both the reactants and products are at the same conditions. A standard state is a commonly accepted set of conditions used as a reference point for the determination of properties under other different conditions. For chemists, the IUPAC standard state refers to materials under a pressure of 1 bar and solutions at 1 M and does not specify a temperature. Many thermochemical tables list values with a standard state of 1 atm. Because...
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Initiation of Translation

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Calculating Standard Free Energy Changes02:49

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The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
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Transcription Initiation01:47

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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
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Entropy is a state function, so the standard entropy change for a chemical reaction (ΔS°rxn) can be calculated from the difference in standard entropy between the products and the reactants.
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Updated: Jan 25, 2026

Toeprinting Analysis of Translation Initiation Complex Formation on Mammalian mRNAs
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Proteomics Standards Initiative Extended FASTA Format.

Pierre-Alain Binz1, Jim Shofstahl2, Juan Antonio Vizcaíno3

  • 1CHUV Centre Hospitalier Universitaire Vaudois , CH-1011 Lausanne 14 , Switzerland.

Journal of Proteome Research
|May 14, 2019
PubMed
Summary
This summary is machine-generated.

The Proteomics Standards Initiative (PSI) developed the Proteomics Standards Initiative extended FASTA format (PEFF) to standardize protein sequence metadata. This new format facilitates the analysis of sequence variants and post-translational modifications (PTMs) in proteomics research.

Keywords:
FASTAPEFFPSIProteomics Standards Initiativefile formatsmass spectrometryproteogenomicsproteomicsstandards

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Mass-spectrometry-based proteomics allows high-throughput protein identification and quantification.
  • Analyzing sequence variants and post-translational modifications (PTMs) requires their inclusion in search algorithms, which is challenging.
  • Existing analysis tools struggle to incorporate diverse protein sequence variations.

Purpose of the Study:

  • To introduce the Proteomics Standards Initiative extended FASTA format (PEFF) for encoding protein sequence metadata.
  • To provide a standardized mechanism for representing known sequence variants, PTMs, and proteoforms.
  • To enhance the analysis of proteogenomics and top-down proteomics data.

Main Methods:

  • Development of the PEFF format based on the FASTA format.
  • Inclusion of a uniform mechanism for encoding metadata, including variants and PTMs.
  • Ensuring backward compatibility with existing FASTA parsers.

Main Results:

  • PEFF offers a standardized way to encode protein sequence variations and PTMs.
  • The format is nearly backward compatible with existing FASTA parsers.
  • PEFF is supported by key software like Comet and knowledge bases like neXtProt and UniProtKB.

Conclusions:

  • PEFF is expected to significantly advance proteogenomics and top-down proteomics.
  • Standardized encoding of protein variations will improve data analysis and interpretation.
  • Widespread adoption of PEFF will facilitate more comprehensive proteomic studies.