Molecules

About

A good general definition of a molecule is given on the wikipedia (August 18, 2010): A molecule is defined as an electrically neutral group of at least two atoms in a definite arrangement held together by very strong (covalent) chemical bonds. Molecules are distinguished from polyatomic ions in this strict sense. In organic chemistry and biochemistry, the term molecule is used less strictly and also is applied to charged organic molecules and biomolecules.

In the context of the analysis of biomolecular NMR data, we can thus limit ourselves to the less strict definition that a molecule is a group of at least 2 covalently bonded atoms, whether charged or not. Molecules are important because these are the physical objects to which we relate observed NMR signals by assignment of NMR resonances to individual nuclear spins or atoms within the molecules. In turn, the NMR signals provide information about the structure and conformations of the molecules used in the NMR experiments.

In general, a molecule can be described by on various levels, of which I will mention 3:

• • Chemical composition: The number of atoms of each element in the molecule.

  • Topology: The description of all the individual atoms and their connections through covalent bonds.

  • 3 dimensional structure: The spatial arrangement of all atoms and their chemical bonds, which can be described by bond lengths, angles, torsion angles and distances.

Biopolymers

In the specific case of (bio)polymers, molecules are often described by the building blocks that make up the polymer chain. For example, proteins these can be described by the sequence of amino acids or residues that are linked by the peptide bonds, whereas in nucleic acids the building blocks would be the nucleotides.

In the case of multimers, where the multimeric complex is made up of a number of polymer chains, the individual chains are distinguished.

Molecules in CcpNmr Analysis

The concepts in CcpNmr Analysis that are used to treat molecules have been designed such that it is possible to deal with a large variety of molecules, complexes and mixtures of molecules.

To understand molecules in CcpNmr Analysis, we have to first distinguish 3 molecule data types or data packages (see Figure 1) in the CCPN Data Model that are used to describe molecules. These are:

• • ChemComps, which is the short name for Chemical Compounds

  • Molecules, which is the short name for Molecule Templates

  • MolSystems, which is the short name for Molecular Systems

ChemComps

The ChemComps data contain reference information, and describe the building blocks of molecules in terms of bonds, angles torsion angles etcetera, and thus provide topologies and 3D models of basic building blocks that can make up a molecule. ChemComps contain for example descriptions of:

• • All amino acids and nucleotides, such as Alanine and Guanine

  • Small molecules, such as ATP

Molecules

Molecules in CcpNmr Analysis are actually template molecules and not the actual molecular structure that you assign NMR resonances to. The template molecules contain a description of the building blocks (ChemComps) within a molecule and how they are connected, such as the primary sequence of a protein. A chain is a subpart of a molecule (or the whole molecule in case of one chain). One molecule can consist of one or several chains and chains can be linked within the molecule (e.g. disulfide bridges). The advantage of using template molecules is that each molecule needs to be defined only once, even if the actual sample contains homo-multimeric complexes.

MolSystems

The actual description of the components in your sample is contained in the MolSystem, or Molecular System. MolSystem describes the chains, residues and atoms in the sample, and are built up using the Molecules and ChemComps. It is the Molecular Systems that are used by CcpNmr Analysis to assign NMR signals to.

Figure 1. Overview of some of the packages that relate to Molecules in the CCPN data model, their sub-packages with building blocks and associated examples.

Alternative description of Core Concepts: Molecules

A description of this subject with emphasis on the data packages is found here