NAMD case study: Water and Ice

Water and Ice

The universal solvent

Water is essential for sustaining life on Earth. Almost 75% of the Earth’s surface is covered by it. It composes roughly 70% of the human body by mass. It is the medium associated with nearly all microscopic life processes. Much of the reason that water can sustain life is due to its unique properties.

水的几个重要性质：

1. 较大的比热容（在同样受热或冷却的条件下，水的温度变化较小）
2. 较高的潜热（high latent heats of vaporization and melting）
3. 在4℃时呈现最大密度
4. 高表面张力（high surface tension）

The Liquid and Solid Phase of water

• 氢键的重组发生在飞秒尺度
• 氢键会诱导水分子形成3-7元的环，有别于冰相中的六元环
• 当降温时，水分子与周围4个分子形成氢键规则网络，来降低相互作用能。
• 冰至少有14种相（相图仍在不断扩展中）
• 计算氢键数目的脚本（count-HBonds.tcl）

set all [atomselect top all]

# determine the dimensions of the water box
set mes [measure minmax $all]
set xmin [lindex [lindex $mes 0] 0]    #利用lindex提取mes数组中的数据
set ymin [lindex [lindex $mes 0] 1]
set zmin [lindex [lindex $mes 0] 2]
set xmax [lindex [lindex $mes 1] 0]
set ymax [lindex [lindex $mes 1] 1]
set zmax [lindex [lindex $mes 1] 2]

set O [atomselect top "name OH2"]　　#选择文件中的O原子

# set the number of atoms for which you want to count H-bonds
set atomcount 300.0
set totalbondnum 0
for {set i 1} {$i <= $atomcount} {incr i} {　　　　　　　　　　　　　　　　　　#循环
  # pick a random water molecule (oxygen atom) and record its position
  set rand [expr int(rand()*[expr [$O num] - 1])]　　　　　　　　　　　　　　　#rand命令取随机数
  set oatom [atomselect top "index [lindex [$O get index] $rand]"]
  set xpos [lindex [lindex [$oatom get {x y z}] 0] 0]
  set ypos [lindex [lindex [$oatom get {x y z}] 0] 1]
  set zpos [lindex [lindex [$oatom get {x y z}] 0] 2]

  set buffer 3
  # the selected atom should be away from the surface (by <buffer> Angstroms)
  if {$xpos < [expr $xmin+$buffer] || $xpos > [expr $xmax-$buffer] || $ypos < [expr $ymin+$buffer] || $ypos > [expr $ymax-$buffer] || $zpos < [expr $zmin+$buffer] || $zpos > [expr $zmax-$buffer]} then {
    set i [expr $i-1]
  } else {
    # set the distance of a H-bond to 3.0 Angstroms and the angle to 30 degrees (default values)
    set dist 3.0
    set ang 30.0

    set temp1 [atomselect top "same residue as index [$oatom get index]"]
    set temp2 [atomselect top "same residue as exwithin 10 of index [$temp1 get index]"]
    # count the number of H-bonds for th molecule

    set count1 [llength [lindex [measure hbonds $dist $ang $temp1 $temp2] 0]]
    set count2 [llength [lindex [measure hbonds $dist $ang $temp2 $temp1] 0]]

    # and add it to the total so far
    set totalbondnum [expr $totalbondnum+$count1 + $count2]
    }
  }

puts "Each water molecule makes [expr double($totalbondnum/$atomcount)] hydrogen bonds on average with its neighbors."

• 鱼类的抗冻蛋白分为四种

AP Type	Typical Size（kDa）	Secondary Structure	Amino Acid Feature
Type I	3.3-4.5	α-helical	ThrX2AsxX7
Type II	6-14	globular	disulfide bridge
Type III	6-14	globular	none
Type IV	12	4 amphipathic α-helices	Glx-rich

• Based on ice etching experiments, it has been determined that HLPC6, a winter flounder type I AP, typically binds to the {2021}plane (equivalently {201} in a , b, c-axis notation) of ice 1h along the <0112> direction in which the ice oxygen atoms have a repeat distance of approximately 16.7A。
• A fundamental question : Is ice more hydrophobic than water?（突变实验和模拟研究指出，抗冻蛋白中的疏水基团在识别冰结合面中有重要作用，之后亲水基团才能与冰面结合）