Proteins have various functions that are precisely controlled.
首先找出句子的重点。此句强调的重点，不是蛋白质功能的多样性，而是这些功能的精确控制。再来，消除不必要的介词短语：使用protein function，而非functions of proteins。
改句：Protein function is precisely controlled.
The release and activation of the proteins were controlled by…
改句：Protein release and activation were controlled by…
The latest analysis methods make it possible to profile all the proteins produced during a given period.
在这里，您可以将短语make it possible to用一个词permit取代。
改句：The latest analysis methods permit profiling of all the proteins produced during a given period.
There is no general method for controlling the timing and location of activity of proteins within cells.
不使用there be句型当主语，且使用简介的术语，即spatiotemporal control（时空控制）来取代controlling the timing and location。
改句：A general method for spatiotemporal control of protein activity within cells is lacking.
Nanoparticles have been successfully used to carry probe molecules into cells.
改句：Nanoparticles have been used to carry probe molecules into cells.
The point of irradiation coincided with the point at which the change in morphology started, suggesting that the change in morphology was initiated by…
改句：The irradiation point coincided with the point at which the morphological change started, suggesting that the change was initiated by…
Nanoparticles were prepared containing proteins, and the nanoparticles were used as carriers of the proteins into cells.
将一个复合句（两个主语、两个动词）改写为具单一主语（nanoparticles）和复合谓语（were prepared and used）的句子。
改句：Nanoparticles containing proteins were prepared and used to carry the proteins into cells.
Enzyme activity was negligible before irradiation, whereas strong enzyme activity was observed after irradiation
很多时候，be observed的句型都是多余的。此处，strong enzyme activity was observed可以改写为enzyme activity…was strong。
改句：Enzyme activity was negligible before irradiation but strong after irradiation.
Changing the reagent concentration resulted in a change in the size of the nanoparticles: a higher reagent concentration produced smaller nanoparticles.
改句：Increasing the reagent concentration decreased the nanoparticle size.
In the merged images obtained immediately after irradiation (Fig. 1, left panels) and 24 h later (Fig. 1, right panels), the fluorescence was visible.
改句：In the merged images obtained immediately after irradiation (Fig. 1, left) and 24 h later (right), the fluorescence was visible.
When a small spot (indicated by the red circle in Fig. 1) was irradiated…
改句：When a small spot (red circle, Fig. 1) was irradiated…