Structural Bioinformatics

what is some information on the proteins of the extracellular matrix

• fibrous proteins, crosslinking enabled by disulfide bridges

• extensively glycosylated, contributes to cell adhesion

• composed of distinct domains with specialised functions

  • cell adhesion

what is some information on membrane transport

• hydrophobic belt of residues

• ATPase activity

• Dimer

• conformational flexibility

• channel specifically matching the chemical nature of small molecules

where is N & C terminus located

N = start (start Now)

C = end (Cut off)

what are the different levels of protein structure

primary - refers to sequence of amino acids

secondary - refers to initial shape formed by H-bonds

• e.g. alpha helices / beta sheets

tertiary - how protein folds into a globular shape

quaternary - structure formed by multiple proteins interacting

what are some different ways to display protein structure

• ribbon representation

• C_alpha trace

• stick representation

• space filling representation

• surface representation

what are some functions of oligomerisation

• allows proteins to function

• increases the stability of the protein

what does folding minimise in the system

minimises the free energy of the system

• the configuration is optimized to minimize the free energy

• partially folded intermediates have higher free energy

how is free energy minimized

through choosing a configuration that maximizes favorable interactions between amino acid residues, this includes maximizing:

• favorable interactions between hydrophobic residues inside the hydrophobic core

• interactions between polar residues on the surface and water

what forces drive the folding process

• van der Waals forces - random dipole moments

  • 3.5-4.0 A

• hydrogen bonds - O, N, F

  • >=3.1 A

• electrostatic interactions - ion pairs

  • >=3.1 A

• hydrophobic interactions - polar vs non-polar interactions

what are domains

structural units that are part of a continuous protein chains, but that fold independently of each other

• different domain often associated with different functions

what is sequence homology analysis

compare the amino acid sequence of a protein with sequences of other known proteins in databases

what information can be learnt from multiple sequence alignments

conserved residues can be identified

• could be important for correct folding

• could be important for function

2 proteins with >25% identity in amino acid sequences usually share the same structure.

• sequences can diverge (evolution) while retaining the same stable structural fold

why might protein structure be challenging to study

• cannot produce protein in high amounts

• unstable or degrades fast

• protein is too big/small for some techniques

what is resolution

the shortest distance between 2 objects where they can still be distinguished as 2 separate entities

what features are discernible at different resolutions

• 10-20 Å – blobs, overall shape of the molecule

  • Can dock/fit a homology model into the overall shape

• 5-10 Å - Can discern secondary structure elements, helices seen as sausages, beta-sheets as plates

• <5 Å - Can perform backbone tracing

• 3.2-3.5 Å - Can see amino acid side chains

• ~1.5 Å - Can resolve individual atoms

what are some different levels of structural information

• 3D atomic structure

• shape & symmetry

• protein contact (interaction)

• subunit proximity (distances)

what is the principle between X-ray crystallography

• electrons within a single molecule will scatter X-rays, however we are unable to measure the scattering

• crystal, containing a repeating pattern of molecules, provides a way of amplifying the signal of the scattered X-rays

what are some pros & cons of X-ray crystallography

PROS:

• ultra-rare resolution

• insight into dynamics

• chemical reaction intermediates trapped in the crystal

CONS:

• not all proteins crystallize

• high protein concentration required

• static picture

what is the principle behind nuclear magnetic resonance

Certain atoms (H, C, N) have a nuclear spin that gives rise to an NMR signal. The signals in the NMR spectra are affected by:

• the chemical environment of the atom and

• how flexible the region is where it is located

what are some limitations of NMR

• high protein concentration required

• requires efficient isotope labeling

• outcome is multiple structure that must be interrupted

what are some advantages of cyro-electron microscopy

• helps us visualize large proteins & protein complexes

• only low concentration are needed

• no need to crystallize

why is the structure of functionally homologous proteins more conserved than the amino acid sequence

Once a protein has evolved and folded into a stable conformation, natural selection will ensure that any subsequent random mutations do not change this fold.

Mutations emerging in the course of evolution may change the properties of the protein (e.g. reaction specificity or substrate specificity) but the stable fold will be retained