The first step to construct any nanomachine is to build the structure. This is not an easy goal, atoms can't be modeled as they were any macroscopic material. They follow a set of rules to interact with another atoms.
Chemists have studied the properties of these atoms and biologists the details of the nanomachines constructed by them. So we have now the knowledge to start creating these new nanomachines. We are going to review the different methods followed to do that.
The natural bionanomachinery is designed for a specific environment. It is done for working inside cells, in a water environment. Without that conditions they don't work properly or don't work at all. The temperature is also important, the most common is 37º. In this environment nanomachines are stable, but they can be destroyed to create new ones with a little energy cost. The life of a nanomachine is between seconds to a year (but this is rare).
The intuitive approach to construct nanomachines is to build them atom by atom. However it is possible to follow a hierarchical strategy. George Whitesides set four different strategies:
- Sequential covalent synthesis: atoms are bonded into covalent molecules. The atoms are placed together piece by piece to build up the structure. The main advantage is the diversity achieved because it is possible to combine in almost any combination.
- Covalent polymerization: some modular units are linked into linear or branched chains. Using this method it is possible to get very large chains. The DNA synthesis is an example of this. There are limitations, for example, once the scheme is chosen it has to be always followed. Another limitation is that only stable chains under reaction conditions can be used to link each other. Enzimes allow the use of many different monomers, it is being studied.
- Self-organizing synthesis: nanostructures are formed by noncovalent bonds from modular units. They bond each other adopting the thermodynamic minimum.
- Self-assembly: as the author says "the spontaneous assembly of molecules into structured, stable, noncovalently joined aggregates". It is the most important in the construction of nanomachines and the less intuitive because it is far from the macroscopic behavior.
The key of bionanotechnology is Carbon. Every organic molecule has carbon. There are other atoms like oxygen and hydrogen also present that bonds to carbon. There are three forces that assure the stability: covalent bonds, nonbonded forces within molecules and interaction with water.
Covalent bonds are the most strong bonds. They are the product of two atoms sharing electrons of their last level. They are expensive in energy to break. Atoms with covalent bonds form the skeleton of the biomolecules. There are a few general rules that control them, so understanding them it is possible to figure out how the molecules are. Single bonds allow rotation, while double or triple don't. The most stable structures are those that are made by carbon bonded. Then nitrogen, oxygen and phosphorus can be bonded. Hydrogen is always present everywhere. The different quantities and order of this elements forms the molecules.
But these rules sometimes are a little bit different. Resonance is a neutral field between double and single covalent bonds. In a ring formed by carbon all the links are equal, no single links and no double links. This allow flexibility in the molecule.
The dispersion and repulsion forces between atoms are powerful. At a close range atoms experiment a dispersion force, but in a closer range a repulsion force begin to work.
Hydrogen bonds are weaker than covalent, but they contribute to stabilize molecules. This bonds are formed between a hydrogen atom covalent bonded to a nitrogen, oxygen or sulfur and another oxygen, nitrogen or sulfur atom. Because of the water environment this is very important for the stability of bionanomachines
.Electrostatic interactions are also active at atom level. They aren't directional and has a wide range. They help to the stability of molecules. These interactions are reduced by the dielectric effect.
Another effect is the hydrophobic. It was explained in chapter 2 and it is still the same. It helps molecules to form aggregates.
The proteins have a structure that provide them the characteristics they have. All the information about the amino-acid sequence and the structure is coded in the DNA. It is really hard to predict the structure from the sequence, but once it will be done custom proteins will be constructed much easily.
But proteins are not always stable. There are many ways for a chain to be stable. Similar proteins tend to have similar structures. That is a really good feature for bionanotechnology because then it is possible to use comparing tables to determine structures. The only but is that a single change where in a wrong place would be fatal for the protein and not match at all the other model.
Proteins have a hierarchical structure that provides them the stability they need. They have some particular structures like the a-helices and b-sheets. This structures provides many hydrogen bonds inside the molecule. This local structures then fold into a stable globular structure.
Those proteins can form a globular structure with a hydrophobic core, this is the positive design. The interaction with water provide most of the energetic stabilization for them. The unfavorable reduction of entropy must be compensated by favorable interactions in the folded structure.
The negative design is to ensure that a single folded conformation is created. The protein is designed to avoid any conformation energetically unfavorable.
To achieve this folding there is a collection of molecules called chaperones that assist proteins. They separate the molecule from the water environment and provide the conditions needed. They are like a box, the protein enter inside and the top is closed. Cells have two chaperones, the first is the formation of disulfide bonds that cross-link cysteine amino acids at distant parts of the polypeptide chain.
There are proteins that can be stable at high temperatures. In nature they are in some bacteria, so it is easier for us to study them and understand how to reproduce it. They are very useful for industry because they are processes where enzimes are needed and they are at high temperatures. The structure of these proteins is almost the same as the heat-labile proteins. The amino acid sequence is not quite different. The major difference is the rigidity. They have in the surface some new ion pair interactions between amino acids, new disulfide linkages or metal ions, incorporation of rigid proline or replacement of flexible glycine amino acids.
Some proteins don't use a static structure, instead they change between structures. This characteristic is attractive in signaling proteins because they can change rapidly to response to some signal. The disorder also allows the protein to have several capacities.
Self-assembly is how most of bionanomachines are build. They associate each other spontaneously in flexible chains that later form compact structures and then into functional complexes. The instructions used are in DNA, but it only specifies the amino acid chain, then they form their own structures. But it is more restrictive than directed construction, where we can specify exactly everything.
This process is modular. Large assemblies may be created with many identical pieces. It requires specific geometry of interaction and unique interaction between subunits to avoid any crosstalk. This can be a serious problem when interaction surface is small because they can interact with another unwanted molecules.
The process is also spontaneous, it doesn't require any guide or additional information. That involves a careful trade-off enthalpy and entropy.
Symmetry is a good help for constructing proteins because it is only needed part of the information to construct the whole thing. It is also good to control the errors. It has also many functional advantages, they can cooperate with their neighboring. And they can use many identical bonding sites to enhance the strength of binding to their target.
There are 3 important classes of geometry: cyclic, dihedral and cubic:
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Cyclic:only one single axis of symmetry forming a ring of symmetrically arranged subunits. Molecules with the higher cyclic groups are used in specialized functions like interaction with membranes or rotational motion.
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Dihedral: a central axis of twofold or higher rotational symmetry perpendicular to another axis of twofold symmetry. They have multiple surfaces of interaction, each different. They are used to construct enzimes that modify their action.
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Cubic: an axis of rotational symmetry with a nonperpendicular threefold axis. There are 3 possible arrangements: tetrahedral, octahedral and icosahedral. Transactional symmetries can be used to extend structures.
Line symmetries: include a transaction in one dimension, adding a rotational symmetry around the transaction axis yields a helix.
Plane symmetries are formed when translational symmetries are applied in two dimensions.
Space group symmetries are rare in nature.
The assembly process can be controlled by enzimes that speed up or stop it.
When it is needed to construct a very large protein the quasisymmetry can be used. It doesn't require as much information as a perfect symmetry. To do that two or more identical molecules are placed at each symmetrical position. This requires that subunits adopt slightly different conformations in the different nonsymmetrical positions.
The self-assembly is promoted by crowded conditions. If there are a lot of molecules in a solution they will tend to interact with each other more frequently than if they are alone. That is why nanomachines work better in crowded conditions, although the larger aggregates are harder to form.
Sometimes a less concrete building material is needed, so self-organization is a perfect method for creating structures that are flexible, resilient and self-repairing. It hasn't the control present in self-assembly, but that's exactly what is needed in some applications. These systems are also modular but don't have specific surfaces of interaction.
Lipids self-organize into bilayers. That is due to the hydrophobic and hydrophilic effect. Each lipid has a distinctive critical concentration and it is very low and lower for lipids with longer carbon chains. They associate to shield the hydrophobic segments of the molecule.
The lipid bilayers are fluid because they are composed of many nonbonded molecules. The lateral motion is fast, but flipping lipids from one surface to the other is not frequent. The fluidity is useful because it allows spontaneous healing of damage. This fluidity is dependent on the structure of the component lipids and on the temperature. They are highly flexible, allowing complex shape transformations. This bilayers can also have proteins to change the permeability or provide some different properties.
Molecular recognition is needed to control the interaction between parts in the bionanomachines.
There are two design concepts postulated by H.R.Crane:
“For a high degree of specificity the contact of combining spots on the two particles must be multiple and weak.”
“One particle must have a geometrical arrangement which is complementary to the arrangement on the other”.
To recognize molecules the nanomachines use some specific spots where the desired molecule, and only it, can be attached. Inside those spots there are a lot of weak interactions between the atoms of both molecules.
It is impossible to achieve high precision in the interaction between molecules because the atoms are spheric and they are discrete, so we can't break them in smaller pieces. Surfaces of interaction are rough, they can't fit exactly.
Because nanotehnology is based on macroscopic engineering the same approach is being taken. So there are rigid components binded by a few mobile bonds or joints. The natural bionanomachines are not like that. Evolution do it the other way around, it take flexible molecules and select some rigid ones for special tasks.
The flexibility in biomolecules is at all levels. From atoms to the higher structure. It is used to enhance their functions. Although many proteins are composed of several rigid domains connected by flexible linkers. Multichain assemblies may shift between specific conformations with different properties. In enzimes this is called “allosteric” motion and is used for regulation.
Biomolecules may incorporate specific levels of rigidity to improve the entropy.
These all kinds of flexibility create a greater level of complexity at design-time. It is harder to predict the structure and properties of the molecules we are trying to construct. But biomolecular flexibility will provide one of the greatest challenges, and potential benefits, of bionanotechnology.
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