아미노산들의 복합체인 단백질 구조

1. 일차구조: 아미노산들은 펩타이결합들로이어져서 폴리펩타이드 사슬을 만든다

2. 이차구조: 폴리펩타이드 사슬은 알파 나선,베타 판, 그리고 회전들과 고리들 같은규칙적인 구조로 접힐 수 있다.

3. 삼차구조: 수용성 단백질들은 무극성중심부를 가진 촘촘한 구조로 접힌다.Subunit의 기본

4. 사차구조:폴리펩타이드 사슬들은 조립되어여러 소단위체(subunit)들로 된 구조를 만들수 있다.

단백질의 아미노산 순서가 단백질의 삼차원 구조를 결정한다.

Peptide bond (선형중합체, 펩티드결합 또는 아미드결합)

A peptide bond (amide bond) is a covalent chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting C(O)NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called a peptide link. Polypeptides and proteins are chains of amino acids held together by peptide bonds

The amine and carboxylic acid functional groups found in amino acids allow them to have amphiprotic properties.[9] Carboxylic acid groups (-CO2H) can be deprotonated to become negative carboxylates (-CO2

- ), and α-amino groups (NH2-) can be protonated to become positive α-ammonium groups (+NH3-). At pH values greater than the pKa of the carboxylic acid group (mean for the 20 common amino acids is about 2.2, see the table of amino acid structures above), the negative carboxylate ion predominates. At pH values lower than the pKa of the α-ammonium group (mean for the 20 common α-amino acids is about 9.4), the nitrogen is predominantly protonated as a positively charged α-ammonium group. Thus, at pH between 2.2 and 9.4, the predominant form adopted by α-amino acids contains a negative carboxylate and a positive α-ammonium group, as shown in structure (2) on the right, so has net zero charge. This molecular state is known as a zwitterion, from the German Zwitter meaning hermaphrodite or hybrid.[18] Below pH 2.2, the predominant form will have a neutral carboxylic acid group and a positive α-ammonium ion (net charge +1), and above pH 9.4, a negative carboxylate and neutral α-amino group (net charge -1). The fully neutral form (structure (1) on the right) is a very minor species in aqueous solution throughout the pH range (less than 1 part in 107). Amino acids also exist as zwitterions in the solid phase, and crystallize with salt-like properties unlike typical organic acids or amines.

Isoelectric point

At pH values between the two pKa values, the zwitterion predominates, but coexists in dynamic equilibrium with small amounts of net negative and net positive ions. At the exact midpoint between the two pKa values, the trace amount of net negative and trace of net positive ions exactly balance, so that average net charge of all forms present is zero.[19] This pH is known as the isoelectric point pI, so pI = ½(pKa1 + pKa2). The individual amino acids all have slightly different pKa values, so have different isoelectric points. For amino acids with charged side-chains, the pKa of the side-chain is involved. Thus for Asp, Glu with negative side-chains, pI = ½(pKa1 + pKaR), where pKaR is the side-chain pKa. Cysteine also has potentially negative side-chain with pKaR = 8.14, so pI should be calculated as for Asp and Glu, even though the side-chain is not significantly charged at neutral pH. For His, Lys, and Arg with positive side-chains, pI = ½(pKaR + pKa2). Amino acids have zero mobility in electrophoresis at their isoelectric point, although this behaviour is more usually exploited for peptides and proteins than single amino acids. Zwitterions have minimum solubility at their isolectric point and some amino acids (in particular, with non-polar side-chains) can be isolated by precipitation from water by adjusting the pH to the required isoelectric point.

alanine arginine isoleucine aspartic acid

pKa= 12.5

pKa= 4.1

pH=6 ?

At pH 6.00 alanine and isoleucine exist on average as neutral zwitterionic molecules, and are not influenced by the electric field. Arginine is a basic amino acid. Both base functions exist as "onium" conjugate acids in the pH 6.00 matrix. The solute molecules of arginine therefore carry an excess positive charge, and they move toward the cathode. The two carboxyl functions in aspartic acid are both ionized at pH 6.00, and the negatively charged solute molecules move toward the anode in the electric field. Structures for all these species are shown to the right of the display

Tyrosine VS Aspartic Acid at pH=5.7

pKa=10.9

pKa=4.1

pKa=9.1 pKa=2.2

Amino acids are linked by peptides bond

Peptide bond: The polymeric structure of a polypeptide is built by linking a serious of amino acids by peptide bonds

선형중합체, 펩타이드 결합 또는 아마이드결합

일차구조:아미노산들은 펩타이드결합들로 이어져서 폴리펩티드 사슬을 만든다.

펩타이드결합으로 결합된 아미노산들은 폴리펩티드 사슬을 형성 하며 폴리펩타이에 있는 각 아미노산을 residue , 잔기라고 함. 펜타펩티드 Tyr이 아미노 말단, Leu- 카르복실기 말단이라고 부름

N 에서 C 의 방향으로 펩타이드가 합성됨

• 50-2000개의 아미노산 잔기 단백질 • 소수의 아미노산 올리고펩티드 • 단백질의 단위:달톤(dalton), 수소 원자의 질량과 거의 같은 질량의 단위

이황화결합(disulfide bond): 폴리펩타이드 사슬의 교차결합이 있는데 시스테인 잔기들의 산화로 형성된다

Figure 2.17 Amino acid sequence of bovine insulin.

Proteins have unique amino acid sequences specified by genes

단백질들은 유전자들에 의해 지정되는 특유한 아미노산순서를 갖고 있으며 이를 일차구조(primary structure)라고 함

Figure 2.18 Peptide bonds are planar.

Polypeptide chains are flexible yet conformationally restricted

Figure 2.19 Typical bond lengths within a peptide unit.

폴리펩티드에 있는 각 아미노산의 구조는 두 단일결합들 둘레에서 회전으로 조정될 수 있다

두원자가 같은 시간에 같은 공간에 있을 수 없으므로 단백질의 입체적구조로 접힐 수 있다.

(A)

(B)

(C)

• Alpha 나선, ß 회전 오메가고리 와 선형결합 순서에서 인접하는아미노산들의 N-H 와 C=O 기들의 수소결합의 규칙적인 방식에 의해 형성

Figure 2.24 Structure of the α helix.

이차구조: 폴리펩티드 사슬은 알파 나선, 베타 판, 그리고 회전들과 고리들 규칙적인 구조로 접힐 수 있다

Figure 2.25 Hydrogen-bonding scheme for an α helix.

알파나선은 사슬안의 수소결합들로 안정하게된 감긴 구조이다.

Figure 2.27 Schematic views of α helices.

α-helix

Figure 2.28 A largely α-helical protein.

Figure 2.31 An antiparallel β sheet. Figure 2.32 A parallel β sheet.

베타판들은 폴리펩타이들 가닥들 사이에 수소결합으로 안정하게 된다

Figure 2.33 Structure of a mixed β sheet.

β sheet

Figure 2.34 A schematic twisted β sheet.

Figure 2.33 A protein rich in β sheets.

Figure 2.36 Structure of a reverse turn.

Polypeptide chains can change direction by making reverse turns and loops

Figure 2.33 Loops on a protein surface.

Figure 2.38 An α-helical coiled coil.

알파케라틴:양모, 머리카락과 피부의 주성분. 감긴 코일형 단백질. Actin filament. 300개 아미노산으로 된 중심부위에 헵타드반복(heptad repeat) 라는 7개의 아미노산- 매 일곱번째 잔기마다 루신임: 반데르발스, 이온결합, 이황화결합 존재

Figure 2.39 Heptad repeats in a coiled-coil protein.

Figure 2.40 Amino acid sequence of a part of a collagen chain.

나선의 다른형태 콜라겐:피부, 뼈, 힘줄, 연골 세개의 나선 폴리펩타이드로 구성( 3000Å , diameter 15Å/개). 글라신은 매 세번째 잔기에 나타남

Figure 2.41 Conformation of a single strand of a collagen triple helix.

The only residue that can fit in an interior position is glycine

(A)

(B)

Figure 2.42 Structure of the protein collagen.

Figure 2.43 Three-dimensional structure of myoglobin.

삼차구조:수용성 단백질들은 무극성 중심부를 가진 촘촘한 구조로 접힌다.: 내부는 루신, 발린, 메타오닌, 페닐알라닌 무극성

The polypeptide chain therefore folds so that its hydrophobic side chains are buried and its polar, charged chains are on the surface.

Figure 2.45 “Inside out” amino acid distribution in porin.

알파나선, 베타가닥으로 형성된 단백질 삼차구조는 내부로 향하는 소수성 표면, 용액으로 향하는 극성인 표면을 가지고 있음.

Figure 2.46 The helix-turn-helix motif, a supersecondary structural element.

몇 개의 폴리펩타이드 사슬이 접혀서 촘촘한구역을 형성하고 있는것을 domain 이라고 하고 약 100개의 아미노산으로 구성됨.

Figure 2.48 Quaternary structure.

사차구조:폴리펩타이드 사슬들이 조립되어 여러 소단위체들로 구성된 구조 (3차구조+3차구조)

Figure 2.50 Complex quaternary structure.

Figure 2.49 The α2β2 tetramer of human hemoglobin.

단백질의 상호 관계

우레아(Urea) , 염화구아니니늄: 단백질의 비공유결합들을 효과적으로 파괴

Figure 2.51 Amino acid sequence of bovine ribonuclease.

The Amino Acid Sequence of a Protein Determines Its Three-Dimensional Structure

Figure 2.52 Role of β-mercaptoethanol in reducing disulfide bonds.

β-mercaptoethanol: denature reagent 단백질을 변성시킴

베타메캅토에탄올은 산화됨

단백질의 기능을 잃게되고 마구잡이로 감긴 펩티드로 전환되었을때 변성된 단백질이라고 함 (denatured protein)

Figure 2.53 Reduction and denaturation of ribonuclease.

random-coil conformation

리보핵산 가수분해 효소의 기능을 잃게 됨

Figure 2.54 Reestablishing correct disulfide pairing.

This process was driven by the decrease in free energy as the scrambled conformations were converted into the stable, native

conformation of the enzyme.:

105가지의 조합이 있음

105가지의 조합이 있으나 original 결합으로 다시 돌아감: 104가지의 잘못된 조합으로 돌아가지 않음. 열역학적 가장 안정된 상태, 에너지가 가장 낮은 조건으로 다시 돌아감.

또한 Chaperone 이라는 단백질들이 부정한 상호작용을 막음

Amino acids have different propensities for forming alpha helices, beta sheets, and beta turns

Figure 2.55 Alternative conformation of a peptide sequence.

Figure 2.56 Transition from folded to unfolded state.

Protein folding is a highly cooperative process

Figure 2.57 Components of a partly denatured protein solution.

Figure 2.58 Typing-monkey analogy.

Proteins fold by progressive stabilization of intermediates rather than by random search

Figure 2.59 Proposed folding pathway of chymotrypsin inhibitor.

The essence of protein folding is the tendency to retainpartly correct intermediates

Figure 2.60 Folding funnel.

Figure 2.61 Lymphotactin exists in two conformations, which are in equilibrium.

Some proteins are inherently unstructured and can exist in multiple conformations

Figure 2.62 A model of the human prion protein amyloid.

Protein misfolding and aggregation are associated with some neurological diseases

Figure 2.63 The protein-only model for prion-disease transmission.

Alzheimer's disease

Figure 2.64 Finishing touches.

Protein modification and cleavage confer new capabilities

Figure 2.65 Chemical rearrangement in GFP.

(A) (B)

Figure 2.66 Space-filling model of lysozyme.

Figure 2.67 Ball-and-stick model of lysozyme.

Figure 2.68 Backbone model of lysozyme.

Ribbon diagrams

Figure 2.69 Ribbon diagram of lysozyme. Figure 2.70 Ribbon diagram of lysozyme with highlights.