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Scientists advance the search for molecular roots of memory

  Scientists accelerate the search for molecular roots of memory
A model of the CaMKII protein shows multiple domains that allow it to bind actin filaments in the dendrites of neurons into bundles, thereby giving dendrites their shape. Researchers at Rice University, the University of Houston and the University of Texas Health Science Center in Houston believe the complex is the key to long-term memory formation. Picture credits: Wolynes Research Lab / Rice University

A new piece of a difficult puzzle ̵

1; the nature of memory – emerged this week with an indication of how brain cells change structure when they learn something.

Interactions between three moving parts-a binding protein, a structural protein, and calcium-are part of the process by which electrical signals enter neuronal cells and transform the molecular structures that allow for the recognition and storage of memories.

Colleagues from Rice University, the University of Houston (UH), and the University of Texas Health Sciences Center in Houston (UTHealth) combined theories, simulations, and experiments to determine how a central binding protein – calcium calmodulin Dependent kinase II (CaMKII) – binds and solves binding from the cytoskeleton of a neuron.

The team's report in the Proceedings of the National Academy of Sciences gives first clear details on how the binding sites of CaMKII affect the alignment of actin filaments – the protein structure – into long, rigid bundles. The bundles serve as supporting skeletons for dendritic spines, prickly protrusions that receive chemical messages through synapses from other neurons. The goal was to understand how signals arrive through dendrites, the branches of nerve cells that transmit information between cells.

Finding the complete structure of CaMKII has proved too complex for X-ray crystallography, although parts of its structure have been known. In combination with the actin that makes up the cytoskeleton, the system also became the largest protein that Wolynes and his team analyzed through their protein-structure prediction program, AWSEM.

When finished, the computer predicted structure was a notable coincidence for two-dimensional electron micrographs of Waxham and his group showing distinctly parallel actin filaments being laddered together by CaMKII rungs.

  Scientists Drive Search for Molecular Roots of Memory
The CaMKII Protein of Researchers from Rice University, the University of Houston, and the University of Texas Health Sciences Center in Houston (UTHealth) say it's important in that twisted actin filaments accumulate in neurons in three pockets to form a long-term memory. The CaMKII regulatory domain (red) also binds to incoming calmodulin proteins, which unpack the entire structure of actin and allow bundled filaments to reorganize. Picture credits: Wolynes Research Lab / Rice University

"There are definitely preparatory chemical steps that affect the enzyme activity of CaMKII before you reach this stage, so we do not have a completely clear picture of how to put it all together," Wolynes said. "However, it is clear that the construction of the complex is the crucial step in which chemistry becomes a larger structure that can store a memory."

CaMKII is uniquely suited for the interaction with actin, the most abundant protein in eukaryotic cells that has special abilities in neurons, where not only do thousands of dendrites (in every billion neurons) have their resting states, but Give them a degree of plasticity to adapt to a constant signal fire.

Actin molecules assemble into long, twisted filaments. The hydrophobic pockets between these molecules are perfectly configured to bind CaMKII, a large protein with multiple parts or domains. These domains bind to three consecutive binding sites on the filament, and the twists place binding sites at regular intervals to prevent the accumulation of proteins.

The "association" domain of CaMKII is a sixfold subunit that also binds to adjacent filaments. To actin bundles, the spines of the dendritic spines are formed, giving shape to these protrusions.

These bundles remain rigid when the dendrite contains little calcium. When calcium ions pass through the synapse, they bind to calmodulin proteins and bind to another part of CaMKII, the floppy regulatory domain. This triggers the cleavage of a domain of CaMKII from the filament, followed by the remainder of the protein, and provides a short window of time in which the bundles can reconfigure.

"When enough calcium enters, the activated calmodulin splits it onto structures, but only for a while," Wolynes said. During this time, the dendritic spine can take on a different shape that could be larger.

"We know that calcium brings information into the cell," Cheung added, "but how nerve cells handle it really depends on how that protein encodes information. Part of our work involves linking them at the molecular level and then projecting how these simple geometric rules develop larger structures on a microscale. "

  Scientists accelerate the search for molecular roots of memory
An electron micrograph shows actin filaments, which are held together by CaMKII proteins in a neuron in parallel or branched arrangements, simulations and experiments conducted at Rice University, the University of Houston, and the University of Texas Health Science Center, Houston, showed that the distance between The scale is 100 nanometers, and the image was taken at the Structural Biology Imaging Center of McGovern Medical School at UTHealth Image credits: Waxham Lab / UTHealth

The team's calculations revealed that the association domain accounts for approximately 40% of the binding strength of the protein to actin. A linker domain adds an additional 40% and the crucial regulatory domain provides the last 20% – a useful strategy, as the regulatory domain looks for incoming calcium calmodulinins that can unpack the entire protein from the filament.

The project came together through Rice's Center for Theoretical Biological Physics (CTBP), of which Wolyne's co-director and Cheung is a senior scientist. Her association dates back to when both were at the University of California at San Diego, he was a professor and she was a PhD student to rice physicist José Onuchic, also CTBP co-director. Wolynes also served in her Thesis Review Panel, she said.

Cheung knew from earlier work by Wolynes and his Rice group that actin stabilizes prion-like fibers that are thought to encode memories in neurons, and decided it fits in well with her research with Waxham how calcium activates CaMKII.

"This is one of the most interesting problems in neuroscience: how do short-term chemical changes lead to something long-term like memory?" Waxham said. "I think one of the most interesting contributions we make is to understand how the system makes changes in milliseconds to seconds and creates something that survives the original signal."

The puzzle is far from complete, Wolynes said. "The earlier work of Margaret and Neal was about triggering remembrance events," he said of his colleagues' calmodulin study. "Our prion paper was about preserving memory at the end of the learning process, and actin is in the middle, and there may be many other things in the middle."

"These questions are an interesting example for many people," he said . " This is a key element of the problem, but it is clearly not the end of the story. "

An unexpected mechanism allows a protein kinase to decode calcium signals in the brain

Further information:
Qian Wang el al., "Calcium / Calmodulin-Dependent Kinase II Actin Aggregates and Their Dynamic Regulation by Calmodulin in Dendritic Spines", PNAS (19459015) (2019). www.pnas.org/cgi/doi/10.1073/pnas.1911452116

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Rice University

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Scientists force search for molecular roots of memory (2019, August 26)
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