Protein function and their role in diseases

Protein structure and function are intrinsically tied to each other as a protein’s function is largely determined by its three-dimensional conformation. Functionally, proteins are versatile macromolecules that evolved to carry out a wide range of functions (Lodish et al., 2007). According to their different cellular roles, proteins can be classified into distinct functional classes:

• Enzymes present the largest class of proteins. They catalyze and accelerate the

2.1 Proteins rates of biochemical reactions that take place in a cell. Enzymes are typically named based on the reaction they facilitate. For instance, the enzyme tripeptide aminopeptidase is a hydrolase that cleaves off the amino-terminal amino acid from a polypeptide.

• Regulatory proteins or messenger proteins regulate the ability of other proteins to perform their biological functions. They transmit signals to coordinate biological processes between different cells, tissues, and organs. A classical regulatory protein is insulin – a hormone that regulates the glucose metabolism.

• Transport proteins serve as carriers that bind and transfer small molecules within cells and throughout the organism. Two different types of transport proteins can be distinguished: (i) those that transport molecules within cells or organisms, such as hemoglobin that transports oxygen from lungs to tissues, and (ii) membrane-bound proteins that serve as gateways for shuttling molecules, such as glucose, vitamins and amino acids, across otherwise impermeable cell membranes.

• Storage proteinsfunction as biological reservoir for small molecules, e.g., metal ions and amino acids, which are mobilized and utilized for maintenance and growth of organisms. For instance, ferritin stores iron, an important component of heme which in turn is essential for binding oxygen by hemoglobin. Others encapsulate small molecules to protect cells, for instance, from metabolites that might be toxic when being released in the wrong cell compartment.

• Contractile and motile proteinsendow cells with unique capacities for special forms of movement. Cell division, muscle contraction and cell motility present basic ways in which cells achieve motion. Prominent examples include actin and myosin as important contractile muscle proteins or tubulin, a major component of micro-tubules which facilitate cell division. Another class of proteins involved in motion are so-called motor proteins that control the movement of vesicles, granules, and organelles.

• Structural proteins are, in terms of molecular weight, the heaviest class of pro-teins. These fibrous molecules, typically insoluble, provide strength, structure and support for cells. α-keratins are the crucial proteins in skin, hair, and fingernails.

Another example is collagen, a major component of bone, connective tissue, ten-dons, and cartilage.

• Scaffold proteinsact as adaptors by linking various proteins to form scaffolds upon which certain protein or protein-DNA complexes are assembled. Scaffold proteins are crucial for regulating signaling pathways by tethering signaling components, localizing these components to specific compartments of the cell, regulating signal transduction by coordinating feedback signals and insulating correct signaling pro-teins from competing propro-teins. Prominent scaffold propro-teins include, for instance, KSR and MEKK1 in the MAPK pathway, HOMER in calcium signaling and DLG1 in T-cell receptor signaling.

• Protective and exploitive proteins are essential elements for cell defense and protec-tion. Classical members of this class are immunoglobulins (or antibodies), critical

components of the immune system that locate and indirectly neutralize molecules that are not intrinsic to the host system. Other important examples are blood clotting proteins, e.g., thrombin and fibrinogen, that help to prevent severe loss of blood upon damage of the circulatory system.

• Transcription factors are proteins involved in the regulation of gene expression.

They recognize and bind specific DNA sequences (motifs), thereby attracting other transcription factors to create a complex which eventually induces the recruitment of RNA polymerase to specific genes. The most common transcription factors include TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH.

It should be emphasized that numerous proteins, particularly in higher eukaryotes, posses multiple different functions rather than only a single one. An intriguing class of such multifunctional proteins are so-called moonlighting proteins that perform mul-tiple autonomous but often unrelated functions without separating these functions into distinct protein domains (Huberts and van der Klei, 2010). Moonlighting proteins con-tribute to basic cellular functions, such as metabolism, angiogenesis, cell motility, DNA synthesis or repair, as well as in physiological functions and biochemical pathways that are involved in cancer and other diseases. Other striking examples are enzymes, which in addition to their catalytic function are involved in completely unrelated processes, such as autophagy, protein transport or DNA maintenance (Huberts and van der Klei, 2010).

Proteins and their role in diseases

A particular important aspect of proteins is their role in human diseases. Diseases are pathological conditions that impair the normal state of an organism by altering or destroying its vital functions (Merskey, 1986). Abnormal functioning is caused by inherited genetical defects or variations, spontaneous mutations, internal dysfunctions and environmental influences, such as stress, infection or other external factors, that directly or indirectly affect genes and their products (Mackenbach, 2006). Even slight alterations, for instance, in a single gene, might yield an aberrant protein, which may lead to cell malfunction and, eventually, to a disease. Furthermore, many known variations do not necessarily cause a disease but might increase the risk of developing a particular disease.

Disease-related alterations, e.g., mutations or dysregulations may affect proteins in various ways and on several functional levels. However, most alterations will eventually perturb the cellular machinery and its biological processes by impairing the natural function of a protein. Protein function can be severely disrupted by aberrations that affect either the specific protein expression, post-translational modification patterns, the folding into a stable tertiary structure or the combination of such events.

Protein expression

The expression of biologically active proteins is determined by the expression of their encoding genes which is regulated in many different ways. Precise expression control

2.1 Proteins is vital for cells to synthesize gene products whenever they are needed and to adapt to environmental changes, external signals or damages to the cell (Perdew et al., 2006).

Gene expression is mostly controlled at the level of the transcription initiation and transcription rate but also through microRNA. Transcriptional activity is responsible for the steady state levels of mRNA of the regulated gene, which in turn correlates with protein levels for most genes. Modifications in the regulatory sequences, chromatin structure and proteins that trigger the transcription of a gene, might alter the cellular concentration of particular proteins which in turn perturbs the sensible balance within a cell. Aberrant expression patterns in central regulatory proteins, such as transcription factors that control cell proliferation and differentiation, are known to be a major cause of cancer (Delgado and León, 2006). In particular, (proto-)oncogenes and tumor sup-pressor proteins that regulate the cell cycle or promote apoptosis are typically over- and underexpressed, respectively, in various types of cancer (Weinberg, 1996; Croce, 2008).

Post-translational modification

Nascent proteins emerging from the translational machinery are often subjected to co-valent chemical modifications that alter their amino acid residues. Post-translational modification is a common biological mechanism contributing to the vast diversity in protein structure, function and dynamics (Seo and Lee, 2004; Walsh, 2006). Various biochemical modifications, such as phosphorylation, glycosylation and proteolysis, in-crease the diversity of functional groups beyond the inherent properties of proteinogenic amino acids and extend the functional and structural repertoire encoded in a genome.

Amino acid substitutions and other sequence variations might disrupt designated post-translational modification sites in proteins. This may have severe functional conse-quences including conformational changes, alterations in subcellular locations, modu-lation of enzyme activity and abnormal interaction patterns (Walsh, 2006). Aberrant post-translational modifications are, for instance, involved in the pathogenesis of Hunt-ington’s disease (Wanget al., 2010), Alzheimer’s disease (Gonget al., 2005) and different types of cancer (Krueger and Srivastava, 2006; Radivojac et al., 2008; Reiset al., 2010).

However, also imbalances and alterations in the close proximity of modification sites have been found to be causative for human diseases (Baenziger, 2003; Liet al., 2010).

Protein folding

The cellular function of proteins depends primarily on their tertiary structure. Alter-ations in the protein sequence, either emerging from inherited or spontaneous variAlter-ations or aberrant amino acid modifications, may interfere with the folding process and result in incorrectly folded proteins. Misfolding of proteins might have serious implications rang-ing from functional insufficiency and loss-of-function to perturbation of cellular pathways to aggregation of abnormally folded proteins causing cell damage (Dobson, 2003).

Different diseases have been associated with protein misfolding (Chiti and Dobson, 2006; Gregersen, 2006), often classified into two types: loss-of-function pathogenesis caused by protein degradation and gain-of-function pathogenesis induced by protein

accumulation (Winklhoferet al., 2008).

• In the first case, aberrant proteins are prematurely eliminated by the degrada-tion systems, which results in loss-of-funcdegrada-tion pathogenesis and protein deficiency diseases (Gregersen, 2006). Cystic fibrosis, Marfan syndrome and some types of cancer, are characterized by the absence of central proteins that have been recog-nized as misfolded and thus degraded by the proteasome. For instance, the loss-of-function of the crucial tumor suppressor p53 induced by misfolding is thought to be a frequent cause of cancer (Nigro et al., 1989; Lubinet al., 2010).

• Aberrant proteins, which circumvent the cellular surveillance and accumulate to intractable aggregates, induce toxic gain-of-function pathogenesis and amyloido-sis (Merlini and Bellotti, 2003; Aigelsreiter et al., 2007). Large quantities of ac-cumulated proteins in the intra- or extracellular space may damage and destroy cells through mechanisms which just have started to be elucidated (Selkoe, 2003).

Alzheimer’s disease, Parkinson’s disease and Type II diabetes, are directly associ-ated with the deposition of such aggregates in tissues, including brain, heart and spleen (Jaikaran and Clark, 2001; Shah et al., 2006; Irvineet al., 2008).