中山大学生物化学幻灯片

1、4 Protein Function,4.1 General features 4.2 Oxygen-binding proteins 4.3 Immunoglobulins 4.4 Muscle contraction,liguofu,4.1 General features,Versatile in function Being hard to study Function via interaction,The interaction with other molecule (ligand) is reversible. The interface between the binding site is complementary in structure, making such interaction highly specific. Structure dynamicness of a protein is usually essential for such interactions.,liguofu,4.1 General features 4.2 Oxygen-bin

2、ding proteins 4.3 Immunoglobulins 4.4 Muscle contraction,4 Protein Function,liguofu,Quantitative description of interaction (1),Protein + nLigand PLn,liguofu,Quantitative description of interaction (2),If kd is constant,liguofu,Quantitative description of interaction (3),If kd is not constant,liguofu,Quantitative description of interaction (4),liguofu,Quantitative description of interaction (5),liguofu,The iron-porphyrin in hemoglobin accounts for the red color of blood, the copper-porphyrin in

3、hemocyanin for blue color of blood, and the magnesium-porphyrin in chlorophyll is responsible for the green of plants.,liguofu,Structure of Porphyrin,Pyrrole ring,Methene bridge,liguofu,Oxygen can be bound to a heme (1),Heme = Protoporphyrin IX + Fe2+,None of the aa side chains in proteins is suited for reversible binding O2,Heme prosthetic group,Transition metals, Fe & Cu, have a strong tendency to bind O2,need,more,commonly,liguofu,Oxygen can be bound to a heme (2),Heme = Protoporphyrin IX + F

4、e2+,Free Iron promotes the formation of highly reactive oxygen species such as hydroxyl radicals. Coordinated N atoms help prevent the conversion of Fe2+ to Fe3+,liguofu,Mb has a single binding site for oxygen,Myoglobin:153 residues, 16700 Da,His93 /F8,His64 /E7,liguofu,Oxygen can be bound to a heme (3),In free heme molecules, reaction of oxygen at one of the two “open” coordination bonds of iron can result in irreversible conversion of Fe2+ to Fe3+ In heme-containing proteins, this reaction is

5、prevented by sequestering the heme deep within a protein structure where acess to the two “open” coordination bonds is restricted. One of these two coordination bonds is occupied by a side-chain N of a His residue.,NO CO,Also,liguofu,Quantitative description of Mb binding O2,liguofu,Protein structure affects ligands bind (1),In free heme,or,In myoglobin,In free heme,In myoglobin heme,or,liguofu,“Breathing” : Molecular motions,The binding of O2 to heme in myoglobin depends on its “breathing”,In m

6、yoglobin,Protein structure affects ligands bind (2),liguofu,Hb is the most-studied and best-understood protein,Hemoglobin was the first protein to be crystallized (in 1849); the first to be associated with a specific physiological function (around 1875); one of the first proteins to have its molecular weight determined correctly (64,500); the first eukaryotic messenger (mRNA) to be isolated and subsequently sequenced. the first eukaryotic protein to be synthesized in a cell-free system in vitro;

7、 the second protein having its 3-D structure determined (1969).,liguofu,The “red coloring matter” (hemoglobin) of animal blood could be brought to crystallization, with crystal forms characteristic of their biological origins (1840s-1860s). Reversible interconversion of oxyhemoglobin and deoxyhemoglobin was revealed by using spectroscope (1860s). Treatment of hemoglobin with acid gave a colorless albuminoid constituent (globin) and a red iron-containing material (by 1870). The structure of heme

8、was elucidated to be a tetrapyrrol (porphyrin) derivative by chemical synthesis (Hans Fischer, 1929). Similar tetrapyrrol derivatives are also used as prosthetic groups of other proteins (e.g., the cytochromes that function in biological oxidation and photosynthesis!,liguofu,Hb has four subunits,Mr = 64,500,141 residues,146 residues,liguofu,Hb subunits are structurally similar to myoglobin, subunit lacks the short D helix,D helix,liguofu,conserved in all known globins,conserved,27 positions are

9、identical, 18%,82,143,liguofu,30 residues,Interactions in the four subunits,19 residues,19 residues,Hydrophobic interactions H bonds Salt bonds,liguofu,This is called Tense state (deoxyHb),Some ion pairs are not shown here,Ion pairs at the 1/2 and 2/1 interface (1),liguofu,Ion pairs at the 1/2 and 2/1 interface (2),Ion pairs stabilize the T state of deoxyHb,liguofu,Quantitative description of Hb binding O2（1）,liguofu,Hill plot,nH: hill coefficient,Quantitative description of Hb binding O2（3）,liguofu,Hb undergoes a structural change on binding O2 (1),Tense state is more stable and thus the predominant conformation of deoxyHb,Relaxed state is the predominant conformation of higher affinity to O2,Binding O2,Val E11,liguofu,In the T state, the porphyrin is slightly puckered, causing the heme iron to protrude somewhat on the proximal His (His F8) side. The binding of O2 causes the heme to assume a more planar conformation, shifting the posit

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