Protein Secondary Structure:- Amino Acid Sequence Affects α Helix Stability

Not all polypeptides can form a stable helix. Interactions between amino acid side chains can stabilize or destabilize this structure. For example, if a polypeptide chain has a long block of Glu residues, this segment of the chain will not forman helix at pH 7.0. The negatively charged carboxyl groups of adjacent Glu residues repel each other so strongly that they prevent formation of the α helix. For the same reason, if there are many adjacent Lys and/or Arg residues, which have positively charged R groups at pH 7.0, they will also repel each other and prevent formation of theα helix. The bulk and shape of Asn, Ser, Thr, and Cys residues can also destabilize an α helix if they are close together in the chain.

The twist of an α helix ensures that critical inter actions occur between an amino acid side chain and the side chain three (and sometimes four) residues away on either side of it (Fig. 4–5). Positively charged amino acids are often found three residues away from negatively charged amino acids, permitting the formation of an ion pair. Two aromatic amino acid residues are often similarly spaced, resulting in a hydrophobic interaction.

FIGURE 4–5 Interactions between R groups of amino acids three residues apart in an α helix. An ionic interaction between Asp¹⁰⁰ and Arg¹⁰³ in an -helical region of the protein troponin C, a calcium binding protein associated with muscle, is shown in this space-filling model (derived from PDB ID 4TNC). The polypeptide backbone (car bons, -amino nitrogens, and -carbonyl oxygens) is shown in gray for a helix segment 13 residues long. The only side chains represented here are the interacting Asp (red) and Arg (blue) side chains.

A constraint on the formation of the helix is the presence of Pro or Gly residues. In proline, the nitrogen atom is part of a rigid ring (see Fig. 4–8b), and rotation about the N-C α bond is not possible. Thus, a Pro residue introduces a destabilizing kink in an α helix. In addition, the nitrogen atom of a Pro residue in peptide linkage has no substituent hydrogen to participate in hydrogen bonds with other residues. For these reasons, proline is only rarely found within an α helix. Glycine occurs infrequently in α helices for a different reason: it has more conformational flexibility than the other amino acid residues. Polymers of glycine tend to take up coiled structures quite different from an α helix. A final factor affecting the stability of an α helix in a polypeptide is the identity of the amino acid residues near the ends of the -helical segment. A small electric dipole exists in each peptide bond (Fig. 4–2a). These dipoles are connected through the hydrogen bonds of the helix, resulting in a net dipole extending along the helix that increases with helix length (Fig. 4–6). The four amino acid residues at each end of the helix do not participate fully in the helix hydrogen bonds. The partial positive and negative charges of the helix dipole actually reside on the peptide amino and carbonyl groups near the amino-terminal and carboxyl-terminal ends of the helix, respectively. For this reason, negatively charged amino acids are often found near the amino terminus of the helical segment, where they have a stabilizing interaction with the positive charge of the helix dipole; a positively charged amino acid at the amino terminal end is destabilizing. The opposite is true at the carboxyl-terminal end of the helical segment.

Thus, five different kinds of constraints affect the stability of an α helix: (1) the electrostatic repulsion (or attraction) between successive amino acid residues with charged R groups, (2) the bulkiness of adjacent R groups, (3) the interactions between R groups spaced three (or four) residues apart, (4) the occurrence of Pro and Gly residues, and (5) the interaction between amino acid residues at the ends of the helical segment and the electric dipole inherent to the helix. The tendency of a given segment of a polypeptide chain to fold up as an α helix therefore depends on the identity and sequence of amino acid residues within the segment.

FIGURE 4–6 Helix dipole. The electric dipole of a peptide bond (see Fig. 4–2a) is transmitted along an -helical segment through the in trachain hydrogen bonds, resulting in an overall helix dipole. In this illustration, the amino and carbonyl constituents of each peptide bond are indicated by + and - symbols, respectively. Non-hydrogen bonded amino and carbonyl constituents in the peptide bonds near each end of the α -helical region are shown in red.

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العتبة العباسية المقدسة: نحو 5 آلاف مستفيد يوميًّا من خدمات المطبخ المركزي في لبنان

العتبة العباسية المقدسة تعلن أسماء الفائزين بمسابقة ذكرى ولادة السيدة فاطمة المعصومة (عليها السلام)

قسم العلاقات يناقش مع المديرية العامّة لتربية كربلاء سبل تعزيز التعاون المشترك

وفد ثقافي عراقي يطّلع على مقتنيات متحف الكفيل ونفائسه ويشيد بطرائق عرضها

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الآخبار الصحية

عدد مرات التبرز يكشف أسرارا عن صحة الأمعاء

علامات جينية طويلة الأمد تتركها الرضاعة الطبيعية في دم الطفل

هل يمكن إعادة برمجة الجهاز المناعي لإنتاج أجسام مضادة نادرة؟

دراسة: أدوية الزهايمر "لا تحدث فرقا يذكر لدى المرضى"

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الآخبار التكنلوجية

روسيا تطور تقنية جديدة لتعديل خصائص البلاديوم

الصين: طاقم مهمة شينتشو-21 سيبقى في الفضاء شهرا آخر

"أبل" تهدد بحذف تطبيق "غروك" من متجرها وتكشف السبب

"أبل" تهدد بحذف تطبيق "غروك" من متجرها وتكشف السبب

المزيد

مواضيع ذات صلة

Protein Tertiary and Quaternary Structures: -Fibrous Proteins Are Adapted for a Structural Function

Protein Secondary Structure:- Common Secondary Structures Have Characteristic Bond Angles and Amino Acid Content

Protein Secondary Structure:- β Turns Are Common in Proteins

Overview of Protein Structure:- The Peptide Bond Is Rigid and Planar

Overview of Protein Structure:- A Protein’s Conformation Is Stabilized Largely by Weak Interactions

Overview of Protein Structure:- The Peptide Bond Is Rigid and Planar

Overview of Protein Structure:- A Protein’s Conformation Is Stabilized Largely by Weak Interactions

Protein Sequences and Evolution:- Protein Sequences Can Elucidate the History of Life on Earth

The Covalent Structure of Proteins:- Amino Acid Sequences Provide Important Biochemical Information

The Covalent Structure of Proteins:- Small Peptides and Proteins Can Be Chemically Synthesized

The Covalent Structure of Proteins:- Amino Acid Sequences Can Also Be Deduced by Other Methods

The Covalent Structure of Proteins:-Large Proteins Must Be Sequenced in Smaller Segments