Bond energy

Interactions that hold molecules together:

1. Covalent bonds (共價鍵)
   (Sharing electrons withina molecule): ~ 100 kcal/mol (Hard to break)

2.Noncovalent bonds
  (Weak interactions between molecules): < 5 kcal/mol (Easily broken)
     a) Ionic bonds (Salt bridge):
          Weak in water (< 3 kcal/mol) but can be very strong within the core of macromolecule
          such as proteins.
     b)  Hydrogen bonds: (0.5 – 3 kcal/mol)
               C-O- ::: +H-N        C-O- ::: +H-O       N- ::: +H-N
     c)  Hydrophobic interaction:
               Nonpolar molecules tends to aggregate to minimize their exposure to water
              (van der Waals forces)
              ( - CH2 -, -CH3, Aliphatic group )
     d)  Hydrophilic molecules:
              Polar molecules like to interactioin with water.
              (-CO, -SH, -NH, PO, N etc)















ref :

Methyl       :  - CH3
Ethyl          :  - CH2 -
Hydroxyl    :  - OH
Carboxyl    : - CO2 –
Amino        : - NH2
Carbony    :  - CO -
Sulfhydryl  :  - SH
Phosphate : - PO4 (3-)
Amide        :  - NH -
Carboxy     : - COOH

Peptide bond: - NH – CO-


Google search : Chap_2_Building Block.pdf

Free enegry 3

Thus, the association reaction of two proteins, say A and B, is determined by the free energy difference ΔG⁰ (19) between the state A + B and the AB final state

protein 摺合 Free energy

在 protein 摺合的過程中，聚肽鏈會經歷多次形態的轉換，以達到一種具有最大穩定性的特定結構。換一句話說，也就是聚肽鏈會尋找一種具有最低自由能(free energy)的結構，顯示出聚肽鏈的一級結構順序，決定了摺合蛋白質分子的最終形態

Link

生命的重要特性之一是具有複雜的結構，這些複雜的結構必須有能力由外界獲取能量，來維持其結構之存在。例如 植物和一些能行光合作用的細菌可先獲取光能再轉變為可供使用的化學能；動物則由食物中之葡萄糖經過氧化產生 水及二氧化碳，同時釋放出能量。葡萄糖的氧化反應可以用下列方程式表示：

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O

這樣一個氧化究竟可以釋放出多少能量？在這裏我們就得先複習一下能量與化學平衡反應之間的關係。簡單的說， 任何一個化學平衡反應都是朝著最低能量與最大亂度的方向趨近。因此我們要推斷一個化學反應是否容易進行就必 須考慮反應物與生成物之間熱含量（enthalpy）與熵（entropy）的差異。為了容易記量化學反應的進行，美國化學 家Gibbs提出了一個方程式來描述化學反應的能量變化：

G=H-TS

其中，G為自由能（free energy）之變化；H為焓（enthalpy）之變化，即反應前後放出（值 為負）或吸收（值為正）的熱量；T為反應之絕對溫度；S為熵（entropy）之變化。 若 G為負值，表示反應可自動發生。 在溫度為25℃，壓力為1大氣壓下，葡萄糖氧化反應自由能的變化為：

G=H - TS = -673 Kcal/mole-298(0.043)Kcal/mole = -686Kcal/mole

Free energy (kcal/mol) 1 - FastContact

Source Link

FastaContact   web


The following energetic, structural and evolutionary properties are computed for each interface residue of a PPI:

• ΔG^FC: an estimate of the change of free energy (kcal/mol) for a residue upon complexation. Computed using FastContact (12). More negative values indicate a stronger interaction. 
  
  
• ΔΔG^R: an estimate of the change in free energy of an alanine mutation. Computed using Rosetta (13). More positive values indicate the mutation destabilizes the complex and thus the original residue has a stronger interaction. 
  
  
• ΔSASA: the change in solvent accessible surface area (SASA) of a residue. This is the difference between the SASA of the bound conformation of a chain in the complexed state and the bound conformation as an independent chain. Computed using naccess (http://www.bioinf.manchester.ac.uk/naccess/). 
  
  
• ΔSASA%: the relative ΔSASA as computed by naccess. Expressed as a percentage.
  
  
• Cons: a conservation score computed using Scorecons (32). A higher score indicates a higher degree of conservation. 
  
  
• Rate: an evolutionary rate computed using Rate4Site (33). A higher score indicates a higher rate and lower degree of conservation.

The full protocol for computing these properties is reported elsewhere (25). Any residue with ΔSASA > 0.05 Ų is treated as an interface residue. All possible clusters of interface residues with a maximal span of 12Å are computed. The cluster properties include the aggregated residue properties (minimum, maximum, average and total values) as well as the types of residues in the cluster, the size of the cluster (number of residues) and the maximal distance between cluster residues.